[1] "ofn"        "-oTSTES-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/STES-TP/15090071/STES-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STES-TP/15125163/STES-TP.mergedcluster.txt"

nPatients in clinical file=612, in cluster file=628, common to both=612
[1]   8 612
[1] "CN_CNMF"
[1] 3
  1   2   3 
163 200 246 
  1   2   3 
163 200 246 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
244 149 171 
  1   2   3 
244 149 171 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
235 121  92 
  1   2   3 
235 121  92 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 76 150  25  80 117 
  1   2   3   4   5 
 76 150  25  80 117 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
154 326 130 
  1   2   3 
154 326 130 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
125 106 227  85  67 
  1   2   3   4   5 
125 106 227  85  67 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
133 208 170 
  1   2   3 
133 208 170 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 47 120 162 100  82 
  1   2   3   4   5 
 47 120 162 100  82 
[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] "NUMBER_PACK_YEARS_SMOKED"              
[17] "COMPLETENESS_OF_RESECTION"             
[18] "NUMBER_OF_LYMPH_NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 612 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=198,	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=324,	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=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=6,	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:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH_NUMBER':	nDistinctValues=34,	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 612 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [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] "NUMBER_PACK_YEARS_SMOKED"              
[10] "COMPLETENESS_OF_RESECTION"             
[11] "NUMBER_OF_LYMPH_NODES"                 
[12] "RACE"                                  
[13] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=56, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  52 126 283 124 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   53   126   283   124 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  52 126 283 124 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   53   126   283   124 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
202 183  96  97 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
202 183  96  97 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
202 183  96  97 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
202 183  96  97 
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
NUMBER_PACK_YEARS_SMOKED, nv=45, binary=FALSE, numeric=TRUE
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  95  59
  subtype2 111  81
  subtype3 148  81
subtype1 subtype2 subtype3 
     154      192      229 
subtype1 subtype2 subtype3 
      59       81       81 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GQ 
       25.78        31.27        14.30         5.92        13.94         4.21 
TCGA-IC-A6RE TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OG 
        7.69       122.10        42.77         8.94         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX 
       32.61         7.17         1.38        58.59         7.13         7.43 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A891 TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NN 
        2.60         0.36         3.95        35.97        12.92         5.49 
TCGA-L5-A8NR TCGA-L5-A8NT TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y0 
        8.71        27.12         7.82        14.70         7.04        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RB 
       15.78         2.89         1.45         7.00        20.02         5.29 
TCGA-V5-AASW TCGA-VR-AA4D TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-B7-A5TJ TCGA-B7-A5TN 
        9.27        46.19        10.16        19.73        11.01         9.44 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
       17.29        19.33         9.17        21.11         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 
       15.42        18.15        28.73         3.45        18.71        11.44 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 
        0.69        12.95         2.66        14.79         5.39         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       20.22        11.54         9.86         8.22        10.68        13.87 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5800 
       22.26         0.72        13.51        20.42         1.15        13.15 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 
        0.30         0.07         0.07         0.13         3.42        11.31 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
       12.20        20.02         7.99        54.08         4.01        29.98 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 
       19.07         7.07        36.00         4.01        69.04        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       11.93        19.13        17.19        10.26        15.22        15.98 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-D7-A6EX 
       11.31        12.33        19.50        14.27        11.24        11.31 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 
        2.96         7.99        72.23        19.53        17.06         0.56 
TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.52        12.59        14.17        12.30        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A7NU 
       11.77         2.10        12.30        27.42        18.38         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZR 
        2.53         5.56        37.64        45.67        18.21         6.08 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N6 TCGA-RD-A8N9 
        9.24         8.61        16.67       122.30         8.94        35.61 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E7 TCGA-VQ-A8PE TCGA-VQ-A8PH 
        5.46        13.25        13.02        34.45        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PY TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
        2.70        14.33        22.68         1.71        36.16         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        9.73        52.24         9.04        64.18        21.04        42.54 
TCGA-VQ-A94U TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-ZQ-A9CR 
       22.09        29.98        17.13         0.79 

$subtype2
TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3I8 
       58.55         7.63         8.94        16.24        32.45        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       20.09         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A4QS TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
        3.88         0.53        17.03         0.79        23.41        12.82 
TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FB 
        9.96         4.67        14.50        12.16        44.75        60.39 
TCGA-JY-A6FE TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
        3.68        23.18        25.22         0.30         4.31        24.00 
TCGA-L5-A4OM TCGA-L5-A4ON TCGA-L5-A4OO TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU 
       47.93        18.35         3.32         3.16         4.90        29.00 
TCGA-L5-A88S TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ 
        6.94         7.40        55.50         2.66        13.48        16.47 
TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
       13.55        13.22        13.41        52.57        46.09        10.36 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R 
        5.92        10.45        12.66        12.43        13.41         0.10 
TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.15        15.35         0.10        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
        0.13         5.16         8.02         7.59         5.06        29.59 
TCGA-R6-A6XQ TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASX 
        6.35        12.69        20.38         3.42         4.80         4.44 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW 
       18.81        19.96        22.82        12.43        18.31         8.12 
TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B 
       28.11        30.71        18.18        42.87        15.06        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-B7-5818 
        9.17        15.91         3.42         2.10         2.66        11.70 
TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-7716 TCGA-BR-8059 
       19.56         6.61        18.35         6.18        28.01        14.43 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8484 TCGA-BR-A4CS TCGA-BR-A4J6 
        2.20         7.40        19.50        25.18         1.48         0.66 
TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8527 
       20.65        13.64         3.25        13.18         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A487 TCGA-CD-A48A 
        0.10         0.16         0.10         0.13         9.34        12.43 
TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4437 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
       11.61         3.02         8.05        47.05        12.03        21.99 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-6519 
       18.97        12.00        22.98        12.03        15.02        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-A4YU 
       18.84        18.54        13.35        12.79        18.21        16.44 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-FP-7735 TCGA-FP-8211 
       15.65         7.40         0.62        16.24         3.48        13.58 
TCGA-HU-8243 TCGA-HU-A4GC TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-IN-7808 
        5.92         3.25         6.25        12.95        23.84         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81         3.39         5.19        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E0 
        6.74         5.56        60.56         0.92        48.79        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PU 
       35.24        21.73         7.73        17.85        13.35        27.35 
TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A94T 
       36.69        18.74        20.81         2.01         4.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6I TCGA-VQ-AA6K 
       18.41        40.08        32.94        54.12        16.14        12.43 

$subtype3
TCGA-IC-A6RF TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A938 
        6.21         9.30        14.86        68.02        41.52        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43E 
       21.70        31.56        24.03         6.28         3.16        30.25 
TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A88T TCGA-L5-A88W TCGA-L5-A893 TCGA-L5-A8NM 
       19.99        21.01         8.71        25.12         3.02         7.76 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-M9-A5M8 TCGA-R6-A6Y2 TCGA-V5-AASV TCGA-VR-A8ET 
       21.37        83.24        33.11         9.30        15.35         1.55 
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-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
       17.49        12.26         9.60        20.55         8.05         0.56 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       16.31        15.58         6.18        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       17.52         0.95        26.33         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 
       11.80        19.17         0.26        15.85         3.72         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         9.34        13.45         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A452 
        0.49        15.81        16.44        15.68        12.56         7.53 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        6.08        13.41        13.51        12.89         8.98        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM 
        0.53        12.82        19.36         0.46        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MG 
        2.83         0.07         0.13         0.10         0.10         6.58 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 
        0.10        12.62        27.02        15.95         1.02        14.01 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        0.00         9.01        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        28.96        79.07        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 
       21.07         7.99        12.36        18.61        17.85        10.55 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        17.19        14.66        21.14        20.91 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        15.16        13.78        14.76        13.71        11.44 
TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A448 
        9.76         8.38         4.34         7.13        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX 
       11.38        14.07        22.29        59.54         5.03         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 
       18.08        26.47         1.51        14.27        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62         0.76        24.30         5.59        11.84        24.20 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        0.26        19.36         9.67         8.88         8.81        21.21 
TCGA-IN-A6RJ TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A93G 
        5.36        12.59         6.51         7.82        13.51        20.15 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 
        3.72        19.73         9.86         8.52        61.25         4.60 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       11.05         5.13        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8P2 
       71.38        57.44        16.87        19.04         5.79        27.88 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       32.48        28.96        34.29        46.26        16.31         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        26.24        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A924 
       65.16        11.70        11.93        61.22         7.36        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6G TCGA-VQ-AA6J 
        6.58         5.72         2.66        28.41        26.04        21.11 
TCGA-ZA-A8F6 
       10.62 

