[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/15090008/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/15114286/STAD-TP.mergedcluster.txt"

nPatients in clinical file=438, in cluster file=443, common to both=438
[1]  10 438
[1] "CN_CNMF"
[1] 3
  1   2   3   4   5 
121 186  36  74  19 
  1   2   3   4   5 
121 186  36  74  19 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
121 120  42 107 
  1   2   3   4 
121 120  42 107 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
82 91 91 
 1  2  3 
82 91 91 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
34 84 55 91 
 1  2  3  4 
34 84 55 91 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
66 63 46 37 62 
 1  2  3  4  5 
66 63 46 37 62 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
38 21 50 62 42 40 21 
 1  2  3  4  5  6  7 
38 21 50 62 42 40 21 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
186 132 119 
  1   2   3 
186 132 119 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 79 174  79 105 
  1   2   3   4 
 79 174  79 105 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5  6 
75 55 61 58 36 58 
 1  2  3  4  5  6 
75 55 61 58 36 58 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
199  72  72 
  1   2   3 
199  72  72 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "COMPLETENESS_OF_RESECTION"             
[17] "NUMBER_OF_LYMPH_NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 438 columns.

[1] "Batch" "20"   
[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=137,	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=248,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=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:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH_NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 438 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"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "COMPLETENESS_OF_RESECTION"             
[10] "NUMBER_OF_LYMPH_NODES"                 
[11] "RACE"                                  
[12] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
 22  90 197 119 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 22  90 197 119 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 22  90 197 119 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 22  90 197 119 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
131 118  84  89 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
131 118  84  89 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
131 118  84  89 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
131 118  84  89 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=34, 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  71  43
  subtype2 111  62
  subtype3  18  16
  subtype4  43  24
  subtype5  11   5
subtype1 subtype2 subtype3 subtype4 subtype5 
     114      173       34       67       16 
subtype1 subtype2 subtype3 subtype4 subtype5 
      43       62       16       24        5 
$subtype1
TCGA-B7-A5TJ TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 
       11.01         6.18        19.33         9.17         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 
       15.42        28.01        18.15        28.73         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8485 
        0.69        12.95         2.66         2.20        14.79         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4PE 
       20.22        11.54        10.68         7.53        22.26        20.42 
TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8535 
       13.64        13.15         0.30         0.07         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 
        3.42         9.34        11.31        12.43        12.20        20.02 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        3.02         7.99        54.08        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 
       21.99        18.97        22.98        15.02         4.01        69.04 
TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
       11.93        17.19        10.26        15.22        15.98        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 
       11.31        12.33        14.27         2.96        15.65         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8211 
        7.99        16.24        72.23         3.48        19.53        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD 
        0.56         5.52         5.92        12.59        14.17        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD 
       25.81        11.77         2.10        12.95        12.30        27.42 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F5 
       18.38         5.19         1.41         6.74         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-RD-A7BT TCGA-RD-A8N6 
       60.56        37.64        45.67        18.21         8.61         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PE 
       35.61         0.92         5.46        13.25        13.02        22.19 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z 
        2.70        17.85        22.68         1.71         9.50        52.24 
TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-A94T 
        9.04         4.54        64.18        21.04        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6G 
       18.41        40.08        32.94        29.98        17.13        26.04 

$subtype2
TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
       26.70         9.47         6.97         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 
       39.12        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        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
       24.76        23.93        15.32        12.43         9.07        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       17.49        14.43        12.26         9.60        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        0.56        16.31         6.18         0.26        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 
        0.95        26.33         4.31        11.80        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
       15.85         3.72         1.12        12.79         9.34        13.45 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 
        6.28         0.49        15.81        15.68        12.56         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       12.82        19.36         0.46        11.57         5.13         2.83 
TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.07         0.13         0.10         0.10         0.10        12.62 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 
        1.02         8.05         0.00         9.01        30.97         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
        0.99         6.02         0.99       105.07        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8570 TCGA-D7-8572 
        7.99        12.36        18.61        17.85        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       17.19        20.91         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       13.71        11.44         9.76         8.38         4.34         7.13 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX 
       14.47        21.27        22.29        59.54         5.03         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       18.08        26.47        14.27        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT 
        0.76         5.59        11.84        21.37        29.98         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RJ TCGA-IN-A7NR 
       10.19         0.26         8.88         8.81         5.36         6.51 
TCGA-IN-AB1X TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZI 
       13.51        20.15         3.72        19.73         9.86        61.25 
TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.60        11.05         5.13        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB 
      116.38        71.38        57.44        16.87        19.04         5.79 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       27.88        32.48        28.96        34.29        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.50         1.87         9.27        23.41        15.65        26.24 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 
       65.16        11.70        61.22         7.36        55.43         6.58 
TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-ZA-A8F6 
        2.66        28.41        54.12        16.14        10.62 

$subtype3
TCGA-B7-5818 TCGA-BR-6801 TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8483 TCGA-BR-8682 
       11.70        21.11        13.08         3.32         5.39        16.44 
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        34.45 
TCGA-VQ-A8PY TCGA-VQ-A91V TCGA-VQ-A923 TCGA-VQ-AA6J 
       14.33        36.16         2.01        21.11 

$subtype4
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-7959 
       19.56         9.44         6.61        18.35        17.29        18.71 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8687 
       15.58         7.40        19.50        25.18        15.81         8.22 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 
        1.48         0.72         0.66        20.65         1.15         3.25 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.07         0.16         0.10         0.13 
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        11.31         7.40        11.38        14.07 
TCGA-FP-8099 TCGA-HU-8238 TCGA-HU-A4G2 TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H6 
       17.06         1.51        24.30         6.25        23.84         9.67 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-A6RP 
       21.21         3.45        18.81         3.39        13.08         6.44 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 
        5.56         1.81         7.82         6.08         9.24        16.67 
TCGA-RD-A8MV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PH TCGA-VQ-A8PS 
      122.30        18.48        35.24         7.73        12.79        13.35 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91Y TCGA-VQ-A94U 
       27.35        64.57        36.69        11.93         9.73        22.09 
TCGA-VQ-AA6K 
       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        19.36        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 
    0.07     0.00     0.10     0.07     0.79 
subtype1 subtype2 subtype3 subtype4 subtype5 
   72.23   116.38    79.07   122.30    24.20 
subtype1 subtype2 subtype3 subtype4 subtype5 
   12.95    12.82    14.10    11.93    12.69 
[1] "0.1 - 72.2 (12.9)"  "0.0 - 116.4 (12.8)" "0.1 - 79.1 (14.1)" 
[4] "0.1 - 122.3 (11.9)" "0.8 - 24.2 (12.7)" 
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        5       15        8        10        16         0
  subtype2       1        3       20       12        18        26         2
  subtype3       0        2        3        2         4         1         0
  subtype4       0        2        2        7         5        11         2
  subtype5       1        2        1        2         1         1         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         28         13          7       14
  subtype2         31         28         17       20
  subtype3          7          8          3        5
  subtype4         17         10         12        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        3        2        2        2
  STAGE IB         15       20        3        2        1
  STAGE II          8       12        2        7        2
  STAGE IIA        10       18        4        5        1
  STAGE IIB        16       26        1       11        1
  STAGE III         0        2        0        2        0
  STAGE IIIA       28       31        7       17        2
  STAGE IIIB       13       28        8       10        3
  STAGE IIIC        7       17        3       12        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 29 56 28
  subtype2  7 36 80 58
  subtype3  2  7 20  7
  subtype4  4 11 35 22
  subtype5  3  7  4  4
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        6        7        2        4        3
  T2       29       36        7       11        7
  T3       56       80       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 38 36 23 19
  subtype2 58 52 32 37
  subtype3 11  5  8 11
  subtype4 18 22 18 14
  subtype5  4  3  3  8
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       38       58       11       18        4
  N1       36       52        5       22        3
  N2       23       32        8       18        3
  N3       19       37       11       14        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  69   2
  subtype5  18   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  106    8
  subtype2  162   16
  subtype3   32    4
  subtype4   69    2
  subtype5   18    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      106      162       32       69       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  84
  subtype2  79 107
  subtype3   7  29
  subtype4  26  48
  subtype5   9  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   84
  subtype2   79  107
  subtype3    7   29
  subtype4   26   48
  subtype5    9   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       37       79        7       26        9
  MALE         84      107       29       48       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"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     7
  subtype2                                    42
  subtype3                                     7
  subtype4                                    12
  subtype5                                     3
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     44
  subtype2                                                     74
  subtype3                                                      8
  subtype4                                                     30
  subtype5                                                      6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                29
  subtype2                                                                27
  subtype3                                                                 9
  subtype4                                                                13
  subtype5                                                                 3
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               30
  subtype2                                               20
  subtype3                                               10
  subtype4                                               13
  subtype5                                                5
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        4
  subtype2                                                       12
  subtype3                                                        1
  subtype4                                                        3
  subtype5                                                        1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         4
  subtype2                                                         2
  subtype3                                                         1
  subtype4                                                         0
  subtype5                                                         1
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        2
  subtype2                                        9
  subtype3                                        0
  subtype4                                        2
  subtype5                                        0
D1V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  44
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        30
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   42
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  74
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 9
                                                                   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  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   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  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[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"
D1V9, binary
          cls
clus         0   1
  subtype1   2 119
  subtype2   1 185
  subtype3   0  36
  subtype4   2  72
  subtype5   1  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  119
  subtype2    1  185
  subtype3    0   36
  subtype4    2   72
  subtype5    1   18
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         2        1        0        2        1
  YES      119      185       36       72       18
[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        R0  R1  R2  RX
  subtype1  95   4   8   5
  subtype2 149   8   8  13
  subtype3  29   2   2   1
  subtype4  56   4   1   5
  subtype5  18   0   0   1
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       95      149       29       56       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                         2
  subtype3     6                         2
  subtype4    18                         2
  subtype5     4                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    69
  subtype2                                         0   129
  subtype3                                         0    18
  subtype4                                         0    49
  subtype5                                         0     9
D1V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           26       34        6       18
  BLACK OR AFRICAN AMERICAN                        5        2        2        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           69      129       18       49
                                           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   1  80
  subtype2   3 142
  subtype3   0  21
  subtype4   0  58
  subtype5   0  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   80
  subtype2    3  142
  subtype3    0   21
  subtype4    0   58
  subtype5    0   12
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        3        0        0        0
  NOT HISPANIC OR LATINO       80      142       21       58       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 68 49
  subtype2 81 34
  subtype3 31 11
  subtype4 63 40
subtype1 subtype2 subtype3 subtype4 
     117      115       42      103 
subtype1 subtype2 subtype3 subtype4 
      49       34       11       40 
$subtype1
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 
       19.56         9.44        17.29         9.17        21.11         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 
       35.24        15.42        28.01        15.32        28.73         3.45 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8483 
       11.44         0.69         2.66         2.20        14.79         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
        9.21        20.22        11.54         9.86         8.22        10.68 
TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 
        7.53         0.72        20.65         3.25        13.15         0.07 
TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A 
        0.07         0.13         0.13         3.42         9.34        12.43 
TCGA-CD-A4MH TCGA-CG-4441 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 
       12.20        14.01        36.00        15.02        79.07         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 
       69.04        12.66        20.55        18.84        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 TCGA-D7-8576 TCGA-D7-A4YT 
       15.98        12.79        11.31        16.80        14.66        14.27 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
       11.31         2.96        15.65         0.62         7.99        16.24 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8243 
       72.23         3.48        17.06        13.58         0.56         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GX 
       12.59        14.17        22.75        25.81        11.77        10.19 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RL 
       12.95        12.30        27.42        21.21        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       13.08         5.56         2.53         5.56        60.56        37.64 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DL 
       18.21         6.08         8.61        37.91         8.94         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE 
        5.46        13.25        13.02        18.48        35.24        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91N TCGA-VQ-A91Q 
       12.79         2.70        17.85        27.35        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       22.68         1.71         9.50        52.24         9.04         4.54 
TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        5.72        21.04        11.24        18.41        32.94        29.98 
TCGA-VQ-AA6D TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       17.13        10.62         0.79 

