[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/19775542/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/20140953/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   5 
123 187  36  76  19 
  1   2   3   4   5 
123 187  36  76  19 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
124 122  42 107 
  1   2   3   4 
124 122  42 107 
[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 
63 63 44 40 64 
 1  2  3  4  5 
63 63 44 40 64 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
110  58 106 
  1   2   3 
110  58 106 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
174 130 132 
  1   2   3 
174 130 132 
[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  4  5  6 
74 57 60 60 33 59 
 1  2  3  4  5  6 
74 57 60 60 33 59 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
85 57 36 76 28 61 
 1  2  3  4  5  6 
85 57 36 76 28 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=149,	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=264,	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 
132 120  86  88 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
132 120  86  88 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
132 120  86  88 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
132 120  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  72  44
  subtype2 102  70
  subtype3  18  16
  subtype4  45  24
  subtype5  11   5
subtype1 subtype2 subtype3 subtype4 subtype5 
     116      172       34       69       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
      44       70       16       24        5 
$subtype1
TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 
       58.03        11.01         6.18        19.33         9.17         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 
       35.24        33.63        39.78        18.15        28.73         3.45 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8373 
       11.44         0.69        29.42         2.66         2.20        14.79 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
        9.21        20.22        24.79        10.68         7.53        34.98 
TCGA-BR-A4PE TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8528 
       20.42        21.44        13.15        13.35        12.59        12.33 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH 
       12.82         3.42         9.34        11.31        12.43        12.20 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 
       20.02         3.02         7.99        54.08        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5725 TCGA-CG-5730 
       19.07        21.99        18.97        22.98        15.02         4.01 
TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       69.04         4.54        17.19        10.26        15.22        15.98 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-D7-A6F2 
       12.36        11.31        12.33        14.27        22.29        15.65 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.99        16.24        72.23         3.48        19.53 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
       13.58         0.56         5.52         5.92        12.59        14.17 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 
       22.75        25.81        11.77         2.10        12.95        12.30 
TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IP-7968 
       27.42        18.38         5.19         1.41         6.74         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        63.62        37.64        14.04        45.67        18.21 
TCGA-RD-A7BT TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
        8.61         8.94        35.61         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8PE TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91S TCGA-VQ-A91U 
       13.02        22.19         2.70        17.85        32.88         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O 
        9.50        55.56         9.04         4.54        66.81        21.04 
TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       42.54        11.24        18.41        43.66        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6G 
       17.13        26.04 

$subtype2
TCGA-3M-AB47 TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       14.01        26.70         9.47         4.64         7.43        30.90 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.87        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       22.32        26.10        32.78        25.61        18.05        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
       12.16         8.98        30.90        31.20        44.94        21.90 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       36.16        35.84        15.32         9.07        29.56        37.25 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       14.43        29.59         9.60        32.25         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.96         6.18         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       26.33         4.31        11.80        31.27         0.26        25.05 
TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        3.72         1.12        12.79         9.34        28.14         6.28 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       26.73        31.96        20.88        34.13         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       28.57        12.89         8.98        14.17         0.53        28.34 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5803 
       32.52         0.46        16.14         5.13         2.83         0.07 
TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 
       12.30        12.59        12.43        11.77        12.62         1.02 
TCGA-CG-4437 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 
        8.05         0.00         9.01        30.97         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
        6.02         0.99       105.07        65.10        21.07         7.99 
TCGA-D7-5577 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       25.71        18.61        17.85        24.72        16.80        17.19 
TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       20.91         5.92        36.43        13.78        14.76        26.43 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 
       11.44        20.32         8.38         4.34         7.13        14.47 
TCGA-F1-A448 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX TCGA-HF-A5NB 
       21.27        22.29        59.54         5.03         0.23        30.51 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       26.47        14.27        11.41        12.10        10.62         0.76 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX 
        5.59        11.84        21.37        29.98         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RJ TCGA-IN-A7NR TCGA-IN-AB1X 
        0.26        14.07        15.68        12.46         6.51        13.51 
TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZI TCGA-R5-A804 
       20.15         3.72        19.73         9.86        74.53         4.60 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       11.05         5.13        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8P2 
       71.38        57.44        16.87        19.04         5.79        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       37.22        30.97        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ 
        1.87         9.27        23.41        15.65        29.59        73.41 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P 
       11.70        61.22        60.85        55.43         6.58         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZA-A8F6 
       28.41        54.12        16.14        17.26 

$subtype3
TCGA-B7-5818 TCGA-BR-6801 TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8483 TCGA-BR-8682 
       11.70        40.21        13.08         3.32         5.39        32.58 
TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CD-A4MG TCGA-CG-4304 
        9.86        13.87        13.51        13.18         6.58        27.02 
TCGA-CG-4440 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        4.01         7.07        36.00        12.03        28.96        79.07 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 
       12.66        19.13        18.54        19.50        14.66        21.14 
TCGA-HU-A4G6 TCGA-HU-A4GQ TCGA-R5-A7ZF TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       12.30         0.10         8.52        48.79        21.73        37.41 
TCGA-VQ-A8PY TCGA-VQ-A91V TCGA-VQ-A923 TCGA-VQ-AA6J 
       14.33        42.64         2.01        27.55 

$subtype4
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-7959 TCGA-BR-8296 
       19.56         9.44        18.35        17.29        33.21        15.58 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8687 TCGA-BR-A4CS 
        7.40        31.10        25.18        27.12         8.22         1.48 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-8524 
        0.72         0.66        20.65         1.15         3.25         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.53         0.07        12.39        11.64        15.39        12.07 
TCGA-CD-A48C TCGA-CG-4472 TCGA-CG-5719 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 
       11.61        12.00         1.02        20.55        18.84        13.35 
TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-7916 
       18.21        16.44         2.83        19.96        11.38        14.07 
TCGA-FP-8099 TCGA-FP-A9TM TCGA-HU-8238 TCGA-HU-A4G2 TCGA-HU-A4GU TCGA-HU-A4H4 
       17.06         6.21         1.51        24.30         6.58        23.84 
TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RN 
        9.67        36.36         3.45        18.81         3.39        19.53 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A93J TCGA-R5-A7ZR 
        6.44        10.62        11.70         7.82        36.95         6.08 
TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        9.24        16.67       122.30        18.48        43.36         7.73 
TCGA-VQ-A8PH TCGA-VQ-A8PS TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E 
       12.79        13.35        27.35        64.57        39.45        21.83 
TCGA-VQ-A91Y TCGA-VQ-A94U TCGA-VQ-AA6K 
        9.73        26.93        12.43 

$subtype5
TCGA-BR-8369 TCGA-BR-8676 TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4455 TCGA-D7-6817 
       14.04         7.53        15.95        14.01        12.03        12.79 
TCGA-D7-A6EV TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4H3 TCGA-IN-A6RS 
       11.24        24.20         3.25         8.98        29.00        12.59 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-ZQ-A9CR 
       18.74        20.81         5.72         0.79 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.56     0.00     0.10     0.07     0.79 
subtype1 subtype2 subtype3 subtype4 subtype5 
   72.23   116.38    79.07   122.30    29.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.465   15.485   14.100   12.790   12.690 
[1] "0.6 - 72.2 (13.5)"  "0.0 - 116.4 (15.5)" "0.1 - 79.1 (14.1)" 
[4] "0.1 - 122.3 (12.8)" "0.8 - 29.0 (12.7)" 
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        5       16        8        11        16         0
  subtype2       1        4       19       12        18        26         2
  subtype3       0        2        3        2         4         1         0
  subtype4       0        2        2        8         6        13         2
  subtype5       1        2        1        2         1         1         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         27         14          7       14
  subtype2         32         28         17       20
  subtype3          7          8          3        5
  subtype4         15         11         10        4
  subtype5          2          3          2        3
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        1        0        0        1
  STAGE IA          5        4        2        2        2
  STAGE IB         16       19        3        2        1
  STAGE II          8       12        2        8        2
  STAGE IIA        11       18        4        6        1
  STAGE IIB        16       26        1       13        1
  STAGE III         0        2        0        2        0
  STAGE IIIA       27       32        7       15        2
  STAGE IIIB       14       28        8       11        3
  STAGE IIIC        7       17        3       10        2
  STAGE IV         14       20        5        4        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  6 31 56 28
  subtype2  7 36 81 58
  subtype3  2  7 20  7
  subtype4  5 12 35 22
  subtype5  3  7  4  4
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        6        7        2        5        3
  T2       31       36        7       12        7
  T3       56       81       20       35        4
  T4       28       58        7       22        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 39 36 23 19
  subtype2 58 52 33 37
  subtype3 11  5  8 11
  subtype4 18 24 19 13
  subtype5  4  3  3  8
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       39       58       11       18        4
  N1       36       52        5       24        3
  N2       23       33        8       19        3
  N3       19       37       11       13        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"
D1V6, binary
          cls
clus         0   1
  subtype1 106   8
  subtype2 162  16
  subtype3  32   4
  subtype4  71   2
  subtype5  18   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  106    8
  subtype2  162   16
  subtype3   32    4
  subtype4   71    2
  subtype5   18    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      106      162       32       71       18
  1        8       16        4        2        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  37  86
  subtype2  79 108
  subtype3   7  29
  subtype4  26  50
  subtype5   9  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   86
  subtype2   79  108
  subtype3    7   29
  subtype4   26   50
  subtype5    9   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       37       79        7       26        9
  MALE         86      108       29       50       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"
D1V8, binary
          cls
clus         0   1
  subtype1  86  23
  subtype2 136  29
  subtype3  27   3
  subtype4  51  17
  subtype5  14   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86   23
  subtype2  136   29
  subtype3   27    3
  subtype4   51   17
  subtype5   14    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        86      136       27       51       14
  YES       23       29        3       17        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"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     7
  subtype2                                    42
  subtype3                                     7
  subtype4                                    13
  subtype5                                     3
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     45
  subtype2                                                     74
  subtype3                                                      8
  subtype4                                                     29
  subtype5                                                      6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                29
  subtype2                                                                28
  subtype3                                                                 9
  subtype4                                                                14
  subtype5                                                                 3
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               30
  subtype2                                               20
  subtype3                                               10
  subtype4                                               14
  subtype5                                                5
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        2
  subtype2                                        9
  subtype3                                        0
  subtype4                                        2
  subtype5                                        0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                               4
  subtype2                                              12
  subtype3                                               1
  subtype4                                               3
  subtype5                                               1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                4
  subtype2                                                2
  subtype3                                                1
  subtype4                                                0
  subtype5                                                1
D1V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  45
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        30
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          4
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         4
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  74
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        20
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 9
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                         12
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         2
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                   8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          1
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        14
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         0
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                   6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          1
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
[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  95   4   8   5
  subtype2 149   8   8  13
  subtype3  29   2   2   1
  subtype4  58   4   1   5
  subtype5  18   0   0   1
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       95      149       29       58       18
  R1        4        8        2        4        0
  R2        8        8        2        1        0
  RX        5       13        1        5        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    26                         5
  subtype2    34                         3
  subtype3     6                         2
  subtype4    18                         2
  subtype5     4                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    71
  subtype2                                         0   129
  subtype3                                         0    18
  subtype4                                         0    51
  subtype5                                         0     9
D1V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           26       34        6       18
  BLACK OR AFRICAN AMERICAN                        5        3        2        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           71      129       18       51
                                           clus
vv                                          subtype5
  ASIAN                                            4
  BLACK OR AFRICAN AMERICAN                        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0
  WHITE                                            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"
D1V13, binary
          cls
clus         0   1
  subtype1   2  81
  subtype2   3 143
  subtype3   0  21
  subtype4   0  59
  subtype5   0  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   81
  subtype2    3  143
  subtype3    0   21
  subtype4    0   59
  subtype5    0   12
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        3        0        0        0
  NOT HISPANIC OR LATINO       81      143       21       59       12
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 71 49
  subtype2 80 37
  subtype3 28 14
  subtype4 57 46
subtype1 subtype2 subtype3 subtype4 
     120      117       42      103 
subtype1 subtype2 subtype3 subtype4 
      49       37       14       46 
$subtype1
TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6801 
       58.03        19.56         9.44        17.29         9.17        40.21 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
        9.21        35.24        33.63        39.78        15.32        28.73 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8373 
        3.45        11.44         0.69         2.66         2.20        14.79 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 
        5.39         9.21        20.22        24.79         9.86         8.22 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-CD-5799 TCGA-CD-5800 
       10.68         7.53         0.72        20.65         3.25        13.15 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
       12.59         0.07        15.39        12.82         3.42         9.34 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4441 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5727 
       12.43        12.20        14.01        36.00        15.02        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 
        4.01        69.04        12.66        20.55        18.84        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8576 
       10.26        15.98        12.79        11.31        16.80        14.66 
TCGA-D7-A4YT TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       14.27         2.83        22.29        15.65         0.62         7.99 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       16.24        72.23         3.48        17.06        13.58         0.56 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.92        12.59        14.17        22.75        25.81        11.77 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI 
       10.19        12.95        12.30        27.42        36.36        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.19        19.53        10.62         2.53         5.56        63.62 
TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT 
       37.64        36.95        14.04        18.21         6.08         8.61 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       37.91         8.94         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       18.48        43.36        22.19        12.79         2.70        17.85 
TCGA-VQ-A8PU TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X 
       27.35        18.74        20.81        32.88         1.71         9.50 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94T 
       55.56         9.04         4.54         5.72        21.04        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       18.41        38.93        32.94        17.13        17.26         0.79 