subtype1 subtype2 subtype3 
    0.07     0.07     0.00 
subtype1 subtype2 subtype3 
  122.30    60.56   116.38 
subtype1 subtype2 subtype3 
  12.315   12.625   13.410 
[1] "0.1 - 122.3 (12.3)" "0.1 - 60.6 (12.6)"  "0.0 - 116.4 (13.4)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       5        6       12       10         9        25         9
  subtype2       2        3       12        9        39        26        18
  subtype3       4       10       24       13        29        33         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         29         17         10       15         1
  subtype2         30         21         14       12         3
  subtype3         38         34         24       24         0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           5        2        4
  STAGE IA          6        3       10
  STAGE IB         12       12       24
  STAGE II         10        9       13
  STAGE IIA         9       39       29
  STAGE IIB        25       26       33
  STAGE III         9       18        2
  STAGE IIIA       29       30       38
  STAGE IIIB       17       21       34
  STAGE IIIC       10       14       24
  STAGE IV         15       12       24
  STAGE IVA         1        3        0
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1  T2  T3  T4
  subtype1    20  31  76  28
  subtype2    15  46 104  25
  subtype3    18  49 100  71
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       20       15       18
  T2          31       46       49
  T3          76      104      100
  T4          28       25       71
[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 42 52 33 23
  subtype2 70 69 24 27
  subtype3 88 61 39 47
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       42       70       88
  N1       52       69       61
  N2       33       24       39
  N3       23       27       47
[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"
D1V6, binary
          cls
clus         0   1
  subtype1 132   9
  subtype2 169  12
  subtype3 212  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  132    9
  subtype2  169   12
  subtype3  212   18
   clus
vv  subtype1 subtype2 subtype3
  0      132      169      212
  1        9       12       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  45 118
  subtype2  37 163
  subtype3 100 146
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45  118
  subtype2   37  163
  subtype3  100  146
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       45       37      100
  MALE        118      163      146
[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                                     6
  subtype2                                    15
  subtype3                                    50
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     42
  subtype2                                                     34
  subtype3                                                     86
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                30
  subtype2                                                                18
  subtype3                                                                33
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               32
  subtype2                                               18
  subtype3                                               28
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        5
  subtype2                                                        3
  subtype3                                                       13
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         5
  subtype2                                                         0
  subtype3                                                         3
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        3
  subtype2                                        1
  subtype3                                        9
D1V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        32
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  86
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       33
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 9
[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"
D1V9, binary
          cls
clus         0   1
  subtype1   1 162
  subtype2   2 198
  subtype3   3 243
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  162
  subtype2    2  198
  subtype3    3  243
     clus
vv    subtype1 subtype2 subtype3
  NO         1        2        3
  YES      162      198      243
[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"
D1V10, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  95   7   6   4
  subtype2  73   3   5   5
  subtype3 179   8   8  16
D1V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       95       73      179
  R1        7        3        8
  R2        6        5        8
  RX        4        5       16
[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"
D1V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    22                         5
  subtype2    60                         3
  subtype3    47                         5
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1   107
  subtype2                                         0   113
  subtype3                                         0   165
D1V13, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  ASIAN                                           22       60       47
  BLACK OR AFRICAN AMERICAN                        5        3        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                          107      113      165
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
          cls
clus         0   1
  subtype1   2  99
  subtype2   1 121
  subtype3   4 174
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   99
  subtype2    1  121
  subtype3    4  174
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        4
  NOT HISPANIC OR LATINO       99      121      174
[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(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1 157  81
  subtype2  88  57
  subtype3  98  68
subtype1 subtype2 subtype3 
     238      145      166 
subtype1 subtype2 subtype3 
      81       57       68 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM 
       25.78        31.27        14.30         7.63         5.92        13.94 
TCGA-2H-A9GN TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FB 
        8.94        32.45         7.69         3.88       122.10        60.39 
TCGA-JY-A93C TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OF TCGA-L5-A4OG 
       23.18        25.22        30.25        24.00         3.68         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
       32.61        19.99        21.01        18.35         7.17         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 
        4.90         7.13         7.43         2.60         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
       55.50        35.97        12.92        16.47        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ 
        8.71        13.41        27.12        52.57        46.09        10.36 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6XG 
       33.11         7.82         8.02         7.59        14.70        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
        6.35         9.30         2.89         1.45         7.00        20.02 
TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
        5.29         4.80         9.27         4.44        22.82        46.19 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-6452 
       10.16        19.73        26.70        11.70        11.01        34.68 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6852 TCGA-BR-7703 
       13.87        19.33        32.78        19.89        32.94        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-7959 
       23.93        15.42        18.15        12.43        12.76        18.71 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8297 
       12.26        20.55         8.05        12.95         2.66         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-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8487 
        3.32        19.17         0.26        15.85         5.39         1.12 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
       15.81        13.45         7.53        15.81        16.44        15.68 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4J8 
       13.87        22.26         1.48        12.89         0.53        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.07         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4437 
       12.43        11.61         6.58         0.10        12.62         8.05 
TCGA-CG-4441 TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       14.01         0.99        12.03        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6525 TCGA-D7-6528 
        4.01        21.07        12.36        12.66        13.35        15.22 
TCGA-D7-6815 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT 
       15.98        12.33        19.50        18.21        14.66        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EV 
       16.44         5.92        15.16        13.78        14.76        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
       11.44         9.76         7.40        14.47        72.23        21.27 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-A5NB 
       19.53        14.07        17.06        11.08         5.52        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G2 
        1.51         5.92        14.27        11.41        12.10        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GN 
        5.59        12.30        11.84        24.20         3.25        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 
        8.98         0.10         6.51         6.25         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 TCGA-IN-8462 
       19.36        23.84         9.67         8.88        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        3.39         5.19         1.41         6.44         6.74        12.59 
TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A5UJ TCGA-R5-A7ZR 
        1.81        13.51         2.53        37.64        19.73         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-SW-A7EA TCGA-VQ-A8DT 
        4.60         9.24         8.61        16.67        19.04        48.79 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       21.73        34.45        27.88        32.48         7.73        28.96 
TCGA-VQ-A8PB TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PY 
       34.29         9.27        23.41        26.24        27.35        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S 
       65.16        36.69        11.70        11.93        61.22        22.68 
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-A925 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-A94U TCGA-VQ-AA68 
        4.54        64.18        42.54        11.24        22.09        40.08 
TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I 
       28.41        29.98        26.04        16.14 

$subtype2
TCGA-2H-A9GG TCGA-2H-A9GJ TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       20.05        58.55         4.21         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        0.85         2.63        18.64         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I 
       23.41        12.82         9.96         4.67        14.50        12.16 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93F 
       44.75        68.02         3.68        41.52        42.77        24.03 
TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z 
        0.30         4.31        47.93         6.94        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NK TCGA-L5-A8NN TCGA-LN-A49K 
        3.95         2.66        13.48        13.55         5.49         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35         0.10        13.25        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.76        12.59         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6Y0 
       12.23        12.03        13.18         0.13         5.16        53.95 
TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
       12.69        20.38         3.42        15.35        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
       12.43        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JE 
       42.87        15.06        11.24         9.17        15.91         2.10 
TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7723 
        9.44        17.29         9.17         9.21        35.24        28.73 
TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8485 
        3.45        11.44         0.69         2.20        14.79         9.21 
TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CD-5800 
       20.22        11.54         8.22         0.72         3.25        13.15 
TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-5718 TCGA-CG-5725 TCGA-D7-6519 
        0.07         3.42        12.20        36.00        15.02        20.55 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6820 TCGA-D7-A6EX TCGA-D7-A6F0 
       18.84        17.19        10.26        11.31        11.31         2.96 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-FP-8631 TCGA-HU-8249 
       15.65         0.62         7.99        16.24         0.56        14.17 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GX TCGA-HU-A4H5 TCGA-HU-A4HD 
       22.75        25.81        11.77        10.19        12.30        27.42 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A7NT TCGA-R5-A7ZE TCGA-RD-A8N6 TCGA-VQ-A8DU 
       18.38        13.08         5.56        18.21         8.94         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       13.25        13.02        35.24        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6A 
       17.85        18.74        52.24         9.04        21.04        32.94 
TCGA-VQ-AA6D 
       17.13 

$subtype3
TCGA-2H-A9GO TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A938 
       16.24        20.78        20.12         9.30        14.86        25.41 
TCGA-JY-A939 TCGA-JY-A93D TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OO 
       21.70        31.56         6.28         3.16         8.94         3.32 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A8NQ TCGA-L5-A8NU 
        1.38        58.59        29.00         8.71        21.37        83.24 
TCGA-LN-A49X TCGA-LN-A4A5 TCGA-R6-A6KZ TCGA-R6-A6L6 TCGA-R6-A8W5 TCGA-VR-A8ET 
        0.10        22.39         5.06         7.04        15.78         1.55 
TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-A5TI TCGA-B7-A5TK TCGA-BR-6453 TCGA-BR-6457 
        3.42         2.66        19.56         9.47        15.95        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 
       39.12        26.10        25.61        18.05        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7716 TCGA-BR-7722 
       21.11        30.90        31.20        12.82        28.01        15.32 
TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8291 
        9.07        17.49        14.43         9.60         0.56        16.31 
TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 
       15.58         0.26        22.19        17.52         0.95        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-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
        9.86        10.68        12.56         7.53         6.08        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
       13.51         8.98        14.17        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5813 
        0.46         2.83        13.18         0.30         0.07         0.39 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-A487 
        0.07         0.07         0.13         0.16         0.10         9.34 
TCGA-CD-A489 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       11.31         6.97         1.02         6.02         0.99       105.07 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 
       69.04         7.99        11.93        19.13        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 
       17.85        12.79        10.55        24.72        16.80        17.19 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A6ET TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       21.14        20.91        13.71         8.38         4.34         7.13 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
       11.38         3.48        22.29        59.54         5.03        13.58 
TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4GJ 
        0.23        26.47        12.59        10.62         0.76        21.37 
TCGA-HU-A4GY TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A7NR TCGA-IN-AB1V 
        0.26         8.81         3.45         5.36         6.51         7.82 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UG TCGA-MX-A663 TCGA-R5-A7O7 
        5.56        60.56        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-A8MW 
        8.52        61.25        11.05         5.13       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
       40.64       115.69       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8PC TCGA-VQ-A8PD 
       16.87         5.79         0.92        18.48        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A91Q 
        2.50         1.87        15.65        13.35        64.57        20.81 
TCGA-VQ-A91Y TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA6F 
        9.73         6.58         5.72         2.66        18.41        54.12 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11        12.43        10.62         0.79 