$subtype2
TCGA-B7-A5TJ TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-7707 
       11.01        34.68        19.33        32.78        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7959 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8297 
       18.15        12.43        18.71         8.05        12.95         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        6.18        19.50        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        19.17         1.12        13.45        15.81        16.44 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF 
       13.87        22.26         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-8536 
       13.64        11.57         5.13         0.07         0.10         0.10 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4437 TCGA-CG-5720 
       11.61         6.58         0.10        12.62         8.05         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6525 TCGA-D7-6528 
       12.03        28.96        65.10        21.07        13.35        15.22 
TCGA-D7-6822 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       12.33        18.21        16.44         5.92        13.78        14.76 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7829 
       11.24        11.44         7.40        14.47        21.27        19.53 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 
       11.08         5.52        18.08         1.51        14.27        11.41 
TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GP 
        5.59        11.84        24.20         3.25        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        6.51         6.25        19.36        23.84         9.67         8.88 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81         3.39         1.41         6.44         6.74        12.59 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-MX-A5UJ TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7C1 
        1.81        13.51        19.73         4.60         9.24        16.67 
TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       19.04        48.79        21.73        34.45        27.88        32.48 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT 
        7.73        28.96        34.29         9.27        23.41        26.24 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91V TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6G 
       36.16        64.18        42.54        22.09        40.08        26.04 
TCGA-VQ-AA6I 
       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 
       32.94        12.82        12.76        12.26        20.55         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        15.85        15.81         7.53 
TCGA-BR-8686 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-CD-5801 TCGA-CD-8531 TCGA-CG-5722 
       15.68        12.89         0.53        13.18         0.10         0.99 
TCGA-D7-5577 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YX TCGA-D7-A6EZ TCGA-FP-7916 
       12.36        24.72        19.50        15.16         9.76        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         7.36         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        39.12        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        17.49        14.43 
TCGA-BR-8080 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8371 
        9.60        16.31        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         0.49 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       12.56         6.08        13.41        13.51         8.98        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5802 
       12.82         0.66        19.36         0.46         2.83         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
        0.07         0.39         0.07         0.13         0.16         0.10 
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 
       11.93        19.13        18.54        18.61        17.85        10.55 
TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A6ET TCGA-D7-A747 TCGA-D7-A748 
       17.19        21.14        20.91        13.71         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         8.81         3.45         5.36 
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        61.25        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        21.11 
TCGA-VQ-AA6K 
       12.43 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.10     0.07 
subtype1 subtype2 subtype3 subtype4 
   79.07    65.16    55.43   122.30 
subtype1 subtype2 subtype3 subtype4 
   12.79    13.64    12.56    12.43 
[1] "0.1 - 79.1 (12.8)"  "0.1 - 65.2 (13.6)"  "0.1 - 55.4 (12.6)" 
[4] "0.1 - 122.3 (12.4)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        3       10        9         9        18         1
  subtype2       2        6       14        8        14        19         0
  subtype3       0        1        2        1         5         8         0
  subtype4       0        3        9       10        11         9         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         30         18         10       12
  subtype2         17         20         13        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        3
  STAGE IB         10       14        2        9
  STAGE II          9        8        1       10
  STAGE IIA         9       14        5       11
  STAGE IIB        18       19        8        9
  STAGE III         1        0        0        2
  STAGE IIIA       30       17        9       23
  STAGE IIIB       18       20        8       15
  STAGE IIIC       10       13        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 28 60 28
  subtype2 10 25 54 31
  subtype3  1  3 22 16
  subtype4  4 19 49 35
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        5       10        1        4
  T2       28       25        3       19
  T3       60       54       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 30 34 29 26
  subtype2 47 23 24 25
  subtype3 14 12  6 10
  subtype4 32 31 19 23
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       30       47       14       32
  N1       34       23       12       31
  N2       29       24        6       19
  N3       26       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 106   5
  subtype2 115   4
  subtype3  38   2
  subtype4  92  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  106    5
  subtype2  115    4
  subtype3   38    2
  subtype4   92   12
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      106      115       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 77
  subtype2 44 76
  subtype3 12 30
  subtype4 36 71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   77
  subtype2   44   76
  subtype3   12   30
  subtype4   36   71
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       44       44       12       36
  MALE         77       76       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"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     6
  subtype2                                    15
  subtype3                                     9
  subtype4                                    36
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     41
  subtype2                                                     42
  subtype3                                                     17
  subtype4                                                     34
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                30
  subtype2                                                                22
  subtype3                                                                 6
  subtype4                                                                14
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               36
  subtype2                                               26
  subtype3                                                9
  subtype4                                                6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        2
  subtype2                                                        9
  subtype3                                                        0
  subtype4                                                        9
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         5
  subtype2                                                         2
  subtype3                                                         1
  subtype4                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        4
  subtype3                                        0
  subtype4                                        8
D2V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  41
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       22
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   36
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 8
[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"
D2V9, binary
          cls
clus         0   1
  subtype1   4 117
  subtype2   1 119
  subtype3   0  42
  subtype4   1 106
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  117
  subtype2    1  119
  subtype3    0   42
  subtype4    1  106
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         4        1        0        1
  YES      117      119       42      106
[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        R0  R1  R2
  subtype1 101   5   6
  subtype2 108   3   1
  subtype3  39   0   1
  subtype4  85   9   4
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      101      108       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                         3
  subtype3    12                         0
  subtype4    25                         2
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1    70
  subtype2                                         0    79
  subtype3                                         0    27
  subtype4                                         0    73
D2V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           26       26       12       25
  BLACK OR AFRICAN AMERICAN                        7        3        0        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                           70       79       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  0 83
  subtype2  1 86
  subtype3  1 35
  subtype4  2 86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   83
  subtype2    1   86
  subtype3    1   35
  subtype4    2   86
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        1        1        2
  NOT HISPANIC OR LATINO       83       86       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 49 21
  subtype2 55 29
  subtype3 52 26
subtype1 subtype2 subtype3 
      70       84       78 
subtype1 subtype2 subtype3 
      21       29       26 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 
       26.70        11.70         6.97        30.90         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 
       34.68        32.78        12.16         8.98        30.90        32.94 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8285 TCGA-BR-8286 
       12.43         3.45        12.76        11.44         0.56        12.95 
TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8372 
        2.66         6.18        19.50         0.26         0.95        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 
        0.26        15.85        25.18        15.81        13.45         7.53 
TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
       15.81        10.68        13.51         1.15        11.57         5.13 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-A487 
        0.07         0.10         0.13         0.10         0.13         9.34 
TCGA-CD-A4MG TCGA-CG-4300 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4469 
        6.58        20.02         1.02         7.99         8.05         7.07 
TCGA-CG-5723 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
      105.07        21.07         7.99        13.35        15.22        15.98 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU TCGA-D7-A4YX 
       11.31        12.33        24.72        19.50        16.44        15.16 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-A4GF TCGA-HU-A4GQ 
        7.99        14.47        26.47        11.41        25.81         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-IP-7968 
        6.51         6.25        10.19         2.53 

$subtype2
TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6456 
        6.61         4.64         7.43         9.57        15.95        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 
       13.68        19.33        26.10        25.61        18.05        21.11 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
       31.20        12.82         9.21        18.15        15.32         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8291 
       18.71        17.49        14.43         9.60        20.55        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
       15.58         7.40        13.08        22.19        17.52        26.33 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 
       14.04         3.32        11.80         3.72         5.39        20.22 
TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A44T 
       12.79         6.28         0.49        16.44         9.86        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY 
        7.53         6.08        22.26         1.48        13.41        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 
        8.98        12.82        19.36         0.46        13.64         2.83 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8530 TCGA-CD-A489 
        0.07         0.39         0.07         0.07         0.16        11.31 
TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
       12.20         3.02        12.03        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 
        6.97        36.00         1.02        65.10        11.93        19.13 
TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-A4Z0 TCGA-F1-A448 
       18.54        17.85        16.80        17.19        14.76        21.27 
TCGA-FP-7916 TCGA-HU-8610 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-8462 
       14.07         0.76        19.36        23.84        12.30        18.81 