$subtype2
TCGA-3M-AB47 TCGA-B7-A5TJ TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-7703 
       14.01        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-8370 TCGA-BR-8372 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8682 
        3.32        31.27         1.12        28.14        31.96        32.58 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF 
       13.87        34.98         1.48        13.51        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8534 
       21.44        16.14         5.13         0.07        12.33        12.07 
TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4437 
       12.43        11.61         6.58        11.77        12.62         8.05 
TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6525 
        0.99        12.03        28.96        65.10        21.07        13.35 
TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY 
       15.22        12.33        18.21        16.44         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-A448 
       14.76        11.24        11.44        19.96        14.47        21.27 
TCGA-FP-7829 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-A5NB TCGA-HU-8238 
       19.53        11.08         5.52         6.21        30.51         1.51 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       14.27        11.41         5.59        11.84        24.20         3.25 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 
       29.98         8.98         6.51         6.58        29.00        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RP 
        9.67        14.07        18.81         3.39         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IN-AB1X TCGA-MX-A5UJ TCGA-R5-A804 
        6.74        12.59        11.70        13.51        19.73         4.60 
TCGA-R5-A805 TCGA-RD-A7C1 TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        9.24        16.67        19.04        48.79        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PO 
       38.14        37.22         7.73        30.97        34.29         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       23.41        29.59        14.33        73.41        39.45        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94U 
       21.83        61.22        42.64        66.81        42.54        26.93 
TCGA-VQ-AA68 TCGA-VQ-AA6G TCGA-VQ-AA6I 
       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-6852 TCGA-BR-7196 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 
       44.94        21.90        29.56        29.59        32.25         0.56 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8589 TCGA-BR-8676 
        0.26         0.95         0.26        25.05        27.12         7.53 
TCGA-BR-8686 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-CD-5801 TCGA-CD-8531 TCGA-CG-5722 
       20.88        12.89         0.53        13.18        12.59         0.99 
TCGA-D7-5577 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YX TCGA-D7-A6EZ TCGA-FP-7916 
       25.71        24.72        19.50        36.43        20.32        14.07 
TCGA-FP-7998 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GQ 
       22.29        12.10        10.62        24.30        12.30         0.10 
TCGA-HU-A4H0 TCGA-VQ-A8PF TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-AA69 
        2.10         2.50        60.85         2.01        55.43        28.41 

$subtype4
TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6709 
       15.95        13.68        22.32        26.10        25.61        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 
        8.98        30.90        31.20         9.07        37.25        14.43 
TCGA-BR-8080 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8371 
        9.60        19.96        15.58        22.19        17.52        11.80 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 
        3.72        25.18        12.79         9.34         6.28        26.73 
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-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5802 
       28.34         0.66        32.52         0.46         2.83        13.35 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
        0.07        12.39        12.53        12.30        12.39        11.64 
TCGA-CD-A489 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5734 
       11.31         6.97         1.02         6.02       105.07         7.99 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 
        4.54        19.13        18.54        18.61        17.85        12.36 
TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A6ET TCGA-D7-A747 TCGA-D7-A748 
       17.19        21.14        20.91        26.43         8.38         4.34 
TCGA-D7-A74B TCGA-F1-A72C TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX TCGA-HJ-7597 
        7.13        11.38        59.54         5.03         0.23        26.47 
TCGA-HU-8610 TCGA-HU-A4GJ TCGA-HU-A4GY TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ 
        0.76        21.37         0.26        15.68         3.45        12.46 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A663 TCGA-R5-A7O7 
        6.51         7.82        20.15         3.72         9.86        45.67 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        8.52        74.53        11.05         5.13       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS 
        5.79        46.26        16.31         1.87        15.65        13.35 
TCGA-VQ-A8PX TCGA-VQ-A91Y TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-AA6F TCGA-VQ-AA6J 
       64.57         9.73         6.58         2.66        54.12        27.55 
TCGA-VQ-AA6K 
       12.43 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.10     0.07 
subtype1 subtype2 subtype3 subtype4 
   79.07    73.41    60.85   122.30 
subtype1 subtype2 subtype3 subtype4 
  13.415   14.330   16.060   13.350 
[1] "0.1 - 79.1 (13.4)"  "0.1 - 73.4 (14.3)"  "0.1 - 60.9 (16.1)" 
[4] "0.1 - 122.3 (13.3)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        3       11       10        11        19         1
  subtype2       2        6       14        8        14        20         0
  subtype3       0        1        2        1         5         8         0
  subtype4       0        4        8       10        11         9         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         28         19          9       12
  subtype2         17         21         12        7
  subtype3          9          8          6        2
  subtype4         23         15         11       14
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        2        0        0
  STAGE IA          3        6        1        4
  STAGE IB         11       14        2        8
  STAGE II         10        8        1       10
  STAGE IIA        11       14        5       11
  STAGE IIB        19       20        8        9
  STAGE III         1        0        0        2
  STAGE IIIA       28       17        9       23
  STAGE IIIB       19       21        8       15
  STAGE IIIC        9       12        6       11
  STAGE IV         12        7        2       14
[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  5 31 60 28
  subtype2 11 25 55 31
  subtype3  1  3 22 16
  subtype4  4 19 49 35
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        5       11        1        4
  T2       31       25        3       19
  T3       60       55       22       49
  T4       28       31       16       35
[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 31 35 30 25
  subtype2 47 24 25 25
  subtype3 14 12  6 10
  subtype4 32 31 19 23
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       31       47       14       32
  N1       35       24       12       31
  N2       30       25        6       19
  N3       25       25       10       23
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus         0   1
  subtype1 107   5
  subtype2 116   4
  subtype3  38   2
  subtype4  92  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  107    5
  subtype2  116    4
  subtype3   38    2
  subtype4   92   12
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      107      116       38       92
  1        5        4        2       12
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 44 80
  subtype2 44 78
  subtype3 12 30
  subtype4 36 71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   80
  subtype2   44   78
  subtype3   12   30
  subtype4   36   71
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       44       44       12       36
  MALE         80       78       30       71
[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"
D2V8, binary
          cls
clus        0  1
  subtype1 92 26
  subtype2 91 26
  subtype3 36  3
  subtype4 81 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92   26
  subtype2   91   26
  subtype3   36    3
  subtype4   81   18
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        92       91       36       81
  YES       26       26        3       18
[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  DIFFUSE TYPE
  subtype1                                     7
  subtype2                                    15
  subtype3                                     8
  subtype4                                    37
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     41
  subtype2                                                     43
  subtype3                                                     17
  subtype4                                                     33
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                30
  subtype2                                                                23
  subtype3                                                                 7
  subtype4                                                                14
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               37
  subtype2                                               26
  subtype3                                                9
  subtype4                                                6
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        4
  subtype3                                        0
  subtype4                                        8
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                               2
  subtype2                                               9
  subtype3                                               0
  subtype4                                               9
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                5
  subtype2                                                2
  subtype3                                                1
  subtype4                                                0
D2V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  41
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        37
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          2
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         5
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  43
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        26
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          9
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         2
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         9
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          0
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   37
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 8
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          9
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY 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
  subtype1 102   5   6
  subtype2 109   3   1
  subtype3  39   0   1
  subtype4  85   9   4
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      102      109       39       85
  R1        5        3        0        9
  R2        6        1        1        4
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    26                         7
  subtype2    26                         4
  subtype3    12                         0
  subtype4    25                         2
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    73
  subtype2                                         0    80
  subtype3                                         0    27
  subtype4                                         0    73
D2V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           26       26       12       25
  BLACK OR AFRICAN AMERICAN                        7        4        0        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           73       80       27       73
[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"
D2V13, binary
          cls
clus        0  1
  subtype1  1 84
  subtype2  1 88
  subtype3  1 35
  subtype4  2 86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   84
  subtype2    1   88
  subtype3    1   35
  subtype4    2   86
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        1        2
  NOT HISPANIC OR LATINO       84       88       35       86
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 18 11
  subtype2 56 30
  subtype3 43 29
  subtype4 47 39
  subtype5 30 20
subtype1 subtype2 subtype3 subtype4 subtype5 
      29       86       72       86       50 
subtype1 subtype2 subtype3 subtype4 subtype5 
      11       30       29       39       20 
$subtype1
TCGA-3M-AB47 TCGA-BR-4191 TCGA-BR-6453 TCGA-BR-6565 TCGA-BR-A4J2 TCGA-BR-A4PE 
       14.01        18.35        15.95         9.17        14.17        20.42 
TCGA-CD-5800 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5721 
       13.15         3.02        27.02        47.05        21.99         6.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-A4YT TCGA-F1-A72C 
       28.96        79.07         4.01        69.04        14.27        11.38 
TCGA-IN-AB1V TCGA-KB-A93G TCGA-SW-A7EB TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS 
        7.82        20.15         5.79        37.41        17.85        13.35 
TCGA-VQ-A8PZ TCGA-VQ-A91X TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
       73.41         9.50        26.04        12.43        17.26 