subtype1 subtype2 subtype3 
    0.07     0.07     0.07 
subtype1 subtype2 subtype3 
  122.10    68.02   122.30 
subtype1 subtype2 subtype3 
  13.285   12.590   12.495 
[1] "0.1 - 122.1 (13.3)" "0.1 - 68.0 (12.6)"  "0.1 - 122.3 (12.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       9       10       18       11        24        43        12
  subtype2       2        4       10        8        31        21        15
  subtype3       0        4       14       10        23        19         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         35         35         21       13         0
  subtype2         21         14          9        8         2
  subtype3         35         22         17       19         2
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           9        2        0
  STAGE IA         10        4        4
  STAGE IB         18       10       14
  STAGE II         11        8       10
  STAGE IIA        24       31       23
  STAGE IIB        43       21       19
  STAGE III        12       15        2
  STAGE IIIA       35       21       35
  STAGE IIIB       35       14       22
  STAGE IIIC       21        9       17
  STAGE IV         13        8       19
  STAGE IVA         0        2        2
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1  T2  T3  T4
  subtype1    32  39 115  48
  subtype2    12  38  74  22
  subtype3     7  34  82  45
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       32       12        7
  T2          39       38       34
  T3         115       74       82
  T4          48       22       45
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 83 68 41 40
  subtype2 59 50 20 15
  subtype3 52 47 29 37
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       83       59       52
  N1       68       50       47
  N2       41       20       29
  N3       40       15       37
[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"
D2V6, binary
          cls
clus         0   1
  subtype1 209   8
  subtype2 129   8
  subtype3 140  16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  209    8
  subtype2  129    8
  subtype3  140   16
   clus
vv  subtype1 subtype2 subtype3
  0      209      129      140
  1        8        8       16
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus         0   1
  subtype1  70 174
  subtype2  40 109
  subtype3  50 121
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   70  174
  subtype2   40  109
  subtype3   50  121
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       70       40       50
  MALE        174      109      121
[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                                    23
  subtype2                                     2
  subtype3                                    41
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     63
  subtype2                                                     24
  subtype3                                                     47
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                35
  subtype2                                                                14
  subtype3                                                                23
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               44
  subtype2                                               19
  subtype3                                               14
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                       10
  subtype2                                                        0
  subtype3                                                       10
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         3
  subtype2                                                         3
  subtype3                                                         2
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        4
  subtype2                                        1
  subtype3                                        8
D2V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  63
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   41
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  47
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       23
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 8
[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"
D2V9, binary
          cls
clus         0   1
  subtype1   2 242
  subtype2   1 148
  subtype3   3 168
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  242
  subtype2    1  148
  subtype3    3  168
     clus
vv    subtype1 subtype2 subtype3
  NO         2        1        3
  YES      242      148      168
[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"
D2V10, continuous
          vv
clus        R0  R1  R2
  subtype1 163   4   4
  subtype2  51   3   3
  subtype3 119  10   5
D2V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      163       51      119
  R1        4        3       10
  R2        4        3        5
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    44                         6
  subtype2    52                         4
  subtype3    34                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1   163
  subtype2                                         0    80
  subtype3                                         0   117
D2V13, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  ASIAN                                           44       52       34
  BLACK OR AFRICAN AMERICAN                        6        4        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                          163       80      117
[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"
D2V14, binary
          cls
clus         0   1
  subtype1   3 150
  subtype2   1  97
  subtype3   3 124
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  150
  subtype2    1   97
  subtype3    3  124
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        3
  NOT HISPANIC OR LATINO      150       97      124
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 147  64
  subtype2  73  46
  subtype3  50  34
subtype1 subtype2 subtype3 
     211      119       84 
subtype1 subtype2 subtype3 
      64       46       34 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK 
       25.78        20.05        31.27        14.30        58.55         7.63 
TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS 
        5.92         8.94        16.24        32.45         7.69         3.88 
TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E 
      122.10        60.39        21.70        23.18         3.16        30.25 
TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON 
        8.94         3.68        32.61        19.99        21.01        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OS TCGA-L5-A4OT TCGA-L5-A4OU 
        7.17         1.38         3.16        58.59         4.90        29.00 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH 
        7.13         7.43        55.50         2.66        35.97        12.92 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS 
       13.48        16.47         7.76         5.49         8.71        13.41 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG 
       52.57        10.36        33.11         7.59         5.06        29.59 
TCGA-R6-A8W5 TCGA-R6-A8WC TCGA-R6-A8WG TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RE 
       15.78         1.45        12.69         7.00        20.02         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-B7-5816 
        9.27         4.44        22.82        46.19        10.16        26.70 
TCGA-B7-5818 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       11.70        18.35         6.18         6.61        34.68        15.95 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 
        9.17        32.78        19.89        21.11        30.90        32.94 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       24.76        23.93        28.01        18.15        15.32        12.43 
TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8286 
        3.45        17.49         0.69        12.26        20.55        12.95 
TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8373 
       16.31        19.50        13.08         4.31        19.17        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8683 
        1.12        12.79        15.81        13.45        15.81         9.86 
TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4PD 
        8.22         7.53         1.48         0.72        12.82        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       20.42         1.15        13.64         3.25        13.15        13.18 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.13         0.10         0.13         0.10         3.42 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
       11.61         6.58        12.20        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       14.01        47.05        19.07        21.99         0.00         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       18.97         7.07        12.00        36.00         1.02         0.99 
TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        0.99        28.96        69.04         7.99        12.36        12.66 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.84        18.54        17.85        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        18.21        14.66        21.14        20.91        14.27 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 
       15.16        13.78        14.76         7.99        16.24        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       21.27         3.48        19.53        17.06        13.58         0.56 
TCGA-FP-A4BE TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       11.08         1.51        14.27        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
        3.25        25.81        11.77        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         2.10        12.95        19.36        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IP-7968 
        2.53 

$subtype2
TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       13.94         4.21         6.21        33.27        20.09         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D 
       20.78         2.63        20.12        18.64         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16        44.75        68.02         3.68        41.52        42.77 
TCGA-JY-A938 TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OE 
       25.41        24.03         6.28         0.30         4.31        24.00 
TCGA-L5-A4OG TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88W 
        4.70        47.93         6.94         8.71         2.60        25.12 
TCGA-L5-A88Y TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NQ 
        0.36         7.40         3.95         3.02        13.55        21.37 
TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       46.09         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
        0.10        13.15        15.35         0.10        13.25         0.10 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 
       12.46        12.59        12.49        12.76        12.59        22.39 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
        0.10        15.52        11.54        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY 
       12.33        25.25        10.52        12.00        12.23        12.03 
TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 
       13.18         0.13         5.16         7.82         8.02        14.70 
TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-S8-A6BW 
        7.04         6.35        53.95         9.30         2.89        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
        5.29         3.42        15.35        18.81        19.96        12.43 
TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ 
        1.55        18.31         8.12        28.11        30.71        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD 
       42.87        15.06        11.24         9.17        15.91         3.42 
TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-8678 TCGA-BR-A4IY TCGA-BR-A4J4 
        2.10         2.66        19.73        11.54        12.89         0.53 
TCGA-CD-8535 TCGA-CG-4443 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5723 TCGA-CG-5724 
        0.13        29.98        30.97         6.97       105.07        12.03 
TCGA-CG-5725 TCGA-D7-6525 TCGA-F1-6875 TCGA-IN-8462 TCGA-IN-8663 
       15.02        13.35        72.23        18.81         3.39 

$subtype3
TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A4OO TCGA-L5-A8NL 
        9.30        14.86        31.56        25.22         3.32        13.22 
TCGA-L5-A8NT TCGA-L5-A8NU TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-6455 
       27.12        83.24         4.64        30.90         9.57        13.87 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 
       17.29        13.68        19.33        39.12        26.10        25.61 
TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
       18.05        12.16         8.98        31.20        12.82         9.21 
TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
       15.42        28.73         9.07        12.76        18.71        14.43 
TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8363 
       11.44         9.60         8.05         2.66         7.40         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
       22.19        17.52         0.95        26.33        14.04        11.80 
TCGA-BR-8384 TCGA-BR-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-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5803 
        0.66        19.36        13.51         0.46         2.83         0.07 
TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-A487 
        0.39         0.07         0.07         0.16         0.10         9.34 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4475 TCGA-CG-5721 TCGA-D7-6518 TCGA-D7-6522 
       11.31         0.10        22.98         6.02        19.13        18.61 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-FP-7916 
       24.72        16.80        17.19        16.44         5.92        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GJ TCGA-HU-A4GY TCGA-IN-7808 
       22.29        59.54         5.03        21.37         0.26         3.45 