$subtype3
TCGA-BR-4191 TCGA-BR-6455 TCGA-BR-6565 TCGA-BR-6707 TCGA-BR-7703 TCGA-BR-7704 
       18.35        13.87         9.17        19.89        24.76        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8368 
       15.42        28.01        28.73         8.05         2.20         4.31 
TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U 
        9.21         9.34        11.54        15.68         8.22        13.87 
TCGA-BR-A4IV TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4PD 
       13.51         0.72        14.17         0.53         0.66        20.65 
TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8527 
       20.42         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.13         0.10         3.42        12.43        11.61 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4438 TCGA-CG-4443 
        0.10        12.62        27.02        15.95        54.08        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-5720 
       47.05        19.07        21.99         9.01        18.97         0.99 
TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        6.02        12.03        15.02        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       69.04        12.36        12.66        20.55        18.84        18.61 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT 
       10.26        12.79        10.55        18.21        21.14        14.27 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7998 TCGA-HU-8608 
        5.92        13.78        16.24        72.23        22.29        10.62 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
        0.26        12.95        27.42        21.21         3.45         3.39 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
  105.07    65.10    79.07 
subtype1 subtype2 subtype3 
  11.425   13.245   13.165 
[1] "0.1 - 105.1 (11.4)" "0.1 - 65.1 (13.2)"  "0.1 - 79.1 (13.2)" 
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        0        9        4        10        12         1
  subtype2       0        2        3       12        10        14         1
  subtype3       2        4       13       12         5        10         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         14         12          8        6
  subtype2         15         11         11        9
  subtype3         13         11          5        8
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        2
  STAGE IA          0        2        4
  STAGE IB          9        3       13
  STAGE II          4       12       12
  STAGE IIA        10       10        5
  STAGE IIB        12       14       10
  STAGE III         1        1        1
  STAGE IIIA       14       15       13
  STAGE IIIB       12       11       11
  STAGE IIIC        8       11        5
  STAGE IV          6        9        8
[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  0 20 39 20
  subtype2  2 16 37 33
  subtype3  6 31 29 21
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        0        2        6
  T2       20       16       31
  T3       39       37       29
  T4       20       33       21
[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 27 22 14 15
  subtype2 26 28 15 20
  subtype3 34 23 13 15
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       27       26       34
  N1       22       28       23
  N2       14       15       13
  N3       15       20       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"
D3V6, binary
          cls
clus        0  1
  subtype1 72  4
  subtype2 84  6
  subtype3 81  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72    4
  subtype2   84    6
  subtype3   81    6
   clus
vv  subtype1 subtype2 subtype3
  0       72       84       81
  1        4        6        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 34 48
  subtype2 37 54
  subtype3 28 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   48
  subtype2   37   54
  subtype3   28   63
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       34       37       28
  MALE         48       54       63
[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                                     9
  subtype2                                    19
  subtype3                                    14
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     45
  subtype2                                                     43
  subtype3                                                     47
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                13
  subtype2                                                                 9
  subtype3                                                                15
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               11
  subtype2                                                4
  subtype3                                               11
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        3
  subtype2                                                       12
  subtype3                                                        1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         3
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        1
  subtype3                                        0
D3V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  45
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   19
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  43
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  47
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[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"
D3V9, binary
          cls
clus        0  1
  subtype1  2 80
  subtype2  0 91
  subtype3  4 87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   80
  subtype2    0   91
  subtype3    4   87
     clus
vv    subtype1 subtype2 subtype3
  NO         2        0        4
  YES       80       91       87
[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       R0 R1 R2 RX
  subtype1 65  3  1 11
  subtype2 72  4  2  7
  subtype3 69  2  5  7
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       65       72       69
  R1        3        4        2
  R2        1        2        5
  RX       11        7        7
[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"
D3V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    15                         0    57
  subtype2    23                         0    57
  subtype3    22                         2    45
D3V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           15       23       22
  BLACK OR AFRICAN AMERICAN        0        0        2
  WHITE                           57       57       45
[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"
D3V13, binary
          cls
clus        0  1
  subtype1  0 72
  subtype2  1 79
  subtype3  1 68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   72
  subtype2    1   79
  subtype3    1   68
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        1        1
  NOT HISPANIC OR LATINO       72       79       68
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 26  6
  subtype2 48 24
  subtype3 33 11
  subtype4 49 35
subtype1 subtype2 subtype3 subtype4 
      32       72       44       84 
subtype1 subtype2 subtype3 subtype4 
       6       24       11       35 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-6710 TCGA-BR-6802 
       26.70        11.70        30.90         6.18         8.98        30.90 
TCGA-BR-6852 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8382 TCGA-BR-8690 TCGA-BR-A4PF 
       32.94        20.55         0.56        15.85        10.68         1.15 
TCGA-CD-8528 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4455 
        0.10         9.34        20.02         7.99         8.05        12.03 
TCGA-CG-5718 TCGA-CG-5723 TCGA-CG-5733 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 
       36.00       105.07        21.07        15.98        11.31        12.33 
TCGA-D7-A4YU TCGA-F1-6874 TCGA-F1-A448 TCGA-HU-8610 TCGA-HU-A4GF TCGA-HU-A4H3 
       16.44        14.47        21.27         0.76        25.81        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 
       23.84        12.30 

$subtype2
TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-7723 
        6.61        18.35        15.95        13.87        19.89        28.73 
TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8368 TCGA-BR-8483 
       11.44        16.31         2.20         7.40         4.31         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-A44U TCGA-BR-A452 
       25.18         9.21        20.22         0.49        13.87         7.53 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        6.08        22.26        13.51         8.98         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        0.53        20.65        20.42         3.25        13.15         0.30 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A4MH 
        0.39         0.07         0.13         0.13         3.42        12.20 
TCGA-CD-A4MI TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4438 
        0.10         3.02        27.02        15.95         1.02        54.08 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        21.99         9.01        18.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99         6.02        15.02        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6817 TCGA-D7-6818 
       69.04        12.66        20.55        18.61        12.79        10.55 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-EQ-A4SO 
       17.19        18.21        21.14        14.27         7.99        16.24 
TCGA-HJ-7597 TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
       26.47         0.26        12.95        27.42        21.21         3.45 

$subtype3
TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-7703 
        6.97         6.61        34.68        32.78        12.16        24.76 
TCGA-BR-7704 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8366 TCGA-BR-8372 
       35.24        12.95         6.18        19.50         0.95        19.17 
TCGA-BR-8381 TCGA-BR-8589 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A4J8 TCGA-BR-A4QL 
        0.26        15.81        11.54        15.81        13.51        11.57 
TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 
        5.13        13.18         0.07         0.10         0.13         0.10 
TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4469 TCGA-CG-5724 TCGA-CG-5734 TCGA-D7-5577 
        6.58        12.62         7.07        12.03         7.99        12.36 
TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YX TCGA-D7-A4YY 
       13.35        15.22        24.72        19.50        15.16        13.78 
TCGA-F1-6875 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       72.23        11.41        10.62         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-IP-7968 
       10.19         2.53 

$subtype4
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        4.64         7.43         9.57        17.29        13.68        19.33 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 
       26.10         9.17        25.61        18.05        21.11        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       12.82         9.21        15.42        28.01        18.15        15.32 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         3.45         9.07        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8296 TCGA-BR-8362 
       14.43         9.60         8.05         2.66        15.58        13.08 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
        0.26        22.19        17.52        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       11.80         3.72        12.79         9.34        13.45         6.28 
TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
        7.53        16.44         9.86        15.68         8.22        12.56 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        1.48        13.41        12.89        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 
        0.46        13.64         2.83         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4472 
        0.16         0.10        11.31        12.43        11.61        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5728 TCGA-D7-5579 
       22.98        30.97         6.97         1.02        65.10        11.93 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-8572 
       19.13        18.84        18.54        17.85        10.26        16.80 
TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-FP-7916 TCGA-FP-7998 TCGA-IN-8462 TCGA-IN-8663 
        5.92        14.76        14.07        22.29        18.81         3.39 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.07     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
  105.07    79.07    72.23    65.10 
subtype1 subtype2 subtype3 subtype4 
  15.160   13.330   11.800   12.805 
[1] "0.1 - 105.1 (15.2)" "0.1 - 79.1 (13.3)"  "0.1 - 72.2 (11.8)" 
[4] "0.1 - 65.1 (12.8)" 
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        1        7        4         3         6         0
  subtype2       0        3       10       11         4         8         1
  subtype3       2        2        4        3         7         4         1
  subtype4       0        0        4       10        11        18         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          3          5          3        0
  subtype2         16         10          2       13
  subtype3         11          8          5        3
  subtype4         12         11         14        7
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        0        2        0
  STAGE IA          1        3        2        0
  STAGE IB          7       10        4        4
  STAGE II          4       11        3       10
  STAGE IIA         3        4        7       11
  STAGE IIB         6        8        4       18
  STAGE III         0        1        1        1
  STAGE IIIA        3       16       11       12
  STAGE IIIB        5       10        8       11
  STAGE IIIC        3        2        5       14
  STAGE IV          0       13        3        7
[1] 11  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1 16  9  7
  subtype2  3 27 27 23
  subtype3  4  8 31 10
  subtype4  0 16 38 34
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        1        3        4        0
  T2       16       27        8       16
  T3        9       27       31       38
  T4        7       23       10       34
[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 14  6  6  6
  subtype2 27 24 13 15
  subtype3 19 15  8 10
  subtype4 27 28 15 19
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       14       27       19       27
  N1        6       24       15       28
  N2        6       13        8       15
  N3        6       15       10       19
[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 34  0
  subtype2 70 10
  subtype3 48  2
  subtype4 85  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    0
  subtype2   70   10
  subtype3   48    2
  subtype4   85    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       34       70       48       85
  1        0       10        2        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 14 20
  subtype2 28 56
  subtype3 22 33
  subtype4 35 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   20
  subtype2   28   56
  subtype3   22   33
  subtype4   35   56
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       14       28       22       35
  MALE         20       56       33       56
[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                                     4
  subtype2                                    15
  subtype3                                     8
  subtype4                                    15
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     14
  subtype2                                                     40
  subtype3                                                     32
  subtype4                                                     49
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 6
  subtype2                                                                13
  subtype3                                                                 7
  subtype4                                                                11
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                                7
  subtype2                                                8
  subtype3                                                7
  subtype4                                                4
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        2
  subtype2                                                        5
  subtype3                                                        0
  subtype4                                                        9
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         1
  subtype2                                                         1
  subtype3                                                         1
  subtype4                                                         1
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        2
  subtype3                                        0
  subtype4                                        0
D4V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  40
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING 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"
D4V9, binary
          cls
clus        0  1
  subtype1  0 34
  subtype2  6 78
  subtype3  0 55
  subtype4  0 91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   34
  subtype2    6   78
  subtype3    0   55
  subtype4    0   91
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        6        0        0
  YES       34       78       55       91
[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       R0 R1 R2 RX
  subtype1 31  0  0  3
  subtype2 60  2  7  7
  subtype3 41  2  1  9
  subtype4 74  5  0  6
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       31       60       41       74
  R1        0        2        2        5
  R2        0        7        1        0
  RX        3        7        9        6
[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 WHITE
  subtype1     7                         0    20
  subtype2    21                         0    39
  subtype3    14                         2    34
  subtype4    18                         0    66
D4V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            7       21       14       18
  BLACK OR AFRICAN AMERICAN        0        0        2        0
  WHITE                           20       39       34       66
[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"
D4V13, binary
          cls
clus        0  1
  subtype1  1 26
  subtype2  0 60
  subtype3  0 50
  subtype4  1 83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   26
  subtype2    0   60
  subtype3    0   50
  subtype4    1   83
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        0        0        1
  NOT HISPANIC OR LATINO       26       60       50       83
[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 51 10
  subtype2 33 24
  subtype3 25 13
  subtype4 24  7
  subtype5 37 18
subtype1 subtype2 subtype3 subtype4 subtype5 
      61       57       38       31       55 
subtype1 subtype2 subtype3 subtype4 subtype5 
      10       24       13        7       18 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4201 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6707 
       26.70        11.70        30.90        34.68        32.78        19.89 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8081 
       30.90        32.94        23.93        12.76        12.26        20.55 
TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8372 
       12.95        19.50         0.26         0.95         4.31        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 
        0.26        15.85         1.12        15.81        13.45        15.81 
TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8531 
       12.89         0.53        20.42        13.18         0.10         0.10 
TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4477 
        0.10        11.61         6.58        12.62        15.95        30.97 
TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-D7-5577 TCGA-D7-6524 
        6.97         6.02       105.07        12.03        12.36        17.85 
TCGA-D7-6525 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YX TCGA-D7-A4YY TCGA-FP-8099 
       13.35        24.72        19.50        15.16        13.78        17.06 
TCGA-FP-A4BE TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G6 
       11.08        11.41        12.10        10.62         0.76        12.30 
TCGA-HU-A4G8 TCGA-HU-A4GN TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-IN-8462 
       11.84        29.98         2.10        19.36        23.84        18.81 
TCGA-IN-8663 
        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        39.12 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 
       26.10        25.61        18.05        21.11        31.20        12.82 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8297 
        9.07        18.71        14.43         9.60         8.05         7.40 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
       13.08        22.19        17.52        26.33        14.04        11.80 
TCGA-BR-8384 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8686 
        3.72         9.34         6.28         0.49        16.44        15.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       12.56         6.08        13.41        13.51         8.98        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5803 
       12.82        19.36        13.51         0.46         2.83         0.07 
TCGA-CD-5813 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4472 TCGA-D7-6518 
        0.39         9.34        11.31         0.10        12.00        19.13 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-FP-7916 TCGA-FP-7998 
       17.19        20.91        16.44         5.92        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GY 
       59.54         5.03         0.26 