$subtype2
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6710 
       26.70        11.70        30.90         6.18         6.61         8.98 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8285 
       30.90        44.94        35.24        11.44        32.25         0.56 
TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8484 
       29.42        15.58         6.18        31.10        25.05        25.18 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4J8 
       27.12        28.14         7.53        10.68        13.87        13.51 
TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 
        1.15         5.13         3.25        12.59        12.33        12.30 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
       12.43         3.42         9.34        12.20        20.02         7.99 
TCGA-CG-4437 TCGA-CG-4455 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5723 
        8.05        12.03         7.07        30.97        36.00       105.07 
TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       12.03        65.10        21.07        15.98        12.36        11.31 
TCGA-D7-6822 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-F1-6874 
       12.33        16.44        36.43        11.24        20.32        14.47 
TCGA-F1-A448 TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       21.27        25.81         6.51        12.95        29.00        23.84 
TCGA-HU-A4H5 TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-AB1X TCGA-RD-A7BT TCGA-RD-A7C1 
       12.30         6.74        10.62        13.51         8.61        16.67 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8E3 
      122.30       115.69        19.04         0.92        18.48        21.73 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PO 
       37.22         7.73        46.26        22.19        12.79         9.27 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91S TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94R 
       27.35        64.57        32.88        55.56        66.81        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA6D 
       18.41        17.13 

$subtype3
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-6452 TCGA-BR-7703 TCGA-BR-7716 
       19.56        11.01         9.47        34.68        36.16        39.78 
TCGA-BR-7723 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8485 
       28.73         8.05         2.20         4.31        31.27         9.21 
TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4IV TCGA-BR-A4J1 
        9.34        24.79        20.88         8.22        28.57         0.72 
TCGA-BR-A4J4 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-A48C TCGA-CD-A4MI 
        0.53        13.18        13.35         0.07        11.61        11.77 
TCGA-CD-A4MJ TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4466 
       12.62        54.08        29.98        19.07         9.01        18.97 
TCGA-CG-5720 TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6817 TCGA-D7-8578 
        0.99        15.02        25.71        12.66        12.79        21.14 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6F0 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-HF-A5NB 
        5.92        13.78        22.29        16.24        72.23        30.51 
TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        0.10         6.58        10.19        27.42        36.36         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-RD-A8N0 
        3.39        18.38         5.19        19.53         1.41        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-B7-A5TN TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6457 TCGA-BR-6458 
        9.44         4.64         7.43         9.57        13.68        19.33 
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-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8080 
       33.63        18.15        15.32         9.07        14.43         9.60 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
       19.96         7.40        13.08        22.19        17.52        26.33 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8588 
        3.32        11.80         3.72         5.39        20.22        12.79 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 
        6.28        26.73        32.58        34.13         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J5 
       34.98         1.48        27.55        12.89         8.98        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 
        0.66        32.52         0.46        21.44         2.83         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-A489 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
       12.39         0.07        11.31        12.00        22.98         6.97 
TCGA-CG-5719 TCGA-D7-5579 TCGA-D7-6524 TCGA-D7-8574 TCGA-D7-A4Z0 TCGA-D7-A6EX 
        1.02         4.54        17.85        17.19        14.76         2.83 
TCGA-D7-A6EY TCGA-D7-A748 TCGA-FP-7998 TCGA-HU-8610 TCGA-HU-A4GY TCGA-IN-8462 
       11.44         4.34        22.29         0.76         0.26        18.81 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG 
       12.59         6.51        11.70         5.56        37.64         3.72 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8NB TCGA-VQ-A8E2 TCGA-VQ-A8PD 
       11.05         5.13        37.91        16.87        43.36        16.31 
TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A928 
        1.87        23.41        15.65         9.73         2.01         5.72 
TCGA-VQ-A94P TCGA-VQ-A94U 
        2.66        26.93 

$subtype5
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       13.87        17.29        32.78        18.05        19.89        12.16 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8289 TCGA-BR-8363 
        3.45        29.56        33.21        37.25         2.66         0.26 
TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A4PD 
        0.95        14.04         0.26        31.96         9.86        20.65 
TCGA-BR-A4QL TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
       16.14        12.53        12.39        12.59        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CG-4305 TCGA-CG-4306 
       12.07        12.82        12.43         6.58        15.95         1.02 
TCGA-CG-5734 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        7.99        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       13.35        10.26        15.22        24.72        16.80        19.50 
TCGA-D7-8575 TCGA-EQ-8122 TCGA-FP-7916 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-8608 
       18.21         7.99        14.07        26.47        11.41        10.62 
TCGA-IP-7968 TCGA-VQ-A8DU 
        2.53         5.46 

subtype1 subtype2 subtype3 subtype4 subtype5 
    3.02     0.56     0.07     0.07     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
   79.07   122.30    72.23    43.36    37.25 
subtype1 subtype2 subtype3 subtype4 subtype5 
  15.950   15.780   16.190   12.195   13.955 
[1] "3.0 - 79.1 (15.9)"  "0.6 - 122.3 (15.8)" "0.1 - 72.2 (16.2)" 
[4] "0.1 - 43.4 (12.2)"  "0.3 - 37.2 (14.0)" 
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       3        4        9        3         2         9         1
  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        5
  subtype3         17         12         13        5
  subtype4         17         11         11       15
  subtype5         15         10          1        4
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        0        3        0        0
  STAGE IA          2        1        4        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        1        1        0
  STAGE IIIA        4       16       17       17       15
  STAGE IIIB        3       16       12       11       10
  STAGE IIIC        1        6       13       11        1
  STAGE IV          6        5        5       15        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 21 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       21       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 65 18
  subtype3 53 18
  subtype4 78  7
  subtype5 40  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    4
  subtype2   65   18
  subtype3   53   18
  subtype4   78    7
  subtype5   40    8
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        21       65       53       78       40
  YES        4       18       18        7        8
[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  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  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                12
  subtype2                                                                25
  subtype3                                                                21
  subtype4                                                                 7
  subtype5                                                                 4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                                2
  subtype2                                               17
  subtype3                                               13
  subtype4                                               10
  subtype5                                                8
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        3
  subtype2                                        2
  subtype3                                        0
  subtype4                                        4
  subtype5                                        1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                               1
  subtype2                                               4
  subtype3                                               3
  subtype4                                               8
  subtype5                                               3
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                1
  subtype2                                                1
  subtype3                                                1
  subtype4                                                1
  subtype5                                                1
D3V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                   9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          1
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        17
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          4
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        13
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          8
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
[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 70 55
  subtype2 34 14
  subtype3 49 26
  subtype4 41 34
subtype1 subtype2 subtype3 subtype4 
     125       48       75       75 
subtype1 subtype2 subtype3 subtype4 
      55       14       26       34 
$subtype1
TCGA-3M-AB47 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4191 TCGA-BR-6453 
       14.01        19.56        11.01         9.47        18.35        15.95 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       13.87        19.33         9.17        18.05        19.89        12.16 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8284 TCGA-BR-8295 
       33.63        39.78        18.15        28.73         8.05         2.20 
TCGA-BR-8296 TCGA-BR-8368 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 
       15.58         4.31        25.18         9.21        20.22         9.34 
TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ 
       24.79        20.88         8.22        13.87         6.08        34.98 
TCGA-BR-A4IV TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4PD TCGA-BR-A4PE 
       28.57         0.72        14.17         0.53        20.65        20.42 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 
        3.25        13.15        13.18        13.35         0.07        12.59 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 
        0.07        12.30        12.59        11.64        15.39         3.42 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       11.61        12.20        11.77         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 
        1.02        29.98        47.05        19.07        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5725 TCGA-CG-5726 
       18.97        22.98         0.99         6.02        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       79.07         4.01        69.04        12.66         4.54        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 
       18.84        18.61        10.26        12.79        12.36        24.72 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-EQ-A4SO TCGA-F1-6875 
       18.21        21.14        14.27        22.29        16.24        72.23 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-HU-8608 TCGA-HU-A4GY 
       11.38        14.07        22.29        26.47        10.62         0.26 
TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
       12.95        27.42        36.36         3.45         3.39        18.38 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT TCGA-RD-A7BS TCGA-RD-A8N0 
       19.53         1.41         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-A94U 
       42.64        60.85         9.50         4.54        21.04        26.93 
TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       38.93        54.12        26.04        16.14        12.43 

$subtype2
TCGA-B7-5816 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-7704 
       26.70         6.61        34.68        32.78        36.16        35.24 
TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8366 TCGA-BR-8372 TCGA-BR-8381 
       29.42         6.18        31.10         0.95        31.27         0.26 
TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4J8 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-8526 
       27.12        31.96        13.51        16.14         5.13        12.53 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4438 TCGA-CG-4469 
       12.82        12.43         6.58        12.62        54.08         7.07 
TCGA-CG-5724 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-A4YY 
       12.03         7.99        25.71        13.35        15.22        13.78 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       30.51        11.41         0.10         6.51         6.58        10.19 
TCGA-IP-7968 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PO TCGA-VQ-A8PT 
        2.53        21.73        38.14        37.22         9.27        29.59 
TCGA-VQ-A8PU TCGA-VQ-A91D TCGA-VQ-A91Z TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6B 
       27.35        11.70        55.56        18.41        28.41        32.94 