subtype1 subtype2 subtype3 
    0.00     0.10     0.07 
subtype1 subtype2 subtype3 
  122.10   105.07    83.24 
subtype1 subtype2 subtype3 
   12.95    12.43    13.02 
[1] "0.0 - 122.1 (12.9)" "0.1 - 105.1 (12.4)" "0.1 - 83.2 (13.0)" 
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       8       10       22       14        24        41        13
  subtype2       2        5        8        3        33        19        13
  subtype3       0        0        4        7        11        13         3
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         31         16         14       20         3
  subtype2         10          9          3        4         1
  subtype3         13         16         13        6         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           8        2        0
  STAGE IA         10        5        0
  STAGE IB         22        8        4
  STAGE II         14        3        7
  STAGE IIA        24       33       11
  STAGE IIB        41       19       13
  STAGE III        13       13        3
  STAGE IIIA       31       10       13
  STAGE IIIB       16        9       16
  STAGE IIIC       14        3       13
  STAGE IV         20        4        6
  STAGE IVA         3        1        0
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    31 56 88 46
  subtype2    13 37 57  6
  subtype3     0 13 48 28
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       31       13        0
  T2          56       37       13
  T3          88       57       48
  T4          46        6       28
[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 79 79 38 25
  subtype2 58 38 11  5
  subtype3 25 24  9 27
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       79       58       25
  N1       79       38       24
  N2       38       11        9
  N3       25        5       27
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus         0   1
  subtype1 190  17
  subtype2  97   5
  subtype3  83   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  190   17
  subtype2   97    5
  subtype3   83    5
   clus
vv  subtype1 subtype2 subtype3
  0      190       97       83
  1       17        5        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"
D3V7, binary
          cls
clus         0   1
  subtype1  76 159
  subtype2  15 106
  subtype3  36  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76  159
  subtype2   15  106
  subtype3   36   56
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       76       15       36
  MALE        159      106       56
[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                                    26
  subtype2                                     2
  subtype3                                    23
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     80
  subtype2                                                     10
  subtype3                                                     41
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                25
  subtype2                                                                 2
  subtype3                                                                 7
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               31
  subtype2                                                0
  subtype3                                                5
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        8
  subtype2                                                        0
  subtype3                                                        6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         5
  subtype2                                                         0
  subtype3                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        1
D3V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   26
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  80
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  41
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
[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   6 229
  subtype2   0 121
  subtype3   0  92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  229
  subtype2    0  121
  subtype3    0   92
     clus
vv    subtype1 subtype2 subtype3
  NO         6        0        0
  YES      229      121       92
[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"
D3V10, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 140   6   9  13
  subtype2  13   0   1   0
  subtype3  64   3   0   9
D3V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      140       13       64
  R1        6        0        3
  R2        9        1        0
  RX       13        0        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    49                         3   136
  subtype2    43                         3    63
  subtype3    22                         0    68
D3V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           49       43       22
  BLACK OR AFRICAN AMERICAN        3        3        0
  WHITE                          136       63       68
[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"
D3V14, binary
          cls
clus         0   1
  subtype1   2 156
  subtype2   2  73
  subtype3   1  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  156
  subtype2    2   73
  subtype3    1   83
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        1
  NOT HISPANIC OR LATINO      156       73       83
[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 = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 40 29
  subtype2 93 41
  subtype3 15 10
  subtype4 51 27
  subtype5 71 37
subtype1 subtype2 subtype3 subtype4 subtype5 
      69      134       25       78      108 
subtype1 subtype2 subtype3 subtype4 subtype5 
      29       41       10       27       37 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-JY-A6FE TCGA-JY-A6FH 
       25.78        20.05         5.92         4.21         3.68        42.77 
TCGA-L5-A4OF TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A891 TCGA-L5-A8NN TCGA-L5-A8NR 
        3.68         1.38        58.59         3.95         5.49         8.71 
TCGA-LN-A49L TCGA-LN-A49V TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6Y2 TCGA-R6-A8W5 
       10.45         0.10         8.02         5.06         9.30        15.78 
TCGA-R6-A8WG TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-ZR-A9CJ TCGA-BR-6456 TCGA-BR-6565 
       12.69        18.81        42.87        19.73        17.29         9.17 
TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
       12.16        21.11         9.21        15.42        28.01        28.73 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 
       11.44         0.69        13.08        14.79         5.39         9.21 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
       11.54         9.86         7.53         1.48        12.89         0.72 
TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-8526 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 
       13.64        13.15         0.07         0.13         0.13         3.42 
TCGA-CD-A4MH TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5724 
       12.20        54.08        29.98        18.97        22.98        12.03 
TCGA-CG-5725 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6822 
       15.02        18.84        13.35        17.19        10.55        12.33 
TCGA-D7-8572 TCGA-D7-A4YT TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 TCGA-HU-A4H5 
       16.80        14.27         7.99        72.23        17.06        12.30 
TCGA-HU-A4HD TCGA-IN-8663 TCGA-IP-7968 
       27.42         3.39         2.53 

$subtype2
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO 
       31.27        14.30        58.55         7.63         8.94        16.24 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A939 TCGA-JY-A93C 
       32.45         7.69       122.10        60.39        21.70        23.18 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A43M TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ 
        3.16        30.25         8.94        32.61        19.99        21.01 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A8NE 
       18.35         7.17         3.16         7.13         7.43        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM 
        2.66        35.97        12.92        13.48        16.47         7.76 
TCGA-L7-A6VZ TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RE 
       10.36         7.59        29.59         1.45         7.00         4.80 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-BR-4191 TCGA-BR-4267 
        9.27         4.44        22.82        46.19        18.35         6.18 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 
        6.61        34.68        32.78         8.98        30.90        32.94 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8078 
       24.76        23.93        12.43         3.45        17.49        12.26 
TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 
       20.55        12.95        19.50         4.31        19.17        15.85 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8680 
       25.18        20.22         1.12        12.79        13.45        15.81 
TCGA-BR-8687 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-8528 
        8.22        20.65        20.42         1.15         3.25         0.10 
TCGA-CD-8529 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.10         6.58        12.62         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99         8.05         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5720 
       47.05        21.99         9.01         7.07        36.00         0.99 
TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6527 
       28.96        69.04         7.99        12.66        18.54        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-8576 
       15.22        15.98        12.79        11.31        18.21        14.66 
TCGA-D7-8578 TCGA-D7-A4YY TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 
       21.14        13.78        16.24        14.47        21.27         3.48 
TCGA-FP-7829 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-HU-8238 TCGA-HU-8244 
       19.53        13.58         0.56        11.08         1.51        14.27 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       11.41        12.10         0.76         5.59        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.51         6.25        10.19        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB 
        8.88         8.81 

$subtype3
TCGA-2H-A9GM TCGA-IG-A4QS TCGA-JY-A938 TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T 
       13.94         3.88        25.41        24.00         4.70         8.71 
TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NV TCGA-L5-A8NW TCGA-M9-A5M8 
        2.60         0.36         3.02        52.57        46.09        33.11 
TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 
        7.82        14.70         7.04         6.35        53.95         2.89 
TCGA-S8-A6BV TCGA-V5-A7RB TCGA-X8-AAAR TCGA-CG-4477 TCGA-CG-5717 TCGA-IN-7806 
       20.02         5.29        10.16        30.97         6.97        21.21 
TCGA-IN-8462 
       18.81 

$subtype4
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12        18.64         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J 
       68.02        41.52        24.03         6.28         0.30         4.31 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ 
       47.93         6.94        25.12         7.40        13.55        21.37 
TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25         0.10        12.46        12.59        12.49 
TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 
       12.76        12.59        22.39         0.10        15.52        11.54 
TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV 
       12.33        13.22         4.47        12.33        25.25        10.52 
TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU 
       12.00        12.23        12.03        13.18         0.13         5.16 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
       20.38         3.42        15.35        19.96        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G 
       18.31         8.12        28.11        30.71        18.18        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       11.24         9.17        15.91         3.42         2.10         2.66 