$subtype3
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6710 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-8058 
       18.35         6.18         8.98        18.15        15.32        17.49 
TCGA-BR-8291 TCGA-BR-8484 TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-CD-8529 TCGA-CD-8532 
       16.31        25.18         0.66        20.65         0.13         0.10 
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-EQ-A4SO TCGA-FP-8211 TCGA-HU-A4G2 TCGA-HU-A4G3 
       18.21        14.66        16.24        13.58        24.30         5.59 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4H2 
       24.20         3.25        21.37         8.98        10.19        12.95 
TCGA-HU-A4H6 TCGA-HU-A4HB 
        9.67         8.81 

$subtype4
TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6565 TCGA-BR-7703 TCGA-BR-7851 TCGA-BR-8486 
        6.61        15.95         9.17        24.76        12.43        20.22 
TCGA-BR-8588 TCGA-BR-8683 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CG-4304 
       12.79         9.86         1.15        13.64         3.25        27.02 
TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5720 
        7.99        14.01        47.05         9.01         7.07         0.99 
TCGA-D7-5578 TCGA-D7-6522 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A4Z0 TCGA-F1-6874 
       12.66        18.61        15.22        15.98        14.76        14.47 
TCGA-F1-A448 TCGA-FP-7829 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-A4GT TCGA-HU-A4H8 
       21.27        19.53         1.51        14.27         6.51         8.88 
TCGA-IN-7806 
       21.21 

$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        15.42        28.01        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        11.54         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         0.07         0.16         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        3.42        12.20        54.08         4.01        29.98        19.07 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5725 TCGA-D7-6519 
       21.99        18.97        22.98        36.00        15.02        20.55 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       18.84        17.19        10.55        11.31        12.33        16.80 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8631 
       21.14        14.27         7.99        72.23         3.48         0.56 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 
       25.81        11.77         6.25        12.30        27.42         3.45 
TCGA-IP-7968 
        2.53 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     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 
  13.180   13.410   11.525   13.640   11.770 
[1] "0.1 - 105.1 (13.2)" "0.1 - 59.5 (13.4)"  "0.0 - 69.0 (11.5)" 
[4] "1.0 - 47.0 (13.6)"  "0.1 - 72.2 (11.8)" 
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        2        8        6        12        12         0
  subtype2       0        0        1        5         7         9         1
  subtype3       0        2        3        4         2         7         0
  subtype4       2        3        8        1         3         7         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         10         12         10        5
  subtype3          7          5          3       10
  subtype4          5          3          0        3
  subtype5         13          5          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        12        7        2        3        5
  STAGE IIB        12        9        7        7        9
  STAGE III         0        1        0        1        1
  STAGE IIIA        7       10        7        5       13
  STAGE IIIB        6       12        5        3        5
  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 24 18
  subtype2  0  5 30 25
  subtype3  3 13 16 13
  subtype4  6 15  8  8
  subtype5  2 18 29 11
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        2        0        3        6        2
  T2       19        5       13       15       18
  T3       24       30       16        8       29
  T4       18       25       13        8       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 30 17  8  9
  subtype2 14 19  8 19
  subtype3 10 15 11  8
  subtype4 17  7  9  3
  subtype5 20 18 10 10
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       30       14       10       17       20
  N1       17       19       15        7       18
  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 63  2
  subtype2 58  3
  subtype3 35  7
  subtype4 34  2
  subtype5 53  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    2
  subtype2   58    3
  subtype3   35    7
  subtype4   34    2
  subtype5   53    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       63       58       35       34       53
  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 28 38
  subtype2 23 40
  subtype3 18 28
  subtype4 14 23
  subtype5 20 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   38
  subtype2   23   40
  subtype3   18   28
  subtype4   14   23
  subtype5   20   42
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       28       23       18       14       20
  MALE         38       40       28       23       42
[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                                    12
  subtype2                                    19
  subtype3                                    10
  subtype4                                     5
  subtype5                                     5
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     42
  subtype2                                                     28
  subtype3                                                     19
  subtype4                                                     13
  subtype5                                                     29
          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  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        0
  subtype2                                                        7
  subtype3                                                        3
  subtype4                                                        3
  subtype5                                                        1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         1
  subtype2                                                         0
  subtype3                                                         1
  subtype4                                                         1
  subtype5                                                         2
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        1
  subtype3                                        0
  subtype4                                        0
  subtype5                                        0
D5V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   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  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[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"
D5V9, binary
          cls
clus        0  1
  subtype1  0 66
  subtype2  0 63
  subtype3  4 42
  subtype4  0 37
  subtype5  2 60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   66
  subtype2    0   63
  subtype3    4   42
  subtype4    0   37
  subtype5    2   60
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         0        0        4        0        2
  YES       66       63       42       37       60
[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       R0 R1 R2 RX
  subtype1 55  1  1  5
  subtype2 48  2  0  6
  subtype3 35  2  5  4
  subtype4 30  1  2  3
  subtype5 49  3  2  4
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       55       48       35       30       49
  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    20                         1    38
  subtype2    19                         0    43
  subtype3    13                         0    19
  subtype4     6                         1    21
  subtype5    15                         2    35
D5V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           20       19       13        6       15
  BLACK OR AFRICAN AMERICAN        1        0        0        1        2
  WHITE                           38       43       19       21       35
[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 59
  subtype2  1 61
  subtype3  0 32
  subtype4  1 27
  subtype5  0 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   59
  subtype2    1   61
  subtype3    0   32
  subtype4    1   27
  subtype5    0   52
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        1        0        1        0
  NOT HISPANIC OR LATINO       59       61       32       27       52
[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 21 13
  subtype2 16  4
  subtype3 27 20
  subtype4 36 16
  subtype5 27 11
  subtype6 26  8
  subtype7 17  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      34       20       47       52       38       34       17 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      13        4       20       16       11        8        0 
$subtype1
TCGA-B7-5816 TCGA-BR-4201 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7717 TCGA-BR-8059 
       26.70        30.90        19.33        12.16        18.15        14.43 
TCGA-BR-8289 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8590 TCGA-BR-A4IY TCGA-BR-A4J6 
        2.66         0.26         0.95         9.34        12.89         0.66 
TCGA-CD-5798 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-A487 TCGA-CD-A48C 
        2.83         0.07         0.16         0.10         9.34        11.61 
TCGA-CD-A4MI TCGA-CG-4449 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        0.10        19.07        12.00        22.98        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6525 
        1.02         6.02       105.07        12.03        20.55        13.35 
TCGA-D7-A4YU TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       16.44        21.21        18.81         3.39 

$subtype2
TCGA-B7-5818 TCGA-BR-6455 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-7196 TCGA-BR-7958 
       11.70        13.87        18.05        19.89        12.82        12.76 
TCGA-BR-8381 TCGA-BR-8589 TCGA-BR-8686 TCGA-BR-A4J4 TCGA-CD-5801 TCGA-D7-5577 
        0.26        15.81        15.68         0.53        13.18        12.36 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YX TCGA-FP-7998 TCGA-HU-8608 TCGA-HU-A4G2 
       24.72        19.50        15.16        22.29        10.62        24.30 
TCGA-HU-A4G6 TCGA-HU-A4H0 
       12.30         2.10 

$subtype3
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        39.12        26.10 
TCGA-BR-6705 TCGA-BR-6803 TCGA-BR-7957 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 
       25.61        31.20         9.07         9.60         8.05        16.31 
TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
        7.40        22.19        17.52        26.33        14.04        11.80 
TCGA-BR-8384 TCGA-BR-8592 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
        3.72         6.28        16.44        12.56         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 
       13.51         8.98        14.17        12.82        19.36        13.51 
TCGA-BR-A4J9 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-A489 TCGA-CG-4462 TCGA-D7-6518 
        0.46         0.07         0.39        11.31         0.00        19.13 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4Z0 
       18.61        17.85        17.19        20.91         5.92        14.76 
TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GY TCGA-IN-7808 
       14.07        59.54         5.03         0.26         3.45 

$subtype4
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-7722 
       18.35         6.18        34.68         8.98        30.90        15.32 
TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8687 TCGA-BR-A4PD 
        3.45        17.49        25.18        12.79         8.22        20.65 
TCGA-BR-A4PE TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8536 TCGA-CG-4301 TCGA-CG-4304 
       20.42         0.13         0.10         0.10         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4460 TCGA-CG-5718 TCGA-CG-5722 
       15.95         1.02         8.05        21.99        36.00         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-D7-6820 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-EQ-A4SO TCGA-FP-7735 
       11.31        18.21        14.66        21.14        16.24         3.48 
TCGA-FP-8211 TCGA-HU-8238 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       13.58         1.51         0.76         5.59        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4H2 
        3.25        11.77        21.37         8.98        10.19        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       23.84         9.67         8.88         8.81 

$subtype5
TCGA-BR-4280 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7703 TCGA-BR-8362 
        6.61         9.17        32.78        21.11        24.76        13.08 
TCGA-BR-8368 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A4PF 
        4.31        20.22         1.12        15.81         9.86         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-8528 TCGA-CD-A4MG TCGA-CG-4436 TCGA-CG-4438 
       13.64         3.25         0.10         6.58         7.99        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
        4.01        14.01        47.05         9.01        18.97         7.07 
TCGA-CG-5720 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-EQ-8122 
        0.99        12.66        17.19        15.22        15.98         7.99 
TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-A4BE TCGA-HU-8244 TCGA-HU-8604 TCGA-HU-A4GF 
       14.47        19.53        11.08        14.27        12.10        25.81 
TCGA-HU-A4GT TCGA-HU-A4GU 
        6.51         6.25 