$subtype3
TCGA-B7-5818 TCGA-B7-A5TN TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6710 
       11.70         9.44        30.90         6.18         9.57         8.98 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 
       30.90        44.94        11.44        32.25         0.56        19.96 
TCGA-BR-8297 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 
        7.40        25.05         5.39        28.14         7.53        26.73 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4IZ TCGA-BR-A4PF TCGA-CD-5813 TCGA-CD-8528 
       10.68         7.53         8.98         1.15        12.39        12.33 
TCGA-CD-8534 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4455 
       12.07         9.34        20.02         7.99         8.05        12.03 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6815 
       30.97        36.00       105.07        65.10        21.07        15.98 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A4YU TCGA-D7-A4YX 
       11.31        12.33        19.50        17.19        16.44        36.43 
TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A748 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 
       11.24        20.32         4.34         7.99        14.47        21.27 
TCGA-HU-8610 TCGA-HU-A4GF TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-AB1V 
        0.76        25.81        29.00        23.84        12.30         7.82 
TCGA-IN-AB1X TCGA-KB-A93G TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 
       13.51        20.15         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-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6705 
        4.64         7.43        17.29        13.68        26.10        25.61 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7722 TCGA-BR-7901 
       40.21        31.20        21.90         9.21        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 
        9.07        29.56        33.21        37.25        14.43         9.60 
TCGA-BR-8289 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        2.66        13.08         0.26        22.19        17.52        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8592 
       14.04         3.32        11.80         3.72        12.79         6.28 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY 
       32.58         9.86        34.13         1.48        27.55        12.89 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 
       28.34         0.66        32.52         0.46        21.44         2.83 
TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-4472 TCGA-CG-5717 
        0.07        12.39        11.31        12.43        12.00         6.97 
TCGA-CG-5719 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-8572 TCGA-D7-A4YV 
        1.02        19.13        18.54        17.85        16.80         5.92 
TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RS 
       14.76         2.83        11.44        18.81         5.19        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-RD-A7BW 
        6.51        11.70         5.56        37.64         3.72         5.13 
TCGA-RD-A8MW TCGA-RD-A8NB TCGA-VQ-A8PD TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A91Y 
       37.91        16.87        16.31        23.41        15.65         9.73 
TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A94P 
        2.01         5.72         2.66 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.10     0.56     0.07 
subtype1 subtype2 subtype3 subtype4 
   79.07    55.56   122.30    40.21 
subtype1 subtype2 subtype3 subtype4 
   14.27    14.50    16.44    12.59 
[1] "0.1 - 79.1 (14.3)"  "0.1 - 55.6 (14.5)"  "0.6 - 122.3 (16.4)"
[4] "0.1 - 40.2 (12.6)" 
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2        5       13       13         8        15         1
  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         32         18         11       16
  subtype2         13          8          7        4
  subtype3         11         14          5        4
  subtype4         13         12          9       11
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           2        1        0        0
  STAGE IA          5        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         1        1        0        1
  STAGE IIIA       32       13       11       13
  STAGE IIIB       18        8       14       12
  STAGE IIIC       11        7        5        9
  STAGE IV         16        4        4       11
[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 45 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       45       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 93 27
  subtype2 36  9
  subtype3 59 14
  subtype4 69  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93   27
  subtype2   36    9
  subtype3   59   14
  subtype4   69    5
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        93       36       59       69
  YES       27        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  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  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                30
  subtype2                                                                13
  subtype3                                                                20
  subtype4                                                                 6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               16
  subtype2                                                8
  subtype3                                               17
  subtype4                                                9
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        6
  subtype2                                        1
  subtype3                                        2
  subtype4                                        1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                               7
  subtype2                                               2
  subtype3                                               3
  subtype4                                               7
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                2
  subtype2                                                1
  subtype3                                                1
  subtype4                                                1
D4V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        16
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 6
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          7
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         2
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          2
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        17
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         9
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          7
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
[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 48 10
  subtype2 29 29
  subtype3 22 15
  subtype4 25  8
  subtype5 37 19
subtype1 subtype2 subtype3 subtype4 subtype5 
      58       58       37       33       56 
subtype1 subtype2 subtype3 subtype4 subtype5 
      10       29       15        8       19 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-6852 
       26.70        11.70        30.90        34.68        30.90        44.94 
TCGA-BR-7707 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8361 
       35.84        29.56        29.59        32.25        29.42        31.10 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
        0.26         0.95         4.31        31.27         0.26        25.05 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4IY TCGA-BR-A4J4 
        1.12        27.12        28.14        31.96        12.89         0.53 
TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A48C 
       20.42        13.18        12.33        12.59        12.43        11.61 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5723 
       12.62        15.95        30.97         6.97         6.02       105.07 
TCGA-CG-5724 TCGA-D7-5577 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-8570 TCGA-D7-8573 
       12.03        25.71        17.85        13.35        24.72        19.50 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-FP-8099 TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-8604 
       36.43        13.78        17.06        11.08        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4H0 
       10.62         0.76        12.30        11.84        29.98         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-IN-8462 TCGA-IN-8663 
       29.00        23.84        18.81         3.39 

$subtype2
TCGA-BR-4187 TCGA-BR-4279 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
        4.64         9.57        13.87        17.29        13.68        22.32 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 
       26.10        25.61        18.05        40.21        31.20        21.90 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 
        9.07        33.21        14.43         9.60         8.05        19.96 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 
        7.40        13.08        22.19        17.52        26.33        14.04 
TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 
       11.80         3.72         9.34         6.28        26.73        32.58 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       20.88        34.13         6.08        27.55        28.57         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 
       14.17        28.34        32.52        13.51         0.46         2.83 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4472 
        0.07        12.39        12.07        11.31        11.77        12.00 
TCGA-D7-6518 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-FP-7916 
       19.13        17.19        20.91        16.44         5.92        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GY 
       22.29        59.54         5.03         0.26 

$subtype3
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-7717 TCGA-BR-7722 
       18.35         6.18        19.89         8.98        18.15        15.32 
TCGA-BR-8058 TCGA-BR-8484 TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-CD-8529 TCGA-CD-8532 
       37.25        25.18         0.66        20.65        12.30        11.64 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4462 TCGA-CG-5719 TCGA-CG-5722 
        3.02         1.02         8.05         0.00         1.02         0.99 
TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6817 
       28.96        69.04         7.99        18.54        10.26        12.79 
TCGA-D7-8575 TCGA-D7-8576 TCGA-FP-8211 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G9 
       18.21        14.66        13.58        24.30         5.59        24.20 
TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 
        3.25        21.37         8.98        10.19        12.95         9.67 
TCGA-HU-A4HB 
       15.68 

$subtype4
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-8486 
        6.61        15.95         9.17        32.78        36.16        20.22 
TCGA-BR-8588 TCGA-BR-8683 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-A4MG 
       12.79         9.86         1.15        21.44         3.25         6.58 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4465 TCGA-CG-4469 
       27.02         7.99        14.01        47.05         9.01         7.07 
TCGA-CG-5720 TCGA-D7-5578 TCGA-D7-6522 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A4Z0 
        0.99        12.66        18.61        15.22        15.98        14.76 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7829 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-A4GT 
       14.47        21.27        19.53         1.51        14.27         6.51 
TCGA-HU-A4GU TCGA-HU-A4H8 TCGA-IN-7806 
        6.58        14.07        36.36 

$subtype5
TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
       19.33        12.16         9.21        33.63        39.78        28.73 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 
        3.45        11.44         0.69         2.66        14.79         5.39 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 
        9.21        24.79         8.22         7.53         1.48         0.72 
TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 
       13.15         0.07        12.53        12.39        15.39        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        3.42         9.34        12.20        54.08         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5725 
       19.07        21.99        18.97        22.98        36.00        15.02 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       20.55        18.84        17.19        12.36        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 
       16.80        21.14        14.27         7.99        16.24        72.23 
TCGA-FP-7735 TCGA-FP-8631 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H5 TCGA-HU-A4HD 
        3.48         0.56        25.81        11.77        12.30        27.42 
TCGA-IN-7808 TCGA-IP-7968 
        3.45         2.53 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.26     0.07     0.00     0.99     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  105.07    59.54    69.04    47.05    72.23 
subtype1 subtype2 subtype3 subtype4 subtype5 
  16.505   14.120   12.790   14.070   12.460 
[1] "0.3 - 105.1 (16.5)" "0.1 - 59.5 (14.1)"  "0.0 - 69.0 (12.8)" 
[4] "1.0 - 47.0 (14.1)"  "0.1 - 72.2 (12.5)" 
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        2        8        6         9        12         0
  subtype2       0        0        1        5         7         9         1
  subtype3       0        2        3        4         3         6         0
  subtype4       2        3        8        1         5         8         1
  subtype5       0        3        7        7         5         9         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          7          6          6        3
  subtype2         11         11         10        5
  subtype3          6          4          3       10
  subtype4          4          3          0        3
  subtype5         14          6          4        4
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        0        0        2        0
  STAGE IA          2        0        2        3        3
  STAGE IB          8        1        3        8        7
  STAGE II          6        5        4        1        7
  STAGE IIA         9        7        3        5        5
  STAGE IIB        12        9        6        8        9
  STAGE III         0        1        0        1        1
  STAGE IIIA        7       11        6        4       14
  STAGE IIIB        6       11        4        3        6
  STAGE IIIC        6       10        3        0        4
  STAGE IV          3        5       10        3        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 19 21 18
  subtype2  0  5 30 25
  subtype3  3 13 15 12
  subtype4  6 15 11  8
  subtype5  2 18 30 12
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        2        0        3        6        2
  T2       19        5       13       15       18
  T3       21       30       15       11       30
  T4       18       25       12        8       12
[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 17  8  9
  subtype2 14 19  8 19
  subtype3 11 12 11  8
  subtype4 19  8  9  3
  subtype5 20 20 10 10
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       27       14       11       19       20
  N1       17       19       12        8       20
  N2        8        8       11        9       10
  N3        9       19        8        3       10
[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 60  2
  subtype2 58  3
  subtype3 34  7
  subtype4 37  2
  subtype5 54  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60    2
  subtype2   58    3
  subtype3   34    7
  subtype4   37    2
  subtype5   54    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       60       58       34       37       54
  1        2        3        7        2        4
[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 27 36
  subtype2 23 40
  subtype3 18 26
  subtype4 15 25
  subtype5 20 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   36
  subtype2   23   40
  subtype3   18   26
  subtype4   15   25
  subtype5   20   44
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       27       23       18       15       20
  MALE         36       40       26       25       44
[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 50  5
  subtype2 55  3
  subtype3 26  7
  subtype4 28  4
  subtype5 44  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50    5
  subtype2   55    3
  subtype3   26    7
  subtype4   28    4
  subtype5   44    7
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        50       55       26       28       44
  YES        5        3        7        4        7
[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  DIFFUSE TYPE
  subtype1                                    11
  subtype2                                    19
  subtype3                                     9
  subtype4                                     7
  subtype5                                     5
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     40
  subtype2                                                     28
  subtype3                                                     18
  subtype4                                                     14
  subtype5                                                     30
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 3
  subtype2                                                                 4
  subtype3                                                                 6
  subtype4                                                                 7
  subtype5                                                                14
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                                8
  subtype2                                                3
  subtype3                                                7
  subtype4                                                8
  subtype5                                               10
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        1
  subtype3                                        0
  subtype4                                        0
  subtype5                                        0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                               0
  subtype2                                               7
  subtype3                                               3
  subtype4                                               3
  subtype5                                               1
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                1
  subtype2                                                0
  subtype3                                                1
  subtype4                                                1
  subtype5                                                2
D5V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          0
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  28
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          7
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         0
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          1
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         2
[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 53  1  1  5
  subtype2 48  2  0  6
  subtype3 33  2  5  4
  subtype4 32  1  2  3
  subtype5 51  3  2  4
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       53       48       33       32       51
  R1        1        2        2        1        3
  R2        1        0        5        2        2
  RX        5        6        4        3        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    19                         1    36
  subtype2    18                         0    44
  subtype3    12                         0    18
  subtype4     8                         1    22
  subtype5    16                         2    36
D5V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           19       18       12        8       16
  BLACK OR AFRICAN AMERICAN        1        0        0        1        2
  WHITE                           36       44       18       22       36
[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"
D5V13, binary
          cls
clus        0  1
  subtype1  0 56
  subtype2  1 61
  subtype3  0 30
  subtype4  1 30
  subtype5  0 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   56
  subtype2    1   61
  subtype3    0   30
  subtype4    1   30
  subtype5    0   54
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        1        0        1        0
  NOT HISPANIC OR LATINO       56       61       30       30       54
[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 66 32
  subtype2 28 25
  subtype3 67 24
subtype1 subtype2 subtype3 
      98       53       91 
subtype1 subtype2 subtype3 
      32       25       24 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 
       26.70        11.70        30.90        13.87        17.29        19.33 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 
       18.05        19.89        12.16        21.90         9.21        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 
       39.78        18.15        28.73         3.45        29.56        33.21 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8363 TCGA-BR-8366 
       14.43        11.44         0.69         2.66         0.26         0.95 
TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8590 
       14.79         0.26         5.39         9.21        27.12         9.34 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IY 
       26.73        24.79        20.88         7.53         1.48        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-CD-5798 TCGA-CD-5800 
        8.98         0.72         0.53         0.66         2.83        13.15 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       13.18         0.07        12.53        12.30        12.39        12.59 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MH 
       15.39        12.82         3.42         9.34        11.61        12.20 
TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       54.08        29.98        19.07        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        6.97         1.02         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 
       15.02        25.71        20.55        18.84        13.35        17.19 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YT 
       12.36        12.33        24.72        16.80        19.50        14.27 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7998 
       16.44        36.43         7.99        72.23         3.48        22.29 
TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4H0 
       17.06         0.56        10.62        24.30        12.30         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.95        12.30        27.42        36.36         3.45        18.81 
TCGA-IN-8663 TCGA-IP-7968 
        3.39         2.53 