$subtype5
TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A4OO TCGA-L5-A4OT 
        9.30        14.86        31.56        25.22         3.32         4.90 
TCGA-L5-A4OU TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-B7-5816 
       29.00        13.22        13.41        27.12        83.24        26.70 
TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 
       11.70         4.64        30.90         9.57        15.95        13.87 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
       13.68        19.33        39.12        26.10        25.61        18.05 
TCGA-BR-6707 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 
       19.89        31.20        12.82        18.15        15.32         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8289 
       12.76        18.71        14.43         9.60         8.05         2.66 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       16.31         7.40         0.26        22.19        17.52         0.95 
TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8589 
       26.33        14.04        11.80         0.26         3.72        15.81 
TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44T 
        9.34         6.28         0.49        16.44        15.68        12.56 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        6.08        13.41        13.51         8.98        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 
       12.82         0.66        19.36        13.51         0.46         2.83 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8531 
       13.18         0.07         0.39         0.07         0.16         0.10 
TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CG-4449 
        0.10         9.34        11.31        11.61         0.10        19.07 
TCGA-CG-4462 TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        0.00        12.00         1.02         6.02         0.99       105.07 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8570 
       12.36        19.13        20.55        18.61        17.85        24.72 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       19.50        17.19        20.91        16.44         5.92        15.16 
TCGA-D7-A4Z0 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-8608 
       14.76        14.07        22.29        59.54         5.03        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-IN-7808 
       24.30        12.30         0.26         2.10        12.95         3.45 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.10     0.36     0.10     0.00 
subtype1 subtype2 subtype3 subtype4 subtype5 
   72.23   122.10    53.95    68.02   105.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  12.200   12.935   10.160   12.540   13.200 
[1] "0.1 - 72.2 (12.2)"  "0.1 - 122.1 (12.9)" "0.4 - 54.0 (10.2)" 
[4] "0.1 - 68.0 (12.5)"  "0.0 - 105.1 (13.2)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        2        6        3         8        12         7
  subtype2       8        9       18        8        13        25         8
  subtype3       2        0        2        1         2         5         1
  subtype4       0        3        4        1        31        12        10
  subtype5       0        1        4       11        14        19         3
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         15          6          5        2         1
  subtype2         15          8         11       13         2
  subtype3          1          3          0        0         0
  subtype4          7          5          2        3         1
  subtype5         16         19         12       12         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        8        2        0        0
  STAGE IA          2        9        0        3        1
  STAGE IB          6       18        2        4        4
  STAGE II          3        8        1        1       11
  STAGE IIA         8       13        2       31       14
  STAGE IIB        12       25        5       12       19
  STAGE III         7        8        1       10        3
  STAGE IIIA       15       15        1        7       16
  STAGE IIIB        6        8        3        5       19
  STAGE IIIC        5       11        0        2       12
  STAGE IV          2       13        0        3       12
  STAGE IVA         1        2        0        1        0
[1] 12  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     2 19 37 12
  subtype2    28 40 44 29
  subtype3     6  5  9  0
  subtype4     7 24 44  4
  subtype5     1 18 59 35
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        2       28        6        7        1
  T2          19       40        5       24       18
  T3          37       44        9       44       59
  T4          12       29        0        4       35
[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 22 24 12 10
  subtype2 56 43 25 17
  subtype3  7 10  3  0
  subtype4 45 24  6  3
  subtype5 32 40 12 27
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       22       56        7       45       32
  N1       24       43       10       24       40
  N2       12       25        3        6       12
  N3       10       17        0        3       27
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus         0   1
  subtype1  63   2
  subtype2 120  12
  subtype3  14   0
  subtype4  69   4
  subtype5 104   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    2
  subtype2  120   12
  subtype3   14    0
  subtype4   69    4
  subtype5  104    9
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       63      120       14       69      104
  1        2       12        0        4        9
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 18 58
  subtype2 53 97
  subtype3  3 22
  subtype4 12 68
  subtype5 41 76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   58
  subtype2   53   97
  subtype3    3   22
  subtype4   12   68
  subtype5   41   76
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       18       53        3       12       41
  MALE         58       97       22       68       76
[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                                     3
  subtype2                                    15
  subtype3                                     1
  subtype4                                     0
  subtype5                                    32
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     32
  subtype2                                                     51
  subtype3                                                      2
  subtype4                                                      0
  subtype5                                                     46
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 8
  subtype2                                                                16
  subtype3                                                                 1
  subtype4                                                                 0
  subtype5                                                                 9
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                                8
  subtype2                                               21
  subtype3                                                0
  subtype4                                                0
  subtype5                                                7
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        0
  subtype2                                                        5
  subtype3                                                        0
  subtype4                                                        0
  subtype5                                                        9
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         2
  subtype2                                                         2
  subtype3                                                         0
  subtype4                                                         0
  subtype5                                                         1
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        0
  subtype3                                        0
  subtype4                                        0
  subtype5                                        1
D4V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  51
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                   2
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  46
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
[1] 7 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
          cls
clus         0   1
  subtype1   2  74
  subtype2   4 146
  subtype3   0  25
  subtype4   0  80
  subtype5   0 117
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   74
  subtype2    4  146
  subtype3    0   25
  subtype4    0   80
  subtype5    0  117
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         2        4        0        0        0
  YES       74      146       25       80      117
[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"
D4V10, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 44  2  1  4
  subtype2 87  4  7  8
  subtype3  4  0  0  0
  subtype4  0  0  0  0
  subtype5 82  3  2 10
D4V11, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype5
  R0       44       87        4       82
  R1        2        4        0        3
  R2        1        7        0        2
  RX        4        8        0       10
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    14                         1    49
  subtype2    31                         3    82
  subtype3     0                         0    20
  subtype4    38                         2    37
  subtype5    31                         0    79
D4V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           14       31        0       38       31
  BLACK OR AFRICAN AMERICAN        1        3        0        2        0
  WHITE                           49       82       20       37       79
[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"
D4V14, binary
          cls
clus         0   1
  subtype1   2  53
  subtype2   1  93
  subtype3   1  11
  subtype4   0  55
  subtype5   1 100
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   53
  subtype2    1   93
  subtype3    1   11
  subtype4    0   55
  subtype5    1  100
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        1        1        0        1
  NOT HISPANIC OR LATINO       53       93       11       55      100
[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(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  86  65
  subtype2 188 111
  subtype3  81  45
subtype1 subtype2 subtype3 
     151      299      126 
subtype1 subtype2 subtype3 
      65      111       45 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL 
       25.78         5.92         4.21         6.21        33.27        20.09 
TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D 
        0.85        20.78        20.12        18.64         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH 
       12.16        44.75        68.02         3.68        41.52        42.77 
TCGA-JY-A93F TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS 
       24.03         0.30         4.31        47.93         1.38        58.59 
TCGA-L5-A4OU TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NK 
       29.00         2.60        25.12         7.40         3.95        13.55 
TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
        5.49        21.37        46.09         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       12.43        13.41         0.10        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
        0.10        12.46        12.59        12.49        12.76        12.59 
TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       22.39         0.10        15.52        11.54        12.33        13.22 
TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX 
        4.47        12.33        25.25        10.52        12.00        12.23 
TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ 
       12.03        13.18         0.13         5.16         8.02         5.06 
TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
       14.70         7.04         6.35         9.30        15.78        12.69 
TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP 
       20.38         5.29         3.42        15.35        18.81        19.96 
TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       12.43         1.55        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        42.87        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-6709 TCGA-BR-7723 
        3.42         2.10         2.66        19.73        12.16        28.73 
TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CS 
       11.44         2.20         7.53        11.54         7.53         1.48 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8531 TCGA-CD-8535 
       12.89         0.72         0.30         0.07         0.10         0.13 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-5724 TCGA-CG-5725 
        3.42         9.34        19.07        21.99        12.03        15.02 
TCGA-D7-6822 TCGA-D7-A6F0 TCGA-HU-8245 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GH 
       12.33         2.96        12.59        12.30        25.81        11.77 
TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
        2.10        12.30        27.42         3.39         5.36        13.08 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
       12.59         5.56        60.56        45.67        18.21         8.52 
TCGA-RD-A8MW TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       37.91        13.25        13.02        35.24        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94T TCGA-VQ-AA69 
       17.85        23.41        52.24         9.04        11.24        28.41 
TCGA-VQ-AA6D 
       17.13 

$subtype2
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FB 
        8.94        16.24        32.45         3.88       122.10        60.39 
TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OE TCGA-L5-A4OG 
       25.41        23.18         3.16        30.25        24.00         4.70 
TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
       32.61        19.99        21.01        18.35         7.17         3.16 
TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NE 
        4.90         7.13         7.43         0.36         3.02        55.50 
TCGA-L5-A8NF TCGA-L5-A8NG TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        2.66        35.97        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DQ 
        7.76         8.71        52.57        10.36        33.11         7.59 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV 
       29.59        53.95         2.89         1.45         7.00        20.02 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR 
        4.80         9.27         4.44        22.82        46.19        10.16 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 
       26.70        11.70        19.56        11.01         9.44         6.61 
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 
        6.97        18.35        30.90         6.18         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6710 
       15.95        13.87        19.33        32.78        19.89         8.98 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       30.90        32.94        24.76        35.24        23.93        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 
       18.15        15.32        12.43        12.76        17.49         0.69 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
       12.26        20.55         8.05         0.56        12.95        16.31 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8368 
       15.58         6.18        19.50        13.08         0.26         4.31 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 
       19.17        14.79         0.26        15.85         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 
        9.21        20.22         1.12        15.81        13.45        15.81 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4PD 
        9.86         8.22        10.68        13.87        22.26        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 
       20.42         1.15        13.64        11.57         5.13         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8528 TCGA-CD-8532 TCGA-CD-8533 
       13.15        13.18         0.39         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ 
        0.10        12.43        11.61         6.58        12.20        12.62 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5718 
       12.03         0.00         9.01        18.97         7.07        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 
        0.99         6.02       105.07        28.96        79.07         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
       69.04        21.07         7.99        12.36        12.66        20.55 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85        13.35        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.79        11.31        24.72        19.50        17.19        18.21 
TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.66        14.27         5.92        15.16        13.78        14.76 
TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-6874 
       11.24         9.76        15.65         7.40        16.24        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 
       72.23        21.27        11.38         3.48        19.53        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       13.58         0.56        11.08         5.52         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        14.27        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       12.10        10.62         0.76        24.30         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT 
       24.20         3.25        22.75        29.98         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.25        10.19        12.95        19.36        23.84         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL 
        8.88         8.81         3.45        18.81        18.38         5.19 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IN-AB1X TCGA-IP-7968 
        1.41         6.44         6.74         1.81        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A93G TCGA-KB-A93H TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 
        5.56        20.15        37.64        61.25         6.08         4.60 
TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-SW-A7EA TCGA-SW-A7EB 
        9.24        16.67       122.30       115.69        19.04         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        0.92        48.79         5.46        18.48        21.73        34.45 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       27.88        32.48         7.73        28.96        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       16.31        22.19         2.50         1.87         9.27        15.65 
TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       13.35        26.24        27.35        64.57        14.33        65.16 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       36.69        11.70        11.93        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 
       22.68         1.71        36.16         7.36         9.50         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
       55.43         4.54         6.58        64.18        21.04        42.54 
TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F 
       22.09        18.41        40.08        32.94        29.98        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       26.04        16.14        21.11        12.43         0.79 

$subtype3
TCGA-IC-A6RE TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A939 TCGA-JY-A93D 
        7.69         2.63         9.30        14.86        21.70        31.56 
TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43M TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A88S 
       25.22         6.28         8.94         3.68         3.32         6.94 
TCGA-L5-A88T TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU TCGA-Q9-A6FW TCGA-B7-A5TK 
        8.71        13.41        27.12        83.24         7.82         9.47 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 
        4.64         7.43         9.57        17.29        13.68        39.12 
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-7901 TCGA-BR-7957 TCGA-BR-7959 
       12.82         9.21        15.42         3.45         9.07        18.71 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 
       14.43         9.60         2.66         7.40        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8384 
        0.95        26.33        14.04         3.32        11.80         3.72 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8686 
       12.79         9.34         6.28         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-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        12.82         0.66        19.36        13.51         0.46 
TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 
        2.83         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        0.16        11.31         0.10        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 
        6.97         1.02         0.99        65.10        11.93        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8578 
       18.84        18.54        18.61        10.55        16.80        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 
       20.91        16.44        13.71        11.31        11.44         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-7998 
        4.34         7.13         0.62         7.99        14.07        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-IN-7806 
       59.54         5.03        21.37         0.10         0.26        21.21 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        6.51         7.82         3.72        19.73         9.86        11.05 
TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
        5.13        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P TCGA-ZA-A8F6 
       35.61        16.87         9.73         5.72         2.66        10.62 