$subtype6
TCGA-BR-6456 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 
       17.29         9.21        15.42        28.01        28.73        18.71 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8678 
       11.44         0.69        14.79         5.39         9.21        11.54 
TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-CD-5800 TCGA-CD-8526 TCGA-CD-8533 
        7.53         1.48         0.72        13.15         0.07         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-4443 TCGA-CG-5725 TCGA-D7-6520 
        0.13         3.42        12.20        29.98        15.02        18.84 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-A4YT TCGA-F1-6875 TCGA-FP-8099 
       10.55        12.33        16.80        14.27        72.23        17.06 
TCGA-FP-8631 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IP-7968 
        0.56        12.30        27.42         2.53 

$subtype7
TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8286 
       32.94        23.93        12.43        12.26        20.55        12.95 
TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8677 TCGA-CD-A4MJ 
       19.50        19.17        15.85        13.45         0.49        12.62 
TCGA-D7-A4YY TCGA-F1-A448 TCGA-HU-8602 TCGA-HU-A4GN TCGA-HU-A4H3 
       13.78        21.27        11.41        29.98        19.36 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.07     0.26     0.00     0.10     0.10     0.07     0.49 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  105.07    24.72    59.54    69.04    54.08    72.23    32.94 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  12.015   13.525   13.510   12.315   12.380   12.250   15.850 
[1] "0.1 - 105.1 (12.0)" "0.3 - 24.7 (13.5)"  "0.0 - 59.5 (13.5)" 
[4] "0.1 - 69.0 (12.3)"  "0.1 - 54.1 (12.4)"  "0.1 - 72.2 (12.2)" 
[7] "0.5 - 32.9 (15.8)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        0        2        6         2         9         1
  subtype2       0        1        1        0         2         4         0
  subtype3       0        0        2        5         7         8         1
  subtype4       0        4        8        7         3        10         0
  subtype5       2        3        7        1         9         5         1
  subtype6       0        2        4        3         4         4         0
  subtype7       0        0        3        1         2         4         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          2          4          1        7
  subtype2          4          6          2        1
  subtype3          8          8          7        3
  subtype4          9          5          4        9
  subtype5          5          2          1        5
  subtype6         13          3          3        0
  subtype7          1          3          5        0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           0        0        0        0        2        0        0
  STAGE IA          0        1        0        4        3        2        0
  STAGE IB          2        1        2        8        7        4        3
  STAGE II          6        0        5        7        1        3        1
  STAGE IIA         2        2        7        3        9        4        2
  STAGE IIB         9        4        8       10        5        4        4
  STAGE III         1        0        1        0        1        0        0
  STAGE IIIA        2        4        8        9        5       13        1
  STAGE IIIB        4        6        8        5        2        3        3
  STAGE IIIC        1        2        7        4        1        3        5
  STAGE IV          7        1        3        9        5        0        0
[1] 11  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  0 10 16 10
  subtype2  1  2 11  7
  subtype3  0  9 23 17
  subtype4  6 21 18 15
  subtype5  5 13 16  8
  subtype6  1 11 18  8
  subtype7  0  4  5 10
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        0        1        0        6        5        1        0
  T2       10        2        9       21       13       11        4
  T3       16       11       23       18       16       18        5
  T4       10        7       17       15        8        8       10
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 10 17  4  4
  subtype2  5  9  2  5
  subtype3 13 12  7 16
  subtype4 18 19 16  7
  subtype5 22  6  9  4
  subtype6 13 10  7  6
  subtype7 10  3  1  7
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       10        5       13       18       22       13       10
  N1       17        9       12       19        6       10        3
  N2        4        2        7       16        9        7        1
  N3        4        5       16        7        4        6        7
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 34  3
  subtype2 19  1
  subtype3 45  4
  subtype4 51  7
  subtype5 37  3
  subtype6 36  0
  subtype7 21  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34    3
  subtype2   19    1
  subtype3   45    4
  subtype4   51    7
  subtype5   37    3
  subtype6   36    0
  subtype7   21    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       34       19       45       51       37       36       21
  1        3        1        4        7        3        0        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 16 22
  subtype2  2 19
  subtype3 21 29
  subtype4 24 38
  subtype5 19 23
  subtype6 10 30
  subtype7 11 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   22
  subtype2    2   19
  subtype3   21   29
  subtype4   24   38
  subtype5   19   23
  subtype6   10   30
  subtype7   11   10
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       16        2       21       24       19       10       11
  MALE         22       19       29       38       23       30       10
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                     8
  subtype2                                     5
  subtype3                                    22
  subtype4                                     9
  subtype5                                     4
  subtype6                                     1
  subtype7                                     2
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     19
  subtype2                                                     11
  subtype3                                                     17
  subtype4                                                     29
  subtype5                                                     16
  subtype6                                                     24
  subtype7                                                     15
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 6
  subtype2                                                                 0
  subtype3                                                                 3
  subtype4                                                                 7
  subtype5                                                                10
  subtype6                                                                 6
  subtype7                                                                 2
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                                1
  subtype2                                                4
  subtype3                                                1
  subtype4                                               13
  subtype5                                               10
  subtype6                                                6
  subtype7                                                1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        2
  subtype2                                                        0
  subtype3                                                        6
  subtype4                                                        3
  subtype5                                                        1
  subtype6                                                        1
  subtype7                                                        1
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         0
  subtype4                                                         1
  subtype5                                                         1
  subtype6                                                         2
  subtype7                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        1
  subtype4                                        0
  subtype5                                        0
  subtype6                                        0
  subtype7                                        0
D6V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   22
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype6
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype7
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
[1] 7 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus        0  1
  subtype1  0 38
  subtype2  0 21
  subtype3  0 50
  subtype4  4 58
  subtype5  0 42
  subtype6  2 38
  subtype7  0 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   38
  subtype2    0   21
  subtype3    0   50
  subtype4    4   58
  subtype5    0   42
  subtype6    2   38
  subtype7    0   21
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO         0        0        0        4        0        2        0
  YES       38       21       50       58       42       38       21
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 28  1  1  5
  subtype2 20  0  0  1
  subtype3 37  3  1  3
  subtype4 48  3  6  4
  subtype5 34  1  2  2
  subtype6 33  1  0  4
  subtype7 17  0  0  3
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       28       20       37       48       34       33       17
  R1        1        0        3        3        1        1        0
  R2        1        0        1        6        2        0        0
  RX        5        1        3        4        2        4        3
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     8                         0    21
  subtype2     7                         0    14
  subtype3    15                         0    34
  subtype4    19                         1    25
  subtype5    10                         2    20
  subtype6    10                         1    26
  subtype7     4                         0    16
D6V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            8        7       15       19       10
  BLACK OR AFRICAN AMERICAN        0        0        0        1        2
  WHITE                           21       14       34       25       20
                           clus
vv                          subtype6 subtype7
  ASIAN                           10        4
  BLACK OR AFRICAN AMERICAN        1        0
  WHITE                           26       16
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
          cls
clus        0  1
  subtype1  0 29
  subtype2  1 20
  subtype3  0 49
  subtype4  0 45
  subtype5  0 32
  subtype6  0 37
  subtype7  1 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   29
  subtype2    1   20
  subtype3    0   49
  subtype4    0   45
  subtype5    0   32
  subtype6    0   37
  subtype7    1   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        0        0        0
  NOT HISPANIC OR LATINO       29       20       49       45       32       37
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO       19
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 109  58
  subtype2  72  52
  subtype3  75  39
subtype1 subtype2 subtype3 
     167      124      114 
subtype1 subtype2 subtype3 
      58       52       39 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56        11.01         6.61         6.97 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-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 
       32.94        24.76        35.24        23.93        12.26        20.55 
TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 
       12.95        15.58         6.18        19.50         0.26         4.31 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
       19.17        15.85        25.18        20.22         1.12        15.81 
TCGA-BR-8680 TCGA-BR-A4CQ TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5801 
       15.81        22.26        11.57         5.13         3.25        13.18 
TCGA-CD-5802 TCGA-CD-5813 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG 
        0.30         0.39         0.10         0.10        11.61         6.58 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
       12.62        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05         4.01        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-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       36.00         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       28.96        79.07         4.01        21.07         7.99        12.36 
TCGA-D7-6519 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       20.55        17.85        13.35        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EZ 
       12.79        24.72        18.21        15.16        13.78         9.76 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-8099 
       15.65         7.40        14.47        21.27        19.53        17.06 
TCGA-FP-8211 TCGA-FP-A4BE TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8604 
       13.58        11.08        26.47         1.51        14.27        12.10 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 
       29.98         8.98         6.51         6.25        10.19        23.84 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RP 
        9.67         8.88         3.45        18.81         3.39         6.44 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7ZI TCGA-R5-A804 
        1.81        13.51        20.15        37.64        61.25         4.60 
TCGA-R5-A805 TCGA-RD-A8MV TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        9.24       122.30        19.04         0.92        21.73        34.45 
TCGA-VQ-A8P3 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM 
       32.48        34.29        46.26        16.31         2.50         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        13.35        26.24        27.35        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        65.16        36.69        11.70        11.93        61.22 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 
        1.71        36.16         7.36         9.50         2.01        55.43 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 
        6.58        64.18        11.24        22.09        18.41        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        29.98        54.12        16.14        21.11 

$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 
       39.12        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-7851 
       21.11        31.20        12.82        18.15        15.32        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        3.45         9.07        12.76        18.71        17.49        14.43 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 
        9.60         8.05         0.56         2.66        16.31         7.40 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 
       13.08        22.19        17.52         0.95        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8590 
        3.32        11.80         3.72         5.39        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       13.45         6.28         0.49        16.44         9.86        15.68 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        8.22        12.56         6.08        13.41        13.51         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8530 
        0.46        13.64         2.83         0.07         0.13         0.16 
TCGA-CD-8532 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 
        0.10        11.31         0.10        12.00         6.97         1.02 
TCGA-CG-5728 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       65.10        69.04        12.66        11.93        19.13        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 
       18.54        18.61        10.55        17.19        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 
       16.44        14.76        13.71        11.31        11.44         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
        4.34         7.13         0.62        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GY 
       22.29        59.54         5.03        21.37         0.10         0.26 
TCGA-IN-7806 TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG TCGA-MX-A663 TCGA-RD-A7BS 
       21.21         6.51         7.82         3.72         9.86        11.05 
TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        5.13        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8P8 TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A928 
       35.61        16.87        28.96        15.65         9.73         5.72 
TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA6K TCGA-ZA-A8F6 
        2.66        42.54        12.43        10.62 