$subtype2
TCGA-BR-4187 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        4.64         9.57        15.95        13.68        22.32        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7957 TCGA-BR-8080 
        9.17        25.61        40.21        31.20         9.07         9.60 
TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 
        8.05        19.96         7.40        13.08        22.19        17.52 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8592 TCGA-BR-8682 
       26.33        14.04        11.80         3.72         6.28        32.58 
TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4J2 
        9.86        34.13         6.08        27.55        28.57        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5803 
       28.34        32.52        13.51         0.46        21.44         0.07 
TCGA-CD-5813 TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4462 TCGA-CG-4472 
       12.39        12.07        11.31        11.77         0.00        12.00 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV 
       19.13        18.61        17.85        17.19        20.91         5.92 
TCGA-D7-A4Z0 TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GY 
       14.76        14.07        59.54         5.03         0.26 

$subtype3
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6710 
       18.35         6.18         6.61        34.68        32.78         8.98 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-8058 
       30.90        44.94        36.16        35.84        15.32        37.25 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 
       29.59        32.25        29.42        31.10         4.31        31.27 
TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 
       25.05        25.18        20.22         1.12        12.79        28.14 
TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 
       31.96         8.22        20.65        20.42         1.15         3.25 
TCGA-CD-8528 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4301 
       12.33        11.64        12.43         6.58        12.62         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5718 
       14.01        47.05        21.99         9.01         7.07        36.00 
TCGA-CG-5720 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6521 
        0.99        28.96        69.04         7.99        12.66        18.54 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8575 
       10.26        15.22        15.98        12.79        11.31        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YY TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 
       14.66        21.14        13.78        16.24        14.47        21.27 
TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-A4BE TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 
       19.53        13.58        11.08         1.51        14.27        11.41 
TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       12.10         0.76         5.59        11.84        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        6.58        10.19        29.00        23.84         9.67        14.07 
TCGA-HU-A4HB 
       15.68 

subtype1 subtype2 subtype3 
    0.07     0.00     0.76 
subtype1 subtype2 subtype3 
  105.07    59.54    69.04 
subtype1 subtype2 subtype3 
   13.05    14.04    14.27 
[1] "0.1 - 105.1 (13.1)" "0.0 - 59.5 (14.0)"  "0.8 - 69.0 (14.3)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        3        9        9         9        19         2
  subtype2       0        0        3        5         9        10         0
  subtype3       2        7       15        9        11        15         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         21         15          6       10
  subtype2          9          8          8        4
  subtype3         12          7          9       11
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        2
  STAGE IA          3        0        7
  STAGE IB          9        3       15
  STAGE II          9        5        9
  STAGE IIA         9        9       11
  STAGE IIB        19       10       15
  STAGE III         2        0        1
  STAGE IIIA       21        9       12
  STAGE IIIB       15        8        7
  STAGE IIIC        6        8        9
  STAGE IV         10        4       11
[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  2 25 53 27
  subtype2  0 10 25 21
  subtype3 11 35 29 27
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        2        0       11
  T2       25       10       35
  T3       53       25       29
  T4       27       21       27
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 32 36 17 18
  subtype2 18 15  7 16
  subtype3 41 25 22 15
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       32       18       41
  N1       36       15       25
  N2       17        7       22
  N3       18       16       15
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 95  7
  subtype2 54  3
  subtype3 94  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   95    7
  subtype2   54    3
  subtype3   94    8
   clus
vv  subtype1 subtype2 subtype3
  0       95       54       94
  1        7        3        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 35 75
  subtype2 22 36
  subtype3 46 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   75
  subtype2   22   36
  subtype3   46   60
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       35       22       46
  MALE         75       36       60
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1 81  9
  subtype2 50  4
  subtype3 72 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   81    9
  subtype2   50    4
  subtype3   72   13
     clus
vv    subtype1 subtype2 subtype3
  NO        81       50       72
  YES        9        4       13
[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  DIFFUSE TYPE
  subtype1                                    16
  subtype2                                    20
  subtype3                                    15
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     57
  subtype2                                                     24
  subtype3                                                     49
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                16
  subtype2                                                                 4
  subtype3                                                                14
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               13
  subtype2                                                2
  subtype3                                               21
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        1
  subtype3                                        0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                               4
  subtype2                                               6
  subtype3                                               4
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                3
  subtype2                                                0
  subtype3                                                2
D6V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  57
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        13
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          4
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         3
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          6
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         0
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        21
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          4
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         2
[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 91  2  2  9
  subtype2 44  3  1  4
  subtype3 82  4  7  9
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       91       44       82
  R1        2        3        4
  R2        2        1        7
  RX        9        4        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    28                         2    66
  subtype2    16                         0    40
  subtype3    29                         2    50
D6V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           28       16       29
  BLACK OR AFRICAN AMERICAN        2        0        2
  WHITE                           66       40       50
[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"
D6V13, binary
          cls
clus        0  1
  subtype1  1 95
  subtype2  0 56
  subtype3  1 80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   95
  subtype2    0   56
  subtype3    1   80
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        1
  NOT HISPANIC OR LATINO       95       56       80
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 96 57
  subtype2 65 57
  subtype3 84 43
subtype1 subtype2 subtype3 
     153      122      127 
subtype1 subtype2 subtype3 
      57       57       43 
$subtype1
TCGA-3M-AB46 TCGA-3M-AB47 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       58.03        14.01        26.70        11.70        19.56        11.01 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 
       13.87        19.33        32.78        19.89        12.16        30.90 
TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 
       44.94        36.16        35.24        35.84        29.59        32.25 
TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 
       29.42        15.58         6.18        31.10         0.26         4.31 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 
       31.27        25.05        25.18         1.12        27.12        31.96 
TCGA-BR-A4CQ TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
       34.98        16.14         5.13         3.25        13.18        13.35 
TCGA-CD-5813 TCGA-CD-8531 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 
       12.39        12.59        11.61         6.58        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        47.05        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5720 
        9.01         7.07        22.98        30.97        36.00         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6524 
        4.01        21.07         7.99        25.71        20.55        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 
       13.35        10.26        15.22        15.98        12.79        24.72 
TCGA-D7-8575 TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A 
       18.21        36.43        13.78        20.32        15.65        19.96 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BE 
       14.47        21.27        19.53        17.06        13.58        11.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4G3 
       26.47         1.51        14.27        12.10        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GT 
       12.30        11.84        24.20         3.25        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7808 
        6.58        10.19        23.84         9.67        14.07         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IN-AB1X TCGA-R5-A7ZI 
       18.81         3.39         6.44        11.70        13.51        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A8MV TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E3 
        4.60         9.24       122.30        19.04         0.92        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       37.41        37.22        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E 
        9.27        23.41        27.35        64.57        39.45        21.83 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 
       61.22         1.71        60.85         9.50         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6B 
        6.58        66.81        11.24        26.93        18.41        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       54.12        16.14        27.55 

$subtype2
TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 
        9.47         4.64         7.43         9.57        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 
       22.32        26.10         9.17        25.61        18.05         8.98 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7901 
       40.21        31.20        21.90        18.15        15.32         3.45 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 
        9.07        29.56        33.21        37.25        14.43         9.60 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 
        8.05         0.56         2.66        19.96         7.40        13.08 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       22.19        17.52         0.95        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       11.80         3.72         5.39        12.79         9.34        28.14 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T 
        6.28        26.73        32.58         9.86        20.88        34.13 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        6.08        27.55        28.57         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI 
       28.34         0.66        32.52        13.51         0.46        21.44 
TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8534 
        2.83         0.07        12.30        12.39        11.64        12.07 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5728 
       11.31        11.77        12.00         6.97         1.02        65.10 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
       69.04        12.66         4.54        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6818 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       18.61        12.36        17.19        21.14        20.91        16.44 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 
       14.76        26.43         2.83        11.44         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        7.13         0.62        11.38         3.48        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-IN-7806 
       59.54         5.03        21.37         0.10         0.26        36.36 
TCGA-IN-A7NR TCGA-MX-A5UG TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 
        6.51         3.72        11.05         5.13        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8P8 
      116.38        71.38        57.44        35.61        16.87        30.97 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R 
        1.87        15.65         9.73         5.72         2.66        42.54 
TCGA-VQ-AA6K TCGA-ZA-A8F6 
       12.43        17.26 