subtype1 subtype2 subtype3 
    0.07     0.00     0.07 
subtype1 subtype2 subtype3 
   68.02   122.30   116.38 
subtype1 subtype2 subtype3 
   12.43    13.87    11.18 
[1] "0.1 - 68.0 (12.4)"  "0.0 - 122.3 (13.9)" "0.1 - 116.4 (11.2)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        5       12        3        36        19        16
  subtype2      11       12       27       21        28        45        13
  subtype3       0        2        9        9        13        20         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         19         14          6       11         2
  subtype2         51         39         29       26         2
  subtype3         27         19         13       13         0
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0       11        0
  STAGE IA          5       12        2
  STAGE IB         12       27        9
  STAGE II          3       21        9
  STAGE IIA        36       28       13
  STAGE IIB        19       45       20
  STAGE III        16       13        1
  STAGE IIIA       19       51       27
  STAGE IIIB       14       39       19
  STAGE IIIC        6       29       13
  STAGE IV         11       26       13
  STAGE IVA         2        2        0
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1  T2  T3  T4
  subtype1    13  38  78  17
  subtype2    35  66 139  71
  subtype3     5  22  64  36
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       13       35        5
  T2          38       66       22
  T3          78      139       64
  T4          17       71       36
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1  62  52  16  14
  subtype2 102  92  60  52
  subtype3  37  39  20  30
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       62      102       37
  N1       52       92       39
  N2       16       60       20
  N3       14       52       30
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus         0   1
  subtype1 125  11
  subtype2 278  18
  subtype3 111  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  125   11
  subtype2  278   18
  subtype3  111   10
   clus
vv  subtype1 subtype2 subtype3
  0      125      278      111
  1       11       18       10
[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"
D5V7, binary
          cls
clus         0   1
  subtype1  27 127
  subtype2 107 219
  subtype3  48  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27  127
  subtype2  107  219
  subtype3   48   82
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27      107       48
  MALE        127      219       82
[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                                     5
  subtype2                                    31
  subtype3                                    35
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     18
  subtype2                                                    103
  subtype3                                                     42
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 9
  subtype2                                                                58
  subtype3                                                                13
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               15
  subtype2                                               55
  subtype3                                                8
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        1
  subtype2                                                       11
  subtype3                                                       10
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         3
  subtype2                                                         4
  subtype3                                                         1
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        1
  subtype2                                       10
  subtype3                                        2
D5V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 1
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   31
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                10
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   35
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  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"
D5V9, binary
          cls
clus         0   1
  subtype1   0 154
  subtype2   5 321
  subtype3   1 129
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0  154
  subtype2    5  321
  subtype3    1  129
     clus
vv    subtype1 subtype2 subtype3
  NO         0        5        1
  YES      154      321      129
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  39   3   4   1
  subtype2 217  11  10  19
  subtype3  92   4   4   5
D5V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       39      217       92
  R1        3       11        4
  R2        4       10        4
  RX        1       19        5
[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"
D5V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    56                         4    77
  subtype2    46                        10   213
  subtype3    27                         0    95
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           56       46       27
  BLACK OR AFRICAN AMERICAN        4       10        0
  WHITE                           77      213       95
[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"
D5V14, binary
          cls
clus         0   1
  subtype1   4  95
  subtype2   2 191
  subtype3   1 108
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   95
  subtype2    2  191
  subtype3    1  108
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        1
  NOT HISPANIC OR LATINO       95      191      108
[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(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  68  50
  subtype2  59  39
  subtype3 137  77
  subtype4  55  28
  subtype5  36  27
subtype1 subtype2 subtype3 subtype4 subtype5 
     118       98      214       83       63 
subtype1 subtype2 subtype3 subtype4 subtype5 
      50       39       77       28       27 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GJ TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ 
       25.78        20.05        58.55         5.92        16.24         4.21 
TCGA-IG-A4QS TCGA-JY-A6FH TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OQ TCGA-L5-A4OS 
        3.88        42.77         3.68        32.61         1.38        58.59 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L7-A6VZ TCGA-R6-A6KZ 
        3.95        55.50         2.66         5.49        10.36         5.06 
TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-ZR-A9CJ TCGA-B7-A5TN TCGA-BR-6456 
        9.30        15.78        12.69        19.73         9.44        17.29 
TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 
        9.17         9.21        28.01        28.73         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8373 TCGA-BR-8483 
        0.69         2.66         2.20         7.40        14.79         5.39 
TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 
        9.21         9.34        11.54         8.22        10.68         7.53 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 
        0.72        20.65        13.15         0.30         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 
        0.07         0.07         0.13         0.16         0.13         3.42 
TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4449 
        9.34        12.20        20.02         1.02        54.08        19.07 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 
       21.99        18.97        36.00        15.02        79.07         4.01 
TCGA-CG-5732 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 
       69.04        18.84        17.19        10.26        15.98        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A6F0 
       11.31        12.33        16.80        21.14         5.92         2.96 
TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8245 TCGA-HU-8249 
        7.99        17.06         0.56         0.23        12.59        14.17 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4HD 
       22.75        25.81        11.77        12.95        12.30        27.42 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93G TCGA-MX-A5UJ 
       18.38         5.19         5.56        60.56        20.15        19.73 
TCGA-MX-A663 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
        9.86        45.67         8.52        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 

$subtype2
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GN TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-L5-A43E 
       31.27        14.30         8.94       122.10        60.39        30.25 
TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A8NI TCGA-L5-A8NJ 
       19.99        18.35         3.16         7.43        13.48        16.47 
TCGA-L5-A8NM TCGA-R6-A6XG TCGA-R6-A8WC TCGA-RE-A7BO TCGA-S8-A6BV TCGA-V5-A7RE 
        7.76        29.59         1.45         7.00        20.02         4.80 
TCGA-V5-AASW TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI 
        9.27        22.82        46.19        26.70        11.70        19.56 
TCGA-B7-A5TJ TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 
       11.01         6.97        30.90         6.61        34.68        32.78 
TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 
       32.94        23.93        12.95         6.18        19.50         4.31 
TCGA-BR-8487 TCGA-BR-A44U TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5799 
        1.12        13.87        20.42         1.15        11.57         3.25 
TCGA-CD-5813 TCGA-CD-8528 TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ 
        0.39         0.10         0.10        11.61         6.58        12.62 
TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 
       15.95         7.99         8.05         4.01        14.01        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5733 TCGA-D7-6528 TCGA-D7-A4YY 
        0.00         9.01         7.07        21.07        15.22        13.78 
TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-A4BE TCGA-FP-A4BF 
       11.24        15.65        14.47        72.23        11.08         5.52 
TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G9 
       18.08         5.92        14.27        11.41         0.76        24.20 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-IN-7808 
       29.98         6.51         6.25        10.19        23.84         3.45 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IP-7968 TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-SW-A7EA 
        1.41         6.44         2.53         6.08        16.67        19.04 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PB 
       21.73        34.45        27.88        32.48         7.73        34.29 
TCGA-VQ-A8PO TCGA-VQ-A91D TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A92D 
        9.27        11.70        20.81         1.71         9.50        64.18 
TCGA-VQ-AA6B TCGA-VQ-AA6I 
       29.98        16.14 

$subtype3
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QT TCGA-JY-A938 
        7.63        13.94        32.45         7.69         9.30        25.41 
TCGA-JY-A939 TCGA-JY-A93C TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG 
       21.70        23.18         3.16         8.94        24.00         4.70 
TCGA-L5-A4OJ TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OW 
       21.01         3.32         7.17         4.90        29.00         7.13 
TCGA-L5-A88T TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NH 
        8.71         2.60         0.36         3.02        35.97        12.92 
TCGA-L5-A8NL TCGA-L5-A8NR TCGA-L5-A8NT TCGA-L5-A8NU TCGA-L5-A8NV TCGA-L5-A8NW 
       13.22         8.71        27.12        83.24        52.57        46.09 
TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 
       33.11         7.82         8.02         7.59        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-V5-A7RB TCGA-V5-AASX TCGA-VR-A8ET 
        6.35        53.95         2.89         5.29         4.44         1.55 
TCGA-X8-AAAR TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6453 TCGA-BR-6455 
       10.16         6.61        18.35         6.18        15.95        13.87 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       19.33        39.12        19.89        12.16         8.98        21.11 
TCGA-BR-6802 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7851 
       30.90        24.76        35.24        15.42        15.32        12.43 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       12.76        17.49        14.43        12.26        20.55         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
        0.56        16.31        15.58        13.08         0.26         0.95 
TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8486 
        3.32        19.17         0.26        15.85        25.18        20.22 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-A4CQ TCGA-BR-A4CS 
       15.81        13.45         7.53        15.81        22.26         1.48 
TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
        8.98         0.53         0.66        13.64         5.13         2.83 
TCGA-CD-5801 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A48A TCGA-CG-4301 
       13.18         0.10         0.10         0.13        12.43         3.02 
TCGA-CG-4304 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       27.02        29.98        47.05        22.98        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
       28.96        65.10         7.99        12.36        12.66        20.55 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8570 
       18.54        18.61        17.85        13.35        12.79        24.72 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YX 
       19.50        17.19        18.21        14.66        14.27        15.16 
TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       14.76        11.31        11.44         9.76         4.34         7.40 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8211 
        0.62        16.24        21.27        11.38        19.53        13.58 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       26.47         1.51        12.10        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GY 
       12.30        11.84         3.25        21.37         8.98         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        2.10        19.36         9.67         8.88         8.81        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81         3.39         5.36        13.08         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A93H TCGA-MX-A5UG 
        6.51         1.81         7.82        13.51        37.64         3.72 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A8MV 
       18.21        61.25         4.60         9.24        11.05       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       40.64       115.69        57.44        16.87         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-A91S TCGA-VQ-A91V 
       65.16        36.69        11.93        61.22        22.68        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-A94T TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 
       42.54        11.24        22.09        18.41        40.08        28.41 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       54.12        26.04        21.11        12.43 

$subtype4
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12        18.64         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H 
       68.02         3.68        41.52        24.03         6.28         0.30 
TCGA-L5-A43J TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK 
        4.31        47.93         6.94        25.12         7.40        13.55 
TCGA-L5-A8NQ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       21.37         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
        0.10        13.15        15.35        13.25         0.10        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.59        12.49        12.76        12.59        22.39         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO 
        0.13         5.16        20.38         3.42        15.35        18.81 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       19.96        12.43        18.31         8.12        28.11        30.71 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        42.87        15.06        11.24         9.17        15.91 
TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-BR-A4IY TCGA-IN-A7NT 
        3.42         2.10         2.66        12.89         5.56 