$subtype3
TCGA-B7-A5TN TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8060 
        9.44         9.21        15.42        28.01        28.73        11.44 
TCGA-BR-8077 TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8485 TCGA-BR-8676 
        0.69         2.20        14.79         0.26         9.21         7.53 
TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IY 
       11.54        10.68        13.87         7.53         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 TCGA-CD-8524 
        0.72        20.65        20.42         1.15        13.15         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.07         0.07         0.10         0.13         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4449 
        3.42         9.34        12.43        12.20        54.08        19.07 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5725 TCGA-D7-6526 TCGA-D7-6820 TCGA-D7-6822 
       21.99        18.97        15.02        17.19        11.31        12.33 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A6EV 
       16.80        19.50        14.66        14.27         5.92        11.24 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-8631 TCGA-FP-A4BF 
        2.96         7.99        16.24        72.23         0.56         5.52 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        0.23        18.08         5.92        12.59        14.17        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H0 
       10.62         0.76        22.75        25.81        11.77         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-A6RI 
       12.95        19.36        12.30         8.81        27.42        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19        13.08         1.41         6.74        12.59 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-R5-A7O7 
        5.56         2.53         5.56        60.56        19.73        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 
       18.21         8.52         6.08        16.67        37.91         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        5.79        48.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       35.24        27.88         7.73        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91Z TCGA-VQ-A922 
       17.85        18.74        20.81        22.68        52.24         9.04 
TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6G TCGA-ZQ-A9CR 
        4.54        21.04        32.94        17.13        26.04         0.79 

subtype1 subtype2 subtype3 
    0.00     0.07     0.07 
subtype1 subtype2 subtype3 
  122.30   116.38    72.23 
subtype1 subtype2 subtype3 
  14.330   12.430   12.315 
[1] "0.0 - 122.3 (14.3)" "0.1 - 116.4 (12.4)" "0.1 - 72.2 (12.3)" 
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2        8       20       18        18        23         2
  subtype2       0        1        9        8        12        16         1
  subtype3       1        5       12        6         9        16         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         33         22         12       18
  subtype2         24         22         18       17
  subtype3         28         18         11       10
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        0        1
  STAGE IA          8        1        5
  STAGE IB         20        9       12
  STAGE II         18        8        6
  STAGE IIA        18       12        9
  STAGE IIB        23       16       16
  STAGE III         2        1        1
  STAGE IIIA       33       24       28
  STAGE IIIB       22       22       18
  STAGE IIIC       12       18       11
  STAGE IV         18       17       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 13 47 85 35
  subtype2  1 21 56 51
  subtype3  8 22 55 33
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       13        1        8
  T2       47       21       22
  T3       85       56       55
  T4       35       51       33
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 60 55 37 26
  subtype2 36 33 23 36
  subtype3 35 30 24 26
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       60       36       35
  N1       55       33       30
  N2       37       23       24
  N3       26       36       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 165  14
  subtype2 116  11
  subtype3 107   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  165   14
  subtype2  116   11
  subtype3  107    5
   clus
vv  subtype1 subtype2 subtype3
  0      165      116      107
  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  70 116
  subtype2  46  86
  subtype3  42  77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70  116
  subtype2   46   86
  subtype3   42   77
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       70       46       42
  MALE        116       86       77
[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                                    25
  subtype2                                    39
  subtype3                                     7
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     69
  subtype2                                                     52
  subtype3                                                     42
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                41
  subtype2                                                                15
  subtype3                                                                24
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               33
  subtype2                                               11
  subtype3                                               34
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        6
  subtype2                                                       10
  subtype3                                                        6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         4
  subtype2                                                         1
  subtype3                                                         3
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        7
  subtype2                                        3
  subtype3                                        3
D7V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  69
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        33
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 7
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   39
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        34
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING 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"
D7V9, binary
          cls
clus         0   1
  subtype1   3 183
  subtype2   1 131
  subtype3   2 117
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  183
  subtype2    1  131
  subtype3    2  117
     clus
vv    subtype1 subtype2 subtype3
  NO         3        1        2
  YES      183      131      117
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 142   6   9  17
  subtype2 107   7   5   6
  subtype3  99   5   4   2
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      142      107       99
  R1        6        7        5
  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    29                         3   115
  subtype2    28                         2    95
  subtype3    32                         7    64
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           29       28       32
  BLACK OR AFRICAN AMERICAN        3        2        7
  WHITE                          115       95       64
[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   2 111
  subtype2   1 117
  subtype3   1  86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  111
  subtype2    1  117
  subtype3    1   86
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        1
  NOT HISPANIC OR LATINO      111      117       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"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  48  23
  subtype2 106  54
  subtype3  43  31
  subtype4  59  41
subtype1 subtype2 subtype3 subtype4 
      71      160       74      100 
subtype1 subtype2 subtype3 subtype4 
      23       54       31       41 
$subtype1
TCGA-B7-5816 TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 
       26.70        11.01         6.97        30.90         6.61        34.68 
TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8286 TCGA-BR-8360 
       19.33        32.78        32.94        23.93        12.95         6.18 
TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8680 TCGA-BR-A44U 
       19.50         4.31        25.18         1.12        15.81        13.87 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5799 TCGA-CD-8528 TCGA-CD-8536 
       20.42         1.15        11.57         3.25         0.10         0.10 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4455 
       11.61         6.58        12.62        15.95         7.99        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5730 TCGA-CG-5733 TCGA-D7-6528 
        0.00         9.01         7.07         4.01        21.07        15.22 
TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-A4BE 
       13.78        11.24        15.65        14.47        19.53        11.08 
TCGA-FP-A4BF TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-A4G9 TCGA-HU-A4GN TCGA-HU-A4GT 
        5.52        14.27        11.41        24.20        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-7808 TCGA-IN-A6RO 
        6.25        19.36        23.84         8.88         3.45         1.41 
TCGA-IN-A6RP TCGA-IP-7968 TCGA-SW-A7EA TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        6.44         2.53        19.04        21.73        34.45        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PO TCGA-VQ-A91D TCGA-VQ-A91S 
       32.48         7.73        34.29         9.27        11.70        22.68 
TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA6B 
        1.71         9.50        64.18        11.24        29.98 

$subtype2
TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6453 
       11.70        19.56         6.61        18.35         6.18        15.95 
TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.87        19.89        12.16         8.98        21.11        30.90 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-8058 
       24.76        35.24        15.32        12.43        12.76        17.49 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 
       12.26        20.55         8.05         0.56        16.31        15.58 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8486 TCGA-BR-8589 
        0.26         0.95        19.17        15.85        20.22        15.81 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
       13.45         7.53         0.49        22.26         1.48        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5813 
        8.98         0.53         0.66         5.13        13.18         0.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 
        0.10         0.10         0.13         3.02        27.02         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       14.01        29.98        47.05        22.98        30.97         6.97 
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-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 
       69.04         7.99        12.36        12.66        20.55        18.54 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       17.85        13.35        12.79        24.72        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EZ 
       18.21        14.66        14.27        15.16        14.76         9.76 
TCGA-D7-A748 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
        4.34         7.40        16.24        72.23        21.27        11.38 
TCGA-FP-8211 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-8608 
       13.58         0.23        26.47         1.51        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC 
        0.76        24.30         5.59        12.30        11.84         3.25 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H6 
       21.37         8.98        10.19         0.26         2.10         9.67 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL 
        8.81        21.21        18.81         3.39         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
       13.08         6.74        12.59         6.51         1.81         7.82 
TCGA-IN-AB1X TCGA-KB-A93H TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       13.51        37.64        61.25         4.60         9.24        11.05 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-VQ-A8DL TCGA-VQ-A8DT 
      122.30        40.64       115.69        57.44         0.92        48.79 
TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PP 
       28.96        46.26        16.31         2.50         1.87        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       15.65        13.35        26.24        27.35        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91V 
       65.16        36.69        11.93        61.22        20.81        36.16 
TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        7.36         2.01        55.43         4.54         6.58         5.72 
TCGA-VQ-A94R TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6F 
       42.54        22.09        18.41        40.08        28.41        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       26.04        16.14        21.11        12.43 

$subtype3
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        39.12 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7715 
       26.10        25.61        18.05        31.20        12.82        15.42 
TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8362 TCGA-BR-8364 
       18.15         9.07        18.71         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-8682 TCGA-BR-8683 TCGA-BR-8686 
        5.39        12.79         6.28        16.44         9.86        15.68 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4J2 TCGA-BR-A4J5 
       12.56         6.08        13.41        13.51        14.17        12.82 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 
       19.36        13.51         0.46        13.64         2.83         0.07 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5728 
       11.31        12.43         0.10        12.00         1.02        65.10 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET 
       11.93        19.13        18.61        20.91        16.44        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A74B TCGA-EQ-5647 TCGA-FP-7735 
       11.31        11.44         8.38         7.13         0.62         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ TCGA-MX-A5UG 
       14.07        22.29        59.54         5.03         0.10         3.72 
TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A91Y 
        5.13       116.38        71.38        35.61        16.87         9.73 
TCGA-VQ-A94P TCGA-ZA-A8F6 
        2.66        10.62 

$subtype4
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        28.01        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        11.54 
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 
        0.30         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 
        0.16         0.13         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-D7-6520 TCGA-D7-6526 TCGA-D7-6527 
       36.00        15.02        79.07        18.84        17.19        10.26 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8578 
       15.98        10.55        11.31        12.33        16.80        21.14 
TCGA-D7-A4YV TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8631 TCGA-HF-A5NB 
        5.92         2.96         7.99        17.06         0.56        18.08 
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-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A7NT TCGA-KB-A6F5 
       12.95        12.30        27.42        18.38         5.56         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       60.56        20.15        19.73         9.86        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
        8.52         6.08        16.67        37.91         8.94         5.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE 
        5.46        13.25        13.02        18.48        35.24        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 
       12.79         2.70        17.85        18.74        52.24         9.04 
TCGA-VQ-A94O TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-ZQ-A9CR 
       21.04        32.94        17.13         0.79 