$subtype3
TCGA-B7-A5TN TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8060 
        9.44         9.21        33.63        39.78        28.73        11.44 
TCGA-BR-8077 TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8485 TCGA-BR-8486 
        0.69         2.20        14.79         0.26         9.21        20.22 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
        7.53        24.79         8.22        10.68        13.87         7.53 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        1.48        12.89         0.72        20.65        20.42         1.15 
TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       13.15         0.07        12.59        12.53         0.07        12.33 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
       15.39        12.82        12.43         3.42         9.34        12.43 
TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5725 
       12.20        54.08        19.07        21.99        18.97        15.02 
TCGA-D7-6526 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 
       17.19        11.31        12.33        16.80        19.50        14.66 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-EQ-A4SO 
       14.27         5.92        11.24        22.29         7.99        16.24 
TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-FP-A9TM TCGA-HF-A5NB 
       72.23         0.56         5.52         0.23         6.21        30.51 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        5.92        12.59        14.17        11.41        10.62         0.76 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 
       22.75        25.81        11.77         8.98         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RJ 
       29.00        12.30        15.68        27.42        18.38        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        5.19        19.53         1.41         6.74        12.59        10.62 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UJ 
        7.82         2.53         5.56        63.62        36.95        19.73 
TCGA-MX-A663 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
        9.86        14.04        45.67        18.21         8.52         6.08 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.67        37.91         8.94         5.79        48.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
       13.25        13.02        18.48        43.36        38.14         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91D TCGA-VQ-A91N 
       22.19        12.79         2.70        17.85        11.70        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91V TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       20.81        32.88        42.64        55.56         9.04         4.54 
TCGA-VQ-A94O TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G 
       21.04        43.66        28.41        38.93        17.13        26.04 
TCGA-ZQ-A9CR 
        0.79 

subtype1 subtype2 subtype3 
    0.00     0.07     0.07 
subtype1 subtype2 subtype3 
  122.30   116.38    72.23 
subtype1 subtype2 subtype3 
  16.140   12.935   12.790 
[1] "0.0 - 122.3 (16.1)" "0.1 - 116.4 (12.9)" "0.1 - 72.2 (12.8)" 
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2        7       20       16        17        22         2
  subtype2       0        0        9        8        11        16         1
  subtype3       1        8       11        8        13        18         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         28         23          9       17
  subtype2         25         21         17       18
  subtype3         29         18         13       10
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        1
  STAGE IA          7        0        8
  STAGE IB         20        9       11
  STAGE II         16        8        8
  STAGE IIA        17       11       13
  STAGE IIB        22       16       18
  STAGE III         2        1        1
  STAGE IIIA       28       25       29
  STAGE IIIB       23       21       18
  STAGE IIIC        9       17       13
  STAGE IV         17       18       10
[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 12 46 79 31
  subtype2  0 21 55 51
  subtype3 11 25 59 36
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       12        0       11
  T2       46       21       25
  T3       79       55       59
  T4       31       51       36
[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 56 52 34 24
  subtype2 34 33 22 37
  subtype3 39 33 29 26
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       56       34       39
  N1       52       33       33
  N2       34       22       29
  N3       24       37       26
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus         0   1
  subtype1 151  14
  subtype2 114  11
  subtype3 119   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  151   14
  subtype2  114   11
  subtype3  119    5
   clus
vv  subtype1 subtype2 subtype3
  0      151      114      119
  1       14       11        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1  64 110
  subtype2  45  85
  subtype3  46  86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   64  110
  subtype2   45   85
  subtype3   46   86
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       64       45       46
  MALE        110       85       86
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus         0   1
  subtype1 113  29
  subtype2 102  17
  subtype3  96  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  113   29
  subtype2  102   17
  subtype3   96   26
     clus
vv    subtype1 subtype2 subtype3
  NO       113      102       96
  YES       29       17       26
[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  DIFFUSE TYPE
  subtype1                                    24
  subtype2                                    39
  subtype3                                     9
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     69
  subtype2                                                     47
  subtype3                                                     47
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                37
  subtype2                                                                16
  subtype3                                                                27
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               29
  subtype2                                               12
  subtype3                                               36
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        4
  subtype2                                        4
  subtype3                                        3
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                               6
  subtype2                                              10
  subtype3                                               6
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                4
  subtype2                                                1
  subtype3                                                3
D7V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  69
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        29
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          6
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         4
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   39
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  47
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        12
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                         10
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  47
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        36
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          6
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         3
[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 128   6   9  17
  subtype2 106   6   5   6
  subtype3 110   6   4   2
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      128      106      110
  R1        6        6        6
  R2        9        5        4
  RX       17        6        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    26                         4   106
  subtype2    28                         2    93
  subtype3    34                         7    74
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           26       28       34
  BLACK OR AFRICAN AMERICAN        4        2        7
  WHITE                          106       93       74
[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"
D7V13, binary
          cls
clus         0   1
  subtype1   3 109
  subtype2   1 114
  subtype3   1  94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  109
  subtype2    1  114
  subtype3    1   94
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        1
  NOT HISPANIC OR LATINO      109      114       94
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 142  78
  subtype2  43  35
  subtype3  60  44
subtype1 subtype2 subtype3 
     220       78      104 
subtype1 subtype2 subtype3 
      78       35       44 
$subtype1
TCGA-3M-AB46 TCGA-3M-AB47 TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       58.03        14.01        26.70        11.70        19.56        11.01 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       13.87        19.33        32.78        19.89        12.16         8.98 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       30.90        44.94        36.16        35.24        35.84        33.63 
TCGA-BR-7722 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       15.32        29.56        37.25        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
        0.56        29.42        19.96        15.58         6.18        31.10 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8484 
        0.26         0.95         4.31        31.27        25.05        25.18 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 
       20.22         1.12        27.12        28.14         7.53        31.96 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.87        34.98         1.48        12.89         0.53         0.66 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5801 
       20.42         1.15        16.14         5.13         3.25        13.18 
TCGA-CD-5813 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 
       12.39        12.33        12.59        11.64        15.39        12.07 
TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       12.43        11.61         6.58        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
       15.95         7.99         8.05        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         0.00         9.01         7.07        22.98        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-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
       16.24        14.47        72.23        21.27        11.38        19.53 
TCGA-FP-8211 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HJ-7597 TCGA-HU-8238 
       13.58        11.08         5.52         6.21        26.47         1.51 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ 
        5.59        12.30        11.84        24.20         3.25        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         6.51         6.58        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        29.00        23.84         9.67        14.07        15.68 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36         3.45        18.81         3.39        12.46         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR 
       19.53         1.41         6.44         6.74        12.59         6.51 
TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-R5-A7ZI TCGA-R5-A804 
       11.70         7.82        13.51         2.53        74.53         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N5 
        9.24        11.05       122.30        40.64       115.69        57.44 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       19.04         0.92        48.79        21.73        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.22         7.73        30.97        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PU 
        2.50         1.87         9.27        23.41        15.65        27.35 
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-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       26.93        18.41        43.66        28.41        32.94        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       26.04        16.14        27.55        12.43 

$subtype2
TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6457 TCGA-BR-6563 
        9.47         4.64         7.43         9.57        13.68        22.32 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 
       26.10        25.61        18.05        40.21        31.20        21.90 
TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8362 TCGA-BR-8364 
       18.15         9.07        33.21         9.60        13.08        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-8483 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
        5.39        12.79         6.28        26.73        32.58         9.86 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       20.88        34.13         6.08        27.55        28.57         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI 
       14.17        28.34        32.52        13.51         0.46        21.44 
TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI TCGA-CG-4472 
        2.83         0.07        11.31        12.43        11.77        12.00 
TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
        1.02       105.07        65.10         4.54        19.13        18.61 
TCGA-D7-6524 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       17.85        20.91        16.44        26.43         2.83        11.44 
TCGA-D7-A747 TCGA-EQ-5647 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
        8.38         0.62         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-HU-A4GQ TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 
        5.03         0.10         3.72         5.13       116.38        71.38 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P TCGA-ZA-A8F6 
       35.61        16.87         9.73         5.72         2.66        17.26 

$subtype3
TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 
        9.44        17.29         9.17         9.21        39.78        28.73 
TCGA-BR-7901 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 
        3.45        14.43        11.44         0.69         2.66         2.20 
TCGA-BR-8297 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 
        7.40        14.79         0.26         9.21         9.34        24.79 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-CD-5800 
        8.22        10.68         7.53         0.72        20.65        13.15 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       13.35         0.07        12.59        12.53         0.07        12.30 
TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 
       12.39        12.82         3.42         9.34        12.20        20.02 
TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4466 
        1.02        54.08         4.01        19.07        21.99        18.97 
TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5732 TCGA-D7-6520 TCGA-D7-6526 
       36.00        15.02        79.07        69.04        18.84        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       10.26        15.98        12.36        11.31        12.33        16.80 
TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A6F0 TCGA-D7-A74B TCGA-EQ-8122 TCGA-FP-8099 
       21.14         5.92        22.29         7.13         7.99        17.06 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 
        0.56         0.23        30.51         5.92        12.59        14.17 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD 
       22.75        25.81        11.77        12.95        12.30        27.42 
TCGA-IN-A6RI TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A5UJ 
       18.38        10.62         5.56        63.62        36.95        19.73 
TCGA-MX-A663 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
        9.86        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     0.07     0.07 
subtype1 subtype2 subtype3 
  122.30   116.38    79.07 
subtype1 subtype2 subtype3 
  14.710   13.860   12.805 
[1] "0.0 - 122.3 (14.7)" "0.1 - 116.4 (13.9)" "0.1 - 79.1 (12.8)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2       14       23       15        25        32         2
  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         43         36         19       23
  subtype2         17         15          9        9
  subtype3         22         11         11       13
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        1
  STAGE IA         14        0        1
  STAGE IB         23        7       10
  STAGE II         15        6       11
  STAGE IIA        25        9        7
  STAGE IIB        32        7       17
  STAGE III         2        0        2
  STAGE IIIA       43       17       22
  STAGE IIIB       36       15       11
  STAGE IIIC       19        9       11
  STAGE IV         23        9       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 24 11 22
  subtype3 27 31 23 22
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       80       22       27
  N1       63       24       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 165  47
  subtype2  68   7
  subtype3  78  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  165   47
  subtype2   68    7
  subtype3   78   18
     clus
vv    subtype1 subtype2 subtype3
  NO       165       68       78
  YES       47        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  DIFFUSE TYPE
  subtype1                                    39
  subtype2                                    25
  subtype3                                     8
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     97
  subtype2                                                     31
  subtype3                                                     35
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                47
  subtype2                                                                 7
  subtype3                                                                26
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               40
  subtype2                                                8
  subtype3                                               29
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        7
  subtype2                                        2
  subtype3                                        2
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                              10
  subtype2                                               7
  subtype3                                               5
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                3
  subtype2                                                1
  subtype3                                                4
D8V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   39
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  97
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       47
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        40
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 7
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                         10
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         3
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          7
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  35
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        29
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          5
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         4
[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 44 28
  subtype2 39 17
  subtype3 34 24
  subtype4 37 18
  subtype5 18 14
  subtype6 28 30
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      72       56       58       55       32       58 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      28       17       24       18       14       30 
$subtype1
TCGA-3M-AB46 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8295 TCGA-BR-8368 
       58.03        28.73        11.44         0.69         2.20         4.31 
TCGA-BR-8485 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A452 
        9.21         7.53        24.79        31.96        10.68         7.53 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-8526 TCGA-CD-8533 
        1.48         0.72        20.65        16.14        12.53        15.39 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-5725 TCGA-CG-5730 
       12.82         3.42         9.34        12.20        15.02         4.01 
TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 
       12.33        14.27        11.24         2.83        20.32        22.29 
TCGA-D7-A74A TCGA-FP-8631 TCGA-FP-A4BE TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GF 
       19.96         0.56        11.08         5.92        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-A6RI TCGA-IN-A7NT 
       11.77         6.51        12.95        12.30        18.38        10.62 
TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-VQ-A8DU 
       63.62        14.04        18.21         8.52         6.08         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8PB 
       13.25        18.48        43.36        38.14         7.73        34.29 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91D TCGA-VQ-A91Q 
       22.19        12.79         2.70        17.85        11.70        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A92D 
       32.88         1.71        60.85        55.56         9.04        66.81 
TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D 
       21.04        11.24        28.41        38.93        32.94        17.13 