$subtype5
TCGA-IG-A7DP TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A8NS TCGA-B7-A5TK TCGA-BR-4187 
       14.86        31.56        25.22        13.41         9.47         4.64 
TCGA-BR-4188 TCGA-BR-4279 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
        7.43         9.57        13.68        26.10        25.61        18.05 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 
       31.20        12.82        18.15         9.07        18.71         9.60 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8384 
       22.19        17.52        26.33        14.04        11.80         3.72 
TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
       12.79         6.28         0.49        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-CD-5803 TCGA-CD-A489 TCGA-CD-A4MI 
       19.36        13.51         0.46         0.07        11.31         0.10 
TCGA-CG-4472 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET 
       12.00        11.93        19.13        20.91        16.44        13.71 
TCGA-D7-A747 TCGA-D7-A74B TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
        8.38         7.13         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-HU-A4GQ TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 
        5.03         0.10         5.13       116.38        71.38        35.61 
TCGA-VQ-A91Y TCGA-VQ-A94P TCGA-ZA-A8F6 
        9.73         2.66        10.62 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.00     0.10     0.10     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
   79.07   122.10   122.30    68.02   116.38 
subtype1 subtype2 subtype3 subtype4 subtype5 
  11.985   12.325   13.285   12.590   13.410 
[1] "0.1 - 79.1 (12.0)"  "0.0 - 122.1 (12.3)" "0.1 - 122.3 (13.3)"
[4] "0.1 - 68.0 (12.6)"  "0.1 - 116.4 (13.4)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       3        1       10       10         6        19         5
  subtype2       5        6       15        8        11        13         8
  subtype3       3        9       14       10        23        32         6
  subtype4       0        3        4        1        31        13        11
  subtype5       0        0        5        4         6         7         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         24         11         12       13         3
  subtype2         10          7          8        6         0
  subtype3         40         34         17       22         0
  subtype4          9          6          2        3         1
  subtype5         14         14          9        6         0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           3        5        3        0        0
  STAGE IA          1        6        9        3        0
  STAGE IB         10       15       14        4        5
  STAGE II         10        8       10        1        4
  STAGE IIA         6       11       23       31        6
  STAGE IIB        19       13       32       13        7
  STAGE III         5        8        6       11        0
  STAGE IIIA       24       10       40        9       14
  STAGE IIIB       11        7       34        6       14
  STAGE IIIC       12        8       17        2        9
  STAGE IV         13        6       22        3        6
  STAGE IVA         3        0        0        1        0
[1] 12  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1  T2  T3  T4
  subtype1     7  28  57  28
  subtype2    17  28  40  15
  subtype3    22  36 106  51
  subtype4     7  24  48   5
  subtype5     0  10  30  25
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        7       17       22        7        0
  T2          28       28       36       24       10
  T3          57       40      106       48       30
  T4          28       15       51        5       25
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 30 41 25 21
  subtype2 42 28 12 15
  subtype3 65 68 45 38
  subtype4 47 27  6  3
  subtype5 17 19  8 19
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       30       42       65       47       17
  N1       41       28       68       27       19
  N2       25       12       45        6        8
  N3       21       15       38        3       19
[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"
D6V6, binary
          cls
clus         0   1
  subtype1 100  12
  subtype2  91   5
  subtype3 191  15
  subtype4  74   4
  subtype5  58   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  100   12
  subtype2   91    5
  subtype3  191   15
  subtype4   74    4
  subtype5   58    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      100       91      191       74       58
  1       12        5       15        4        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  36  89
  subtype2  36  70
  subtype3  73 154
  subtype4  13  72
  subtype5  24  43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   89
  subtype2   36   70
  subtype3   73  154
  subtype4   13   72
  subtype5   24   43
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       36       36       73       13       24
  MALE         89       70      154       72       43
[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                                     5
  subtype2                                    12
  subtype3                                    33
  subtype4                                     0
  subtype5                                    21
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     34
  subtype2                                                     33
  subtype3                                                     70
  subtype4                                                      2
  subtype5                                                     24
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                26
  subtype2                                                                19
  subtype3                                                                32
  subtype4                                                                 0
  subtype5                                                                 3
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               27
  subtype2                                               14
  subtype3                                               31
  subtype4                                                0
  subtype5                                                6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        4
  subtype2                                                        4
  subtype3                                                        8
  subtype4                                                        0
  subtype5                                                        6
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         4
  subtype2                                                         1
  subtype3                                                         3
  subtype4                                                         0
  subtype5                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        3
  subtype2                                        2
  subtype3                                        6
  subtype4                                        0
  subtype5                                        2
D6V8, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
     103       85      183        2       62 
  [1] "subtype2" "subtype2" "subtype2" "subtype2" "subtype5" "subtype1"
  [7] "subtype3" "subtype2" "subtype5" "subtype5" "subtype3" "subtype2"
 [13] "subtype3" "subtype5" "subtype3" "subtype2" "subtype3" "subtype5"
 [19] "subtype2" "subtype2" "subtype1" "subtype1" "subtype3" "subtype2"
 [25] "subtype3" "subtype1" "subtype2" "subtype3" "subtype1" "subtype3"
 [31] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
 [37] "subtype5" "subtype3" "subtype3" "subtype5" "subtype1" "subtype2"
 [43] "subtype5" "subtype5" "subtype3" "subtype3" "subtype3" "subtype3"
 [49] "subtype3" "subtype5" "subtype2" "subtype5" "subtype1" "subtype3"
 [55] "subtype3" "subtype2" "subtype3" "subtype1" "subtype5" "subtype3"
 [61] "subtype1" "subtype3" "subtype1" "subtype5" "subtype3" "subtype5"
 [67] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype5"
 [73] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype3"
 [79] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
 [85] "subtype3" "subtype5" "subtype5" "subtype3" "subtype5" "subtype2"
 [91] "subtype5" "subtype3" "subtype5" "subtype3" "subtype1" "subtype5"
 [97] "subtype3" "subtype3" "subtype5" "subtype1" "subtype3" "subtype1"
[103] "subtype3" "subtype2" "subtype5" "subtype3" "subtype1" "subtype3"
[109] "subtype5" "subtype3" "subtype5" "subtype1" "subtype3" "subtype3"
[115] "subtype5" "subtype5" "subtype5" "subtype1" "subtype1" "subtype5"
[121] "subtype2" "subtype1" "subtype5" "subtype3" "subtype1" "subtype3"
[127] "subtype5" "subtype5" "subtype3" "subtype1" "subtype5" "subtype3"
[133] "subtype5" "subtype3" "subtype5" "subtype5" "subtype5" "subtype1"
[139] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[145] "subtype2" "subtype1" "subtype3" "subtype1" "subtype5" "subtype5"
[151] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[157] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype5"
[163] "subtype1" "subtype2" "subtype1" "subtype1" "subtype5" "subtype3"
[169] "subtype2" "subtype2" "subtype1" "subtype5" "subtype2" "subtype1"
[175] "subtype3" "subtype3" "subtype2" "subtype1" "subtype2" "subtype2"
[181] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[187] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[193] "subtype2" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[199] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[205] "subtype3" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
[211] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype5"
[217] "subtype5" "subtype3" "subtype1" "subtype3" "subtype3" "subtype3"
[223] "subtype3" "subtype1" "subtype1" "subtype2" "subtype1" "subtype3"
[229] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype3"
[235] "subtype3" "subtype3" "subtype3" "subtype1" "subtype5" "subtype3"
[241] "subtype5" "subtype1" "subtype3" "subtype2" "subtype3" "subtype5"
[247] "subtype2" "subtype3" "subtype3" "subtype3" "subtype1" "subtype2"
[253] "subtype5" "subtype3" "subtype3" "subtype5" "subtype3" "subtype1"
[259] "subtype3" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[265] "subtype5" "subtype3" "subtype5" "subtype5" "subtype1" "subtype5"
[271] "subtype5" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[277] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[283] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
[289] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[295] "subtype3" "subtype3" "subtype2" "subtype3" "subtype1" "subtype1"
[301] "subtype1" "subtype3" "subtype2" "subtype3" "subtype5" "subtype2"
[307] "subtype2" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[313] "subtype2" "subtype1" "subtype3" "subtype3" "subtype3" "subtype1"
[319] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[325] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[331] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[337] "subtype1" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[343] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype3"
[349] "subtype3" "subtype3" "subtype5" "subtype2" "subtype3" "subtype1"
[355] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype1"
[361] "subtype5" "subtype3" "subtype2" "subtype1" "subtype3" "subtype3"
[367] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[373] "subtype2" "subtype2" "subtype2" "subtype2" "subtype3" "subtype2"
[379] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype1"
[385] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[391] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[397] "subtype2" "subtype3" "subtype3" "subtype1" "subtype2" "subtype3"
[403] "subtype2" "subtype3" "subtype3" "subtype2" "subtype5" "subtype1"
[409] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[415] "subtype2" "subtype1" "subtype5" "subtype3" "subtype3" "subtype3"