subtype1 subtype2 subtype3 subtype4 
    0.00     0.10     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
   64.18   122.30   116.38    79.07 
subtype1 subtype2 subtype3 subtype4 
  12.030   13.480   12.805   12.250 
[1] "0.0 - 64.2 (12.0)"  "0.1 - 122.3 (13.5)" "0.1 - 116.4 (12.8)"
[4] "0.1 - 79.1 (12.2)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2        3       12        6        11        10         2
  subtype2       0       10       10       12        13        22         0
  subtype3       0        0        8        4         9         7         0
  subtype4       1        1       11       10         6        16         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          9          8          4        6
  subtype2         37         29         18       19
  subtype3         16         15          9        8
  subtype4         23         10         10       12
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           2        0        0        1
  STAGE IA          3       10        0        1
  STAGE IB         12       10        8       11
  STAGE II          6       12        4       10
  STAGE IIA        11       13        9        6
  STAGE IIB        10       22        7       16
  STAGE III         2        0        0        2
  STAGE IIIA        9       37       16       23
  STAGE IIIB        8       29       15       10
  STAGE IIIC        4       18        9       10
  STAGE IV          6       19        8       12
[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  8 22 31 15
  subtype2 11 35 78 48
  subtype3  0 12 37 27
  subtype4  3 21 50 29
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        8       11        0        3
  T2       22       35       12       21
  T3       31       78       37       50
  T4       15       48       27       29
[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 32 21 12  9
  subtype2 48 45 39 39
  subtype3 23 22 10 21
  subtype4 28 30 23 19
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       32       48       23       28
  N1       21       45       22       30
  N2       12       39       10       23
  N3        9       39       21       19
[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"
D8V6, binary
          cls
clus         0   1
  subtype1  70   6
  subtype2 158  10
  subtype3  69   5
  subtype4  91   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70    6
  subtype2  158   10
  subtype3   69    5
  subtype4   91    9
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       70      158       69       91
  1        6       10        5        9
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  33  46
  subtype2  57 117
  subtype3  30  49
  subtype4  38  67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   46
  subtype2   57  117
  subtype3   30   49
  subtype4   38   67
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       33       57       30       38
  MALE         46      117       49       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"
          vv
clus       STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  subtype1                                    10
  subtype2                                    31
  subtype3                                    24
  subtype4                                     6
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     34
  subtype2                                                     63
  subtype3                                                     32
  subtype4                                                     34
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                16
  subtype2                                                                33
  subtype3                                                                 6
  subtype4                                                                25
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               13
  subtype2                                               29
  subtype3                                                7
  subtype4                                               29
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        3
  subtype2                                                        7
  subtype3                                                        7
  subtype4                                                        5
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         1
  subtype2                                                         3
  subtype3                                                         0
  subtype4                                                         4
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        2
  subtype2                                        7
  subtype3                                        2
  subtype4                                        2
D8V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 7
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   24
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        29
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
[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"
D8V9, binary
          cls
clus         0   1
  subtype1   0  79
  subtype2   4 170
  subtype3   0  79
  subtype4   2 103
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   79
  subtype2    4  170
  subtype3    0   79
  subtype4    2  103
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        4        0        2
  YES       79      170       79      103
[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        R0  R1  R2  RX
  subtype1  60   2   3   8
  subtype2 145   8   7   9
  subtype3  59   4   3   5
  subtype4  84   4   5   3
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       60      145       59       84
  R1        2        8        4        4
  R2        3        7        3        5
  RX        8        9        5        3
[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"
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    18                         3    47
  subtype2    27                         3   115
  subtype3    20                         1    55
  subtype4    24                         5    57
D8V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                           18       27       20       24
  BLACK OR AFRICAN AMERICAN        3        3        1        5
  WHITE                           47      115       55       57
[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"
D8V13, binary
          cls
clus         0   1
  subtype1   0  55
  subtype2   2 113
  subtype3   1  73
  subtype4   1  73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   55
  subtype2    2  113
  subtype3    1   73
  subtype4    1   73
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        2        1        1
  NOT HISPANIC OR LATINO       55      113       73       73
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 46 27
  subtype2 38 17
  subtype3 37 21
  subtype4 38 16
  subtype5 22 13
  subtype6 29 27
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      73       55       58       54       35       56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      27       17       21       16       13       27 
$subtype1
TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8295 TCGA-BR-8368 TCGA-BR-8485 
       28.73        11.44         0.69         2.20         4.31         9.21 
TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CS 
        7.53        11.54        15.81        10.68         7.53         1.48 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-8526 TCGA-CD-8533 
        0.72        20.65        13.64        11.57         0.07         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-5725 TCGA-CG-5730 
        0.13         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        11.31         9.76         2.96 
TCGA-D7-A74A TCGA-FP-8631 TCGA-FP-A4BE TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GF 
        7.40         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         5.56 
TCGA-KB-A6F7 TCGA-KB-A93G TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A8MW 
       60.56        20.15        18.21         8.52         6.08        37.91 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P2 
        5.79         5.46        13.25        18.48        35.24        27.88 
TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        7.73        34.29        22.19        12.79         2.70        17.85 
TCGA-VQ-A91D TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z 
       11.70        20.81        22.68         1.71         7.36        52.24 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        9.04        21.04        11.24        28.41        32.94        29.98 
TCGA-VQ-AA6D 
       17.13 

$subtype2
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-6453 TCGA-BR-7703 TCGA-BR-A4QM TCGA-CD-A4MG 
       19.56        11.01        15.95        24.76         5.13         6.58 
TCGA-CG-5717 TCGA-D7-6521 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A6F2 
        6.97        18.54         5.92        14.76        11.44        15.65 
TCGA-F1-A448 TCGA-FP-8211 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ 
       21.27        13.58         5.59        11.84         3.25        21.37 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         0.26        23.84         9.67         8.88         8.81 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
        5.36         5.19         6.44         6.51         1.81         7.82 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7C1 
        3.72        19.73        61.25         4.60         9.24        16.67 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PT 
      122.30       115.69        46.26        16.31         1.87        26.24 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91V 
       27.35        64.57        65.16        11.93        18.74        36.16 
TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A94U TCGA-VQ-AA6F TCGA-VQ-AA6I 
        9.50         4.54         6.58        22.09        54.12        16.14 
TCGA-VQ-AA6J 
       21.11 

$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        21.11 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8363 
       30.90        32.94         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         0.30         0.07         0.39 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        8.05        14.01        19.07        36.00         1.02         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-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        69.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       11.93        20.55        18.84        17.85        13.35        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 
       10.26        15.22        15.98        12.79        11.31        24.72 
TCGA-D7-A4YY TCGA-EQ-5647 TCGA-F1-6874 TCGA-HU-A4GN 
       13.78         0.62        14.47        29.98 

$subtype4
TCGA-B7-A5TK TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7958 
        9.47        35.24        23.93        18.15        12.43        12.76 
TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8372 TCGA-BR-8381 
       17.49        12.26        12.95        19.50        19.17         0.26 
TCGA-BR-8382 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-CD-8525 
       15.85        20.22         1.12        12.79        13.45         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-D7-8575 
        0.07         0.13         0.10         0.10         0.10        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        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RN TCGA-IN-AB1X TCGA-IP-7968 TCGA-R5-A7O7 
       18.81         3.39        13.08        13.51         2.53        45.67 
TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A91K 
        0.92        21.73         2.50         9.27        13.35        61.22 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A92D TCGA-VQ-AA68 TCGA-VQ-AA6G TCGA-VQ-AA6K 
        2.01        55.43        64.18        40.08        26.04        12.43 

$subtype5
TCGA-B7-A5TN TCGA-BR-6705 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-8059 TCGA-BR-8291 
        9.44        25.61         9.21        15.42        14.43        16.31 
TCGA-BR-8373 TCGA-BR-8677 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J5 
       14.79         0.49        22.26        12.89         8.98        12.82 
TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-A48C TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8574 
        0.07         0.16        11.61        10.55        16.80        17.19 
TCGA-D7-8578 TCGA-D7-A748 TCGA-EQ-8122 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 
       21.14         4.34         7.99         5.56        37.64         9.86 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-SW-A7EA TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8PP 
       57.44        35.61        19.04        34.45        32.48        23.41 
TCGA-VQ-A91A TCGA-VQ-A928 TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-ZQ-A9CR 
       36.69         5.72        42.54        18.41         0.79 