$subtype2
TCGA-3M-AB47 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-6453 TCGA-BR-7703 TCGA-BR-A4QI 
       14.01        19.56        11.01        15.95        36.16        21.44 
TCGA-BR-A4QM TCGA-CD-A4MG TCGA-D7-6528 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-D7-A6EY 
        5.13         6.58        15.22         5.92        14.76        11.44 
TCGA-D7-A6F2 TCGA-F1-A448 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HU-A4G3 TCGA-HU-A4G8 
       15.65        21.27        13.58         6.21         5.59        11.84 
TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H4 
        3.25        21.37        29.98        10.19         0.26        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP 
        9.67        14.07        15.68        12.46         5.19         6.44 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI 
        6.51        11.70         7.82         3.72        19.73        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-SW-A7EB 
        4.60         9.24        16.67       122.30       115.69         5.79 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91E TCGA-VQ-A91N 
       46.26        16.31         1.87        64.57        21.83        18.74 
TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94U TCGA-VQ-AA6F 
       42.64         9.50         4.54         6.58        26.93        54.12 
TCGA-VQ-AA6I TCGA-VQ-AA6J 
       16.14        27.55 

$subtype3
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 
       26.70        11.70        34.68        13.87        19.33         9.17 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        18.05        19.89        12.16         8.98        40.21 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8363 
       30.90        44.94         8.05        15.58         6.18         0.26 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        3.25        13.15        13.18        13.35         0.07        12.39 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        8.05        14.01        19.07         6.97        36.00         1.02 
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-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        69.04        21.07         7.99        25.71 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 
       12.66         4.54        20.55        18.84        17.85        13.35 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19        10.26        15.98        12.79        12.36        11.31 
TCGA-D7-8570 TCGA-D7-A4YY TCGA-EQ-5647 TCGA-F1-6874 
       24.72        13.78         0.62        14.47 

$subtype4
TCGA-B7-A5TK TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7958 TCGA-BR-8058 
        9.47        35.24        35.84        18.15        29.56        37.25 
TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       29.59        29.42        31.10        31.27         0.26        25.05 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-A4CQ TCGA-CD-8525 
       20.22         1.12        12.79        28.14        34.98        12.59 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-D7-8575 
        0.07        12.30        12.59        11.64        12.43        18.21 
TCGA-D7-8576 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       14.66        72.23         3.48        19.53        22.29        17.06 
TCGA-HU-8238 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-IN-7806 TCGA-IN-7808 
        1.51        11.41        12.10        10.62        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J 
       18.81         3.39        19.53        13.51         2.53        36.95 
TCGA-R5-A7O7 TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8P8 TCGA-VQ-A8PF TCGA-VQ-A8PO 
       45.67         0.92        21.73        30.97         2.50         9.27 
TCGA-VQ-A8PU TCGA-VQ-A91K TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-AA68 TCGA-VQ-AA6G 
       27.35        61.22         2.01        55.43        43.66        26.04 
TCGA-VQ-AA6K 
       12.43 

$subtype5
TCGA-B7-A5TN TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-8059 TCGA-BR-8291 TCGA-BR-8373 
        9.44         9.21        33.63        14.43        19.96        14.79 
TCGA-BR-8677 TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-CD-8524 TCGA-CD-8530 
       26.73        12.89         8.98        28.34         0.07        12.39 
TCGA-CD-A48C TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-A748 TCGA-EQ-8122 
       11.61        16.80        17.19        21.14         4.34         7.99 
TCGA-KB-A6F5 TCGA-MX-A663 TCGA-RD-A8MW TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-SW-A7EA 
        5.56         9.86        37.91        57.44        35.61        19.04 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PP TCGA-VQ-A91A TCGA-VQ-A928 TCGA-VQ-A94R 
       37.41        37.22        23.41        39.45         5.72        42.54 
TCGA-VQ-AA64 TCGA-ZQ-A9CR 
       18.41         0.79 

$subtype6
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6803 
       17.29        13.68        22.32        26.10        25.61        31.20 
TCGA-BR-7196 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 
       21.90         3.45         9.07        33.21         9.60         2.66 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8370 
        7.40        13.08        22.19        17.52        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8682 
       11.80         3.72         5.39         9.34         6.28        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        9.86         8.22        34.13         6.08        27.55        28.57 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-8534 
        0.66        32.52        13.51         0.46         2.83        12.07 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-8579 
       11.31        11.77        19.13        18.54        18.61        20.91 
TCGA-D7-A4YU TCGA-D7-A6ET TCGA-D7-A747 TCGA-D7-A74B TCGA-FP-8209 TCGA-FP-8210 
       16.44        26.43         8.38         7.13        59.54         5.03 
TCGA-HU-A4GQ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N6 TCGA-RD-A8NB 
        0.10        11.05         5.13        40.64         8.94        16.87 
TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A94P TCGA-ZA-A8F6 
       15.65         9.73         2.66        17.26 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.56     0.26     0.07     0.07     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   66.81   122.30   105.07    72.23    57.44    59.54 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  12.885   14.040   13.565   18.210   16.995   12.575 
[1] "0.6 - 66.8 (12.9)"  "0.3 - 122.3 (14.0)" "0.1 - 105.1 (13.6)"
[4] "0.1 - 72.2 (18.2)"  "0.1 - 57.4 (17.0)"  "0.1 - 59.5 (12.6)" 
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        1       10        2         7         7         1
  subtype2       0        4        4        0         4        11         0
  subtype3       1        1        6       13         7         6         0
  subtype4       1        2        3        8         8        11         1
  subtype5       0        0        3        4         2         6         1
  subtype6       0        0        4        2         7         7         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         19         13          7        6
  subtype2         10         13          5        6
  subtype3         14          4          2        6
  subtype4          9          6          7        3
  subtype5          6          5          1        5
  subtype6         11         12         10        6
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           1        0        1        1        0        0
  STAGE IA          1        4        1        2        0        0
  STAGE IB         10        4        6        3        3        4
  STAGE II          2        0       13        8        4        2
  STAGE IIA         7        4        7        8        2        7
  STAGE IIB         7       11        6       11        6        7
  STAGE III         1        0        0        1        1        0
  STAGE IIIA       19       10       14        9        6       11
  STAGE IIIB       13       13        4        6        5       12
  STAGE IIIC        7        5        2        7        1       10
  STAGE IV          6        6        6        3        5        6
[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  3 14 38 19
  subtype2  7 10 26 14
  subtype3  2 25 26  7
  subtype4  3  9 27 21
  subtype5  0  6 16 11
  subtype6  0  8 30 21
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        3        7        2        3        0        0
  T2       14       10       25        9        6        8
  T3       38       26       26       27       16       30
  T4       19       14        7       21       11       21
[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 21 19 16 16
  subtype2 11 13 20 12
  subtype3 22 17 11 10
  subtype4 26 17  8  9
  subtype5  9 11  6  6
  subtype6 14 12 13 18
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       21       11       22       26        9       14
  N1       19       13       17       17       11       12
  N2       16       20       11        8        6       13
  N3       16       12       10        9        6       18
[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"
D9V6, binary
          cls
clus        0  1
  subtype1 67  4
  subtype2 51  4
  subtype3 55  4
  subtype4 52  3
  subtype5 29  2
  subtype6 52  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67    4
  subtype2   51    4
  subtype3   55    4
  subtype4   52    3
  subtype5   29    2
  subtype6   52    5
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       67       51       55       52       29       52
  1        4        4        4        3        2        5
[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"
D9V7, binary
          cls
clus        0  1
  subtype1 26 48
  subtype2 16 41
  subtype3 21 39
  subtype4 22 38
  subtype5 11 22
  subtype6 22 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   48
  subtype2   16   41
  subtype3   21   39
  subtype4   22   38
  subtype5   11   22
  subtype6   22   37
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       26       16       21       22       11       22
  MALE         48       41       39       38       22       37
[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"
D9V8, binary
          cls
clus        0  1
  subtype1 52 18
  subtype2 43 12
  subtype3 44  6
  subtype4 46 11
  subtype5 23 10
  subtype6 53  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52   18
  subtype2   43   12
  subtype3   44    6
  subtype4   46   11
  subtype5   23   10
  subtype6   53    6
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        52       43       44       46       23       53
  YES       18       12        6       11       10        6
[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  DIFFUSE TYPE
  subtype1                                     2
  subtype2                                    14
  subtype3                                     7
  subtype4                                     7
  subtype5                                     6
  subtype6                                    22
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     24
  subtype2                                                     13
  subtype3                                                     23
  subtype4                                                     27
  subtype5                                                     11
  subtype6                                                     18
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                19
  subtype2                                                                 9
  subtype3                                                                17
  subtype4                                                                 9
  subtype5                                                                 8
  subtype6                                                                 6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               26
  subtype2                                               14
  subtype3                                                8
  subtype4                                               11
  subtype5                                                4
  subtype6                                                6
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        3
  subtype3                                        0
  subtype4                                        2
  subtype5                                        0
  subtype6                                        2
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                               1
  subtype2                                               3
  subtype3                                               3
  subtype4                                               4
  subtype5                                               3
  subtype6                                               5
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                2
  subtype2                                                1
  subtype3                                                2
  subtype4                                                0
  subtype5                                                1
  subtype6                                                0
D9V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        26
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          1
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         2
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        14
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         2
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          4
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         0
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype6
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          5
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         0
[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
  subtype1 63  2  2
  subtype2 45  3  2
  subtype3 50  3  3
  subtype4 56  1  0
  subtype5 29  1  0
  subtype6 48  4  3
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       63       45       50       56       29       48
  R1        2        3        3        1        1        4
  R2        2        2        3        0        0        3
[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"
D9V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    18                         6    41
  subtype2    13                         2    38
  subtype3     6                         1    36
  subtype4    11                         3    41
  subtype5     7                         0    24
  subtype6    12                         0    47
D9V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           18       13        6       11        7
  BLACK OR AFRICAN AMERICAN        6        2        1        3        0
  WHITE                           41       38       36       41       24
                           clus
vv                          subtype6
  ASIAN                           12
  BLACK OR AFRICAN AMERICAN        0
  WHITE                           47
[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"
D9V13, binary
          cls
clus        0  1
  subtype1  1 44
  subtype2  2 40
  subtype3  0 43
  subtype4  2 42
  subtype5  0 25
  subtype6  0 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   44
  subtype2    2   40
  subtype3    0   43
  subtype4    2   42
  subtype5    0   25
  subtype6    0   56
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        2        0        2        0        0
  NOT HISPANIC OR LATINO       44       40       43       42       25       56
[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(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 53 29
  subtype2 29 27
  subtype3 23 12
  subtype4 46 26
  subtype5 15 11
  subtype6 34 26
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      82       56       35       72       26       60 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      29       27       12       26       11       26 
$subtype1
TCGA-3M-AB46 TCGA-BR-6565 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8486 
       58.03         9.17         6.18        31.10         4.31        20.22 
TCGA-BR-8487 TCGA-BR-A4CS TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-8533 
        1.12         1.48        20.65        16.14        13.15        15.39 
TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5727 TCGA-CG-5730 
       12.43         6.58        36.00         0.99        79.07         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       69.04        12.66        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-D7-A6EZ 
       12.79        11.31        18.21        14.27        11.24        20.32 
TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-A4BE TCGA-HU-8243 TCGA-HU-8602 
       19.96        14.47        21.27        11.08         5.92        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GF TCGA-HU-A4GH 
       12.10        10.62         5.59        11.84        25.81        11.77 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       29.98         6.51        10.19        12.95        23.84        12.30 
TCGA-HU-A4H8 TCGA-IN-A6RI TCGA-IN-AB1X TCGA-KB-A93J TCGA-R5-A7ZI TCGA-R5-A7ZR 
       14.07        18.38        13.51        36.95        74.53         6.08 
TCGA-R5-A805 TCGA-RD-A7C1 TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        9.24        16.67         0.92        18.48        21.73        38.14 
TCGA-VQ-A8PB TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D 
       34.29        17.85         9.27        27.35        64.57        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       21.83        61.22        18.74        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A94T TCGA-VQ-AA68 
       60.85         9.50        55.43         4.54        11.24        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6I 
       28.41        38.93        17.13        16.14 