$subtype6
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6803 TCGA-BR-7196 
       17.29        13.68        39.12        26.10        31.20        12.82 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 
        3.45         9.07        18.71         9.60         2.66         7.40 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       13.08        22.19        17.52        14.04         3.32        11.80 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8682 TCGA-BR-8683 
        3.72         5.39         9.34         6.28        16.44         9.86 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4J6 
        8.22        12.56         6.08        13.41        13.51         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-A489 TCGA-CD-A4MI 
       19.36        13.51         0.46         2.83        11.31         0.10 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET TCGA-D7-A747 
       19.13        18.61        20.91        16.44        13.71         8.38 
TCGA-D7-A74B TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ TCGA-RD-A7BS TCGA-RD-A7BW 
        7.13        59.54         5.03         0.10        11.05         5.13 
TCGA-RD-A8N0 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8P8 TCGA-VQ-A8PQ TCGA-VQ-A91Y 
       40.64         8.94        16.87        28.96        15.65         9.73 
TCGA-VQ-A94P TCGA-ZA-A8F6 
        2.66        10.62 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.07     0.26     0.07     0.07     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   60.56   122.30   105.07    72.23    57.44    59.54 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  11.540   11.930   13.825   13.015   14.790   11.555 
[1] "0.1 - 60.6 (11.5)"  "0.3 - 122.3 (11.9)" "0.1 - 105.1 (13.8)"
[4] "0.1 - 72.2 (13.0)"  "0.1 - 57.4 (14.8)"  "0.1 - 59.5 (11.6)" 
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        1        9        2         7         6         1
  subtype2       0        3        4        2         2        10         0
  subtype3       1        1        7       12         8         6         0
  subtype4       1        2        4        7         7        10         1
  subtype5       0        0        3        4         2         7         1
  subtype6       0        0        4        2         7         8         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         22         13          7        6
  subtype2         11         12          6        5
  subtype3         13          4          2        7
  subtype4          9          6          8        3
  subtype5          8          5          1        5
  subtype6          9         12         10        6
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           1        0        1        1        0        0
  STAGE IA          1        3        1        2        0        0
  STAGE IB          9        4        7        4        3        4
  STAGE II          2        2       12        7        4        2
  STAGE IIA         7        2        8        7        2        7
  STAGE IIB         6       10        6       10        7        8
  STAGE III         1        0        0        1        1        0
  STAGE IIIA       22       11       13        9        8        9
  STAGE IIIB       13       12        4        6        5       12
  STAGE IIIC        7        6        2        8        1       10
  STAGE IV          6        5        7        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 12 41 19
  subtype2  6 10 24 15
  subtype3  2 25 26  8
  subtype4  3  9 28 18
  subtype5  0  7 17 12
  subtype6  0  7 29 22
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        3        6        2        3        0        0
  T2       12       10       25        9        7        7
  T3       41       24       26       28       17       29
  T4       19       15        8       18       12       22
[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 18 16
  subtype2 11 13 18 12
  subtype3 23 17 12  9
  subtype4 26 15  7 10
  subtype5  9 13  5  8
  subtype6 15 12 12 17
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       21       11       23       26        9       15
  N1       19       13       17       15       13       12
  N2       18       18       12        7        5       12
  N3       16       12        9       10        8       17
[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 70  4
  subtype2 51  3
  subtype3 55  5
  subtype4 50  3
  subtype5 32  2
  subtype6 51  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70    4
  subtype2   51    3
  subtype3   55    5
  subtype4   50    3
  subtype5   32    2
  subtype6   51    5
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       70       51       55       50       32       51
  1        4        3        5        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 27 48
  subtype2 16 39
  subtype3 22 39
  subtype4 20 38
  subtype5 13 23
  subtype6 22 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   48
  subtype2   16   39
  subtype3   22   39
  subtype4   20   38
  subtype5   13   23
  subtype6   22   36
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       27       16       22       20       13       22
  MALE         48       39       39       38       23       36
[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                                    15
  subtype3                                     6
  subtype4                                     7
  subtype5                                     7
  subtype6                                    20
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     24
  subtype2                                                     11
  subtype3                                                     23
  subtype4                                                     26
  subtype5                                                     13
  subtype6                                                     18
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                20
  subtype2                                                                 9
  subtype3                                                                17
  subtype4                                                                 8
  subtype5                                                                 7
  subtype6                                                                 7
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               24
  subtype2                                               13
  subtype3                                               10
  subtype4                                               11
  subtype5                                                5
  subtype6                                                6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        2
  subtype2                                                        2
  subtype3                                                        3
  subtype4                                                        4
  subtype5                                                        3
  subtype6                                                        5
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         2
  subtype2                                                         1
  subtype3                                                         2
  subtype4                                                         0
  subtype5                                                         1
  subtype6                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        4
  subtype3                                        0
  subtype4                                        2
  subtype5                                        0
  subtype6                                        2
D9V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype6
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
[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"
D9V9, binary
          cls
clus        0  1
  subtype1  1 74
  subtype2  0 55
  subtype3  1 60
  subtype4  2 56
  subtype5  1 35
  subtype6  0 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   74
  subtype2    0   55
  subtype3    1   60
  subtype4    2   56
  subtype5    1   35
  subtype6    0   58
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         1        0        1        2        1        0
  YES       74       55       60       56       35       58
[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       R0 R1 R2
  subtype1 66  2  2
  subtype2 45  3  1
  subtype3 50  3  4
  subtype4 54  1  0
  subtype5 32  1  0
  subtype6 47  4  3
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       66       45       50       54       32       47
  R1        2        3        3        1        1        4
  R2        2        1        4        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    42
  subtype2    12                         1    38
  subtype3     7                         1    36
  subtype4    11                         2    40
  subtype5     8                         0    26
  subtype6    12                         1    45
D9V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           18       12        7       11        8
  BLACK OR AFRICAN AMERICAN        6        1        1        2        0
  WHITE                           42       38       36       40       26
                           clus
vv                          subtype6
  ASIAN                           12
  BLACK OR AFRICAN AMERICAN        1
  WHITE                           45
[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  0 46
  subtype2  2 35
  subtype3  0 44
  subtype4  2 41
  subtype5  0 27
  subtype6  0 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   46
  subtype2    2   35
  subtype3    0   44
  subtype4    2   41
  subtype5    0   27
  subtype6    0   54
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        2        0        2        0        0
  NOT HISPANIC OR LATINO       46       35       44       41       27       54
[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 118  71
  subtype2  43  28
  subtype3  49  22
subtype1 subtype2 subtype3 
     189       71       71 
subtype1 subtype2 subtype3 
      71       28       22 
$subtype1
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN 
       26.70        11.70        19.56        11.01         9.47         9.44 
TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 
       34.68        13.87        17.29        19.33         9.17        32.78 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 
       12.16         8.98        30.90        32.94         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 
       35.24        23.93        15.42        18.15        28.73        12.43 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
        3.45        12.76        17.49        14.43        11.44        12.26 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8362 
        8.05        12.95         2.66         2.20        15.58        13.08 
TCGA-BR-8363 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 
        0.26         3.32        19.17        14.79         0.26        15.85 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8678 
        5.39         9.21        20.22        12.79        13.45        11.54 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
       15.81         9.86         8.22        10.68         7.53        22.26 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5799 
        1.48        12.89         0.72        13.64         5.13         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5813 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.30         0.39         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4437 
        0.13         3.42         9.34        11.61        12.20         8.05 
TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       14.01        19.07         6.97         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        15.02        28.96        69.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
        7.99        12.36        12.66        20.55        18.54        13.35 
TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       17.19        12.79        10.55        12.33        24.72        16.80 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY 
       14.66        21.14        14.27        16.44         5.92        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 
       14.76        11.31        11.44         2.96        15.65         7.99 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8211 
       72.23         3.48        19.53        22.29        17.06        13.58 
TCGA-FP-8631 TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4H6 
        0.56         1.51        12.10         3.25        21.37         9.67 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
        8.81        21.21         3.45        18.81         3.39         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
        5.19        13.08         6.44         6.51         5.56         1.81 
TCGA-IN-AB1V TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UJ TCGA-MX-A663 
        7.82         2.53         5.56        60.56        19.73         9.86 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS 
       45.67        18.21         8.52         4.60         9.24        11.05 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL 
      122.30        37.91         8.94        19.04         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        5.46        13.25        35.24        34.45        32.48         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       28.96        46.26        16.31        22.19         2.50        12.79 
TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PZ TCGA-VQ-A91K TCGA-VQ-A91Q 
        1.87        23.41        15.65        65.16        61.22        20.81 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D 
       52.24         9.04         2.01        55.43         6.58        64.18 
TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA6B TCGA-VQ-AA6F 
       21.04        11.24        22.09        18.41        29.98        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       26.04        21.11        12.43 

$subtype2
TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
       15.95        13.68        39.12        26.10        25.61        18.05 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 
       21.11        31.20        12.82         9.07        18.71         9.60 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8371 
       16.31         7.40        22.19        17.52        14.04        11.80 
TCGA-BR-8384 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-A44T 
        3.72         9.34         6.28         0.49        16.44        12.56 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 
        6.08        13.41        13.51         8.98        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-8524 
       19.36        13.51         0.46         2.83         0.07         0.07 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-5719 TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 
       11.31         0.10         1.02        65.10        11.93        19.13 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A6ET 
       18.84        18.61        17.85        17.19        20.91        13.71 
TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-FP-8209 TCGA-FP-8210 
        8.38         4.34         7.13         0.62        59.54         5.03 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-KB-A93H TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8N0 
        0.10         0.26        37.64         3.72         5.13        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A91A TCGA-VQ-A91Y 
      115.69        57.44        35.61        16.87        36.69         9.73 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72         2.66        42.54        10.62         0.79 

$subtype3
TCGA-BR-6707 TCGA-BR-8077 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 
       19.89         0.69         6.18        19.50         4.31         1.12 
TCGA-BR-8676 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-CG-5718 
        7.53        20.65        11.57         0.10         6.58        36.00 
TCGA-CG-5727 TCGA-CG-5730 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       79.07         4.01        10.26        15.22        15.98        11.31 
TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-A448 
       18.21        11.24         9.76         7.40        14.47        21.27 
TCGA-FP-A4BE TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 
       11.08         5.92        11.41        10.62         5.59        11.84 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX 
       22.75        25.81        11.77        29.98         6.51        10.19 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-IN-A6RI TCGA-IN-AB1X 
       12.95        23.84        12.30         8.88        18.38        13.51 
TCGA-KB-A93G TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-VQ-A8E0 TCGA-VQ-A8E3 
       20.15        61.25         6.08        16.67        18.48        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8PB TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PS 
       27.88        34.29         2.70        17.85         9.27        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91N 
       26.24        27.35        64.57        11.70        11.93        18.74 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A925 
       22.68         1.71        36.16         7.36         9.50         4.54 
TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6I 
       40.08        28.41        32.94        17.13        16.14 

subtype1 subtype2 subtype3 
    0.07     0.07     0.10 
subtype1 subtype2 subtype3 
  122.30   115.69    79.07 
subtype1 subtype2 subtype3 
   12.66    12.82    13.35 
[1] "0.1 - 122.3 (12.7)" "0.1 - 115.7 (12.8)" "0.1 - 79.1 (13.3)" 
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        5       19       19        14        30         2
  subtype2       0        0        5        5         9         7         0
  subtype3       2        2        7        5        10        10         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         45         26         19       19
  subtype2         14         14          9        9
  subtype3         13         12          6        4
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        0        2
  STAGE IA          5        0        2
  STAGE IB         19        5        7
  STAGE II         19        5        5
  STAGE IIA        14        9       10
  STAGE IIB        30        7       10
  STAGE III         2        0        1
  STAGE IIIA       45       14       13
  STAGE IIIB       26       14       12
  STAGE IIIC       19        9        6
  STAGE IV         19        9        4
[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  9 43 97 50
  subtype2  0 12 36 24
  subtype3  5 15 32 20
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        9        0        5
  T2       43       12       15
  T3       97       36       32
  T4       50       24       20
[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 61 53 42 41
  subtype2 18 18 13 21
  subtype3 26 18 17 10
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       61       18       26
  N1       53       18       18
  N2       42       13       17
  N3       41       21       10
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus         0   1
  subtype1 178  13
  subtype2  63   6
  subtype3  68   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  178   13
  subtype2   63    6
  subtype3   68    3
   clus
vv  subtype1 subtype2 subtype3
  0      178       63       68
  1       13        6        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  63 136
  subtype2  30  42
  subtype3  27  45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63  136
  subtype2   30   42
  subtype3   27   45
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       63       30       27
  MALE        136       42       45
[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                                    25
  subtype2                                    25
  subtype3                                     7
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     81
  subtype2                                                     22
  subtype3                                                     12
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                40
  subtype2                                                                 7
  subtype3                                                                21
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               38
  subtype2                                                6
  subtype3                                               25
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        8
  subtype2                                                        9
  subtype3                                                        2
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         2
  subtype2                                                         1
  subtype3                                                         3
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        5
  subtype2                                        2
  subtype3                                        2
D10V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  81
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 5
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   25
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING 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"
D10V9, binary
          cls
clus         0   1
  subtype1   5 194
  subtype2   0  72
  subtype3   0  72
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  194
  subtype2    0   72
  subtype3    0   72
     clus
vv    subtype1 subtype2 subtype3
  NO         5        0        0
  YES      194       72       72
[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        R0  R1  R2
  subtype1 170   8   4
  subtype2  58   6   3
  subtype3  66   0   3
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      170       58       66
  R1        8        6        0
  R2        4        3        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    32                         6   134
  subtype2    18                         0    52
  subtype3    18                         5    41
D10V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           32       18       18
  BLACK OR AFRICAN AMERICAN        6        0        5
  WHITE                          134       52       41
[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"
D10V13, binary
          cls
clus         0   1
  subtype1   2 142
  subtype2   0  64
  subtype3   2  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  142
  subtype2    0   64
  subtype3    2   41
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        0        2
  NOT HISPANIC OR LATINO      142       64       41
[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"