$subtype2
TCGA-3M-AB47 TCGA-BR-6453 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6803 
       14.01        15.95        22.32        26.10        25.61        31.20 
TCGA-BR-7196 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8364 
       21.90         9.07        33.21         9.60         7.40        22.19 
TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8590 TCGA-BR-8592 
       17.52        14.04        11.80         3.72         9.34         6.28 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       26.73        32.58        34.13         6.08        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        8.98        28.34         0.66        32.52        13.51         0.46 
TCGA-CD-8524 TCGA-CD-A489 TCGA-CD-A4MI TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-8574 
        0.07        11.31        11.77        19.13        18.61        17.19 
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-A4GQ TCGA-HU-A4GY TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8N0 
        5.03         0.10         0.26         3.72         5.13        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P 
      115.69        35.61        16.87         9.73         5.72         2.66 
TCGA-VQ-A94R TCGA-ZA-A8F6 
       42.54        17.26 

$subtype3
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
       26.70        11.70        34.68        13.87        13.68        19.33 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       32.78        18.05        19.89         8.98        40.21        30.90 
TCGA-BR-6852 TCGA-BR-8676 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 
       44.94         7.53         2.83         3.25        13.18         0.07 
TCGA-CD-5813 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5721 
       12.39         8.05        14.01         6.97         1.02         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 
        0.99       105.07        28.96        65.10        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6524 TCGA-EQ-5647 
       25.71         4.54        18.84        17.85         0.62 

$subtype4
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-6709 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       19.56        11.01        12.16        36.16        35.24        35.84 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8680 TCGA-BR-A4CQ 
       33.63        18.15        29.42        15.58        31.96        34.98 
TCGA-BR-A4IY TCGA-BR-A4QM TCGA-CD-8534 TCGA-CD-A48C TCGA-CG-5724 TCGA-D7-6519 
       12.89         5.13        12.07        11.61        12.03        20.55 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY 
       18.54        13.35         5.92        13.78        14.76        11.44 
TCGA-D7-A6F2 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-A9TM 
       15.65        72.23         3.48        19.53        13.58         6.21 
TCGA-HU-8238 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-IN-7806 
        1.51         3.25        21.37         9.67        15.68        36.36 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81         3.39        12.46         5.19        19.53 
TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 
        6.44         6.51        11.70         7.82         2.53         5.56 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-SW-A7EA TCGA-VQ-A8E7 
        4.60        11.05       122.30        57.44        19.04        37.41 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PP 
       37.22        30.97        46.26        16.31         1.87        23.41 
TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94U TCGA-VQ-AA64 
       39.45        20.81         6.58        66.81        26.93        18.41 
TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       32.94        54.12        26.04        27.55        12.43         0.79 

$subtype5
TCGA-B7-A5TK TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8291 
        9.47        29.56        37.25        29.59         8.05        19.96 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 
       13.08         0.26         3.32        31.27         0.26        25.05 
TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8683 TCGA-BR-A4QI TCGA-CD-8531 
        5.39        12.79        28.14         9.86        21.44        12.59 
TCGA-CD-8532 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A4YU TCGA-FP-7998 TCGA-VQ-A8PF 
       11.64        24.72        14.66        16.44        22.29         2.50 
TCGA-VQ-A8PQ TCGA-VQ-A923 
       15.65         2.01 

$subtype6
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-8485 
       11.44         0.69         2.66         2.20        14.79         9.21 
TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4J1 TCGA-CD-5802 
       24.79         8.22        10.68         7.53         0.72        13.35 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8535 
       12.59        12.53         0.07        12.30        12.39        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4449 TCGA-CG-5725 TCGA-D7-6818 
        3.42         9.34        12.20        19.07        15.02        12.36 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-8122 
       12.33        16.80        21.14         2.83        22.29         7.99 
TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-A4GD TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A5UJ 
       17.06         0.56        22.75        10.62        63.62        19.73 
TCGA-MX-A663 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A8MW 
        9.86        14.04        45.67        18.21         8.52        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        8.94         5.79         5.46        13.25        43.36         7.73 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O 
       22.19        12.79         2.70        55.56         9.04        21.04 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.92     0.07     0.07     0.79     0.26     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   79.07   115.69   105.07   122.30    37.25    63.62 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  15.305   14.995   13.870   15.665   13.870   12.345 
[1] "0.9 - 79.1 (15.3)"  "0.1 - 115.7 (15.0)" "0.1 - 105.1 (13.9)"
[4] "0.8 - 122.3 (15.7)" "0.3 - 37.2 (13.9)"  "0.1 - 63.6 (12.3)" 
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2        3        8        9        12        10         1
  subtype2       0        0        4        2         7         5         0
  subtype3       0        1        3        8         6         3         0
  subtype4       1        4        6        4         3        15         1
  subtype5       0        0        2        1         1         5         0
  subtype6       0        0        7        5         6        10         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         17         11          8        4
  subtype2         11         13          8        7
  subtype3          9          1          0        5
  subtype4         12         13          7        9
  subtype5          4          8          6        1
  subtype6         16          7          3        6
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           2        0        0        1        0        0
  STAGE IA          3        0        1        4        0        0
  STAGE IB          8        4        3        6        2        7
  STAGE II          9        2        8        4        1        5
  STAGE IIA        12        7        6        3        1        6
  STAGE IIB        10        5        3       15        5       10
  STAGE III         1        0        0        1        0        1
  STAGE IIIA       17       11        9       12        4       16
  STAGE IIIB       11       13        1       13        8        7
  STAGE IIIC        8        8        0        7        6        3
  STAGE IV          4        7        5        9        1        6
[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  6 20 39 20
  subtype2  0  9 27 21
  subtype3  1 12 18  5
  subtype4  7 16 35 18
  subtype5  0  2 12 14
  subtype6  1 13 32 15
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        6        0        1        7        0        1
  T2       20        9       12       16        2       13
  T3       39       27       18       35       12       32
  T4       20       21        5       18       14       15
[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 33 17 20 14
  subtype2 12 13 12 18
  subtype3 15 11  7  3
  subtype4 19 20 19 17
  subtype5  8  6  3 11
  subtype6 16 22 13  8
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       33       12       15       19        8       16
  N1       17       13       11       20        6       22
  N2       20       12        7       19        3       13
  N3       14       18        3       17       11        8
[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"
D10V6, binary
          cls
clus        0  1
  subtype1 81  2
  subtype2 50  4
  subtype3 32  4
  subtype4 65  6
  subtype5 26  1
  subtype6 52  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   81    2
  subtype2   50    4
  subtype3   32    4
  subtype4   65    6
  subtype5   26    1
  subtype6   52    5
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       81       50       32       65       26       52
  1        2        4        4        6        1        5
[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"
D10V7, binary
          cls
clus        0  1
  subtype1 32 53
  subtype2 24 33
  subtype3 12 24
  subtype4 17 59
  subtype5 11 17
  subtype6 22 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   53
  subtype2   24   33
  subtype3   12   24
  subtype4   17   59
  subtype5   11   17
  subtype6   22   39
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       32       24       12       17       11       22
  MALE         53       33       24       59       17       39
[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"
D10V8, binary
          cls
clus        0  1
  subtype1 62 19
  subtype2 47 10
  subtype3 27  0
  subtype4 54 20
  subtype5 26  1
  subtype6 45 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   62   19
  subtype2   47   10
  subtype3   27    0
  subtype4   54   20
  subtype5   26    1
  subtype6   45   13
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        62       47       27       54       26       45
  YES       19       10        0       20        1       13
[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  DIFFUSE TYPE
  subtype1                                     9
  subtype2                                    24
  subtype3                                     3
  subtype4                                    15
  subtype5                                     4
  subtype6                                     3
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     19
  subtype2                                                     17
  subtype3                                                     17
  subtype4                                                     26
  subtype5                                                     13
  subtype6                                                     24
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                20
  subtype2                                                                 5
  subtype3                                                                11
  subtype4                                                                13
  subtype5                                                                 4
  subtype6                                                                15
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               30
  subtype2                                                3
  subtype3                                                2
  subtype4                                               12
  subtype5                                                7
  subtype6                                               15
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        2
  subtype3                                        0
  subtype4                                        4
  subtype5                                        0
  subtype6                                        0
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE
  subtype1                                               2
  subtype2                                               5
  subtype3                                               3
  subtype4                                               5
  subtype5                                               0
  subtype6                                               4
          vv
clus       STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE
  subtype1                                                4
  subtype2                                                1
  subtype3                                                0
  subtype4                                                1
  subtype5                                                0
  subtype6                                                0
D10V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        30
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          2
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         4
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          5
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          3
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        12
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          5
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         1
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          0
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         0
                                                                   clus
vv                                                                  subtype6
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        15
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
  STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE                          4
  STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE                         0
[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
  subtype1 78  0  2
  subtype2 47  4  2
  subtype3 27  2  3
  subtype4 65  5  1
  subtype5 26  0  1
  subtype6 48  3  1
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       78       47       27       65       26       48
  R1        0        4        2        5        0        3
  R2        2        2        3        1        1        1
[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"
D10V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    20                         5    49
  subtype2    15                         0    42
  subtype3     5                         0    19
  subtype4    10                         5    54
  subtype5     3                         0    24
  subtype6    14                         2    39
D10V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           20       15        5       10        3
  BLACK OR AFRICAN AMERICAN        5        0        0        5        0
  WHITE                           49       42       19       54       24
                           clus
vv                          subtype6
  ASIAN                           14
  BLACK OR AFRICAN AMERICAN        2
  WHITE                           39
[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"
D10V13, binary
          cls
clus        0  1
  subtype1  3 50
  subtype2  0 53
  subtype3  0 24
  subtype4  0 53
  subtype5  1 24
  subtype6  1 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   50
  subtype2    0   53
  subtype3    0   24
  subtype4    0   53
  subtype5    1   24
  subtype6    1   46
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            3        0        0        0        1        1
  NOT HISPANIC OR LATINO       50       53       24       53       24       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"