[421] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[427] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype5"
[433] "subtype1"
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 3
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   33
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  70
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        31
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 6
                                                                   clus
vv                                                                  subtype5
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  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"
D6V9, binary
          cls
clus         0   1
  subtype1   2 123
  subtype2   0 106
  subtype3   4 223
  subtype4   0  85
  subtype5   0  67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  123
  subtype2    0  106
  subtype3    4  223
  subtype4    0   85
  subtype5    0   67
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         2        0        4        0        0
  YES      123      106      223       85       67
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       8        6       26       50        1 
 [1] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [7] "subtype4" "subtype3" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype4"
[19] "subtype3" "subtype2" "subtype4" "subtype4" "subtype3" "subtype3"
[25] "subtype1" "subtype2" "subtype4" "subtype2" "subtype3" "subtype3"
[31] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype4"
[37] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[43] "subtype3" "subtype4" "subtype1" "subtype4" "subtype3" "subtype3"
[49] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[55] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[61] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
[67] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[73] "subtype3" "subtype2" "subtype2" "subtype3" "subtype4" "subtype4"
[79] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[85] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype4"
          vv
clus        R0  R1  R2  RX
  subtype1  84   3   5   4
  subtype2  62   3   3   8
  subtype3 152   9   8   9
  subtype4   2   0   0   0
  subtype5  48   3   2   4
D6V11, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      96       76      178        2       57 
  [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype5" "subtype5"
  [7] "subtype3" "subtype2" "subtype3" "subtype5" "subtype3" "subtype2"
 [13] "subtype3" "subtype5" "subtype2" "subtype2" "subtype1" "subtype1"
 [19] "subtype3" "subtype2" "subtype3" "subtype1" "subtype2" "subtype3"
 [25] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
 [31] "subtype3" "subtype1" "subtype5" "subtype3" "subtype3" "subtype5"
 [37] "subtype1" "subtype2" "subtype5" "subtype5" "subtype3" "subtype3"
 [43] "subtype3" "subtype3" "subtype3" "subtype5" "subtype2" "subtype5"
 [49] "subtype1" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
 [55] "subtype5" "subtype3" "subtype1" "subtype3" "subtype1" "subtype5"
 [61] "subtype3" "subtype5" "subtype3" "subtype3" "subtype1" "subtype1"
 [67] "subtype3" "subtype5" "subtype3" "subtype3" "subtype3" "subtype2"
 [73] "subtype1" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
 [79] "subtype2" "subtype3" "subtype3" "subtype5" "subtype5" "subtype3"
 [85] "subtype5" "subtype2" "subtype5" "subtype3" "subtype5" "subtype3"
 [91] "subtype1" "subtype5" "subtype3" "subtype3" "subtype5" "subtype1"
 [97] "subtype3" "subtype1" "subtype3" "subtype2" "subtype5" "subtype3"
[103] "subtype1" "subtype3" "subtype5" "subtype3" "subtype5" "subtype1"
[109] "subtype3" "subtype3" "subtype5" "subtype5" "subtype5" "subtype1"
[115] "subtype1" "subtype5" "subtype2" "subtype1" "subtype5" "subtype3"
[121] "subtype1" "subtype3" "subtype5" "subtype5" "subtype3" "subtype1"
[127] "subtype5" "subtype3" "subtype5" "subtype3" "subtype5" "subtype5"
[133] "subtype5" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[139] "subtype3" "subtype1" "subtype3" "subtype5" "subtype1" "subtype1"
[145] "subtype1" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[151] "subtype3" "subtype3" "subtype5" "subtype1" "subtype2" "subtype1"
[157] "subtype1" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[163] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype3"
[169] "subtype3" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[175] "subtype1" "subtype2" "subtype5" "subtype3" "subtype3" "subtype1"
[181] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype3"
[187] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[193] "subtype1" "subtype3" "subtype1" "subtype1" "subtype2" "subtype3"
[199] "subtype3" "subtype3" "subtype5" "subtype5" "subtype3" "subtype1"
[205] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[211] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[217] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[223] "subtype1" "subtype5" "subtype3" "subtype5" "subtype1" "subtype3"
[229] "subtype2" "subtype3" "subtype5" "subtype2" "subtype3" "subtype3"
[235] "subtype3" "subtype1" "subtype2" "subtype5" "subtype3" "subtype3"
[241] "subtype5" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[247] "subtype3" "subtype3" "subtype5" "subtype3" "subtype5" "subtype1"
[253] "subtype5" "subtype3" "subtype1" "subtype2" "subtype2" "subtype1"
[259] "subtype3" "subtype3" "subtype3" "subtype2" "subtype1" "subtype2"
[265] "subtype3" "subtype3" "subtype2" "subtype2" "subtype1" "subtype1"
[271] "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[277] "subtype3" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[283] "subtype3" "subtype2" "subtype3" "subtype5" "subtype2" "subtype2"
[289] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
[295] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype3"
[301] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[307] "subtype2" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[313] "subtype3" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
[319] "subtype3" "subtype3" "subtype1" "subtype1" "subtype3" "subtype3"
[325] "subtype5" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[331] "subtype5" "subtype5" "subtype3" "subtype1" "subtype5" "subtype3"
[337] "subtype2" "subtype1" "subtype3" "subtype3" "subtype1" "subtype1"
[343] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[349] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype3"
[355] "subtype1" "subtype3" "subtype1" "subtype1" "subtype1" "subtype3"
[361] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[367] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[373] "subtype3" "subtype1" "subtype2" "subtype3" "subtype2" "subtype3"
[379] "subtype3" "subtype2" "subtype5" "subtype1" "subtype1" "subtype3"
[385] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[391] "subtype5" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[397] "subtype3" "subtype1" "subtype2" "subtype1" "subtype3" "subtype3"
[403] "subtype2" "subtype3" "subtype3" "subtype5" "subtype1"
    clus
vv   subtype1 subtype2 subtype3 subtype5
  R0       84       62      152       48
  R1        3        3        9        3
  R2        5        3        8        2
  RX        4        8        9        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      86       71      173        2       55 
  [1] "subtype2" "subtype2" "subtype3" "subtype2" "subtype5" "subtype3"
  [7] "subtype3" "subtype5" "subtype3" "subtype3" "subtype5" "subtype2"
 [13] "subtype3" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [19] "subtype3" "subtype3" "subtype1" "subtype5" "subtype3" "subtype3"
 [25] "subtype5" "subtype1" "subtype2" "subtype5" "subtype5" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype3" "subtype5" "subtype2"
 [37] "subtype5" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
 [43] "subtype1" "subtype5" "subtype3" "subtype1" "subtype3" "subtype1"
 [49] "subtype5" "subtype3" "subtype5" "subtype3" "subtype3" "subtype1"
 [55] "subtype1" "subtype3" "subtype5" "subtype3" "subtype3" "subtype3"
 [61] "subtype2" "subtype1" "subtype3" "subtype1" "subtype3" "subtype1"
 [67] "subtype2" "subtype2" "subtype3" "subtype3" "subtype5" "subtype5"
 [73] "subtype3" "subtype5" "subtype2" "subtype5" "subtype3" "subtype5"
 [79] "subtype3" "subtype1" "subtype5" "subtype3" "subtype3" "subtype5"
 [85] "subtype1" "subtype3" "subtype1" "subtype3" "subtype2" "subtype5"
 [91] "subtype3" "subtype1" "subtype3" "subtype5" "subtype3" "subtype5"
 [97] "subtype1" "subtype3" "subtype3" "subtype5" "subtype5" "subtype5"
[103] "subtype1" "subtype1" "subtype5" "subtype2" "subtype1" "subtype5"
[109] "subtype3" "subtype1" "subtype3" "subtype5" "subtype5" "subtype3"
[115] "subtype1" "subtype5" "subtype3" "subtype5" "subtype3" "subtype5"
[121] "subtype5" "subtype1" "subtype2" "subtype2" "subtype3" "subtype2"
[127] "subtype3" "subtype5" "subtype1" "subtype1" "subtype3" "subtype1"
[133] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[139] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[145] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[151] "subtype2" "subtype5" "subtype3" "subtype3" "subtype1" "subtype3"
[157] "subtype3" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[163] "subtype3" "subtype3" "subtype1" "subtype3" "subtype1" "subtype3"
[169] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[175] "subtype5" "subtype5" "subtype3" "subtype1" "subtype3" "subtype3"
[181] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype1"
[187] "subtype3" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[193] "subtype3" "subtype3" "subtype3" "subtype3" "subtype1" "subtype5"
[199] "subtype3" "subtype5" "subtype1" "subtype3" "subtype2" "subtype3"
[205] "subtype5" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
[211] "subtype2" "subtype5" "subtype3" "subtype3" "subtype5" "subtype3"
[217] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[223] "subtype3" "subtype5" "subtype3" "subtype5" "subtype5" "subtype1"
[229] "subtype5" "subtype5" "subtype3" "subtype1" "subtype2" "subtype2"
[235] "subtype1" "subtype3" "subtype3" "subtype3" "subtype2" "subtype1"
[241] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype1"
[247] "subtype1" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[253] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype1"
[259] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype5"
[265] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype1"
[271] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[277] "subtype1" "subtype3" "subtype2" "subtype3" "subtype3" "subtype1"
[283] "subtype3" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[289] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[295] "subtype1" "subtype1" "subtype1" "subtype3" "subtype3" "subtype1"
[301] "subtype1" "subtype3" "subtype3" "subtype5" "subtype2" "subtype3"
[307] "subtype1" "subtype3" "subtype3" "subtype5" "subtype5" "subtype3"
[313] "subtype1" "subtype5" "subtype3" "subtype2" "subtype1" "subtype3"
[319] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[325] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype3"
[331] "subtype2" "subtype3" "subtype3" "subtype1" "subtype3" "subtype1"
[337] "subtype1" "subtype1" "subtype3" "subtype2" "subtype3" "subtype3"
[343] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[349] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype2"
[355] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype5"
[361] "subtype1" "subtype1" "subtype3" "subtype3" "subtype3" "subtype3"
[367] "subtype3" "subtype2" "subtype1" "subtype3" "subtype3" "subtype3"
[373] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype1"
[379] "subtype3" "subtype3" "subtype2" "subtype3" "subtype3" "subtype5"
[385] "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    23                         4    73
  subtype2    19                         4    66
  subtype3    29                         3   159
  subtype4    40                         2    40
  subtype5    18                         1    47
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           23       19       29       40       18
  BLACK OR AFRICAN AMERICAN        4        4        3        2        1
  WHITE                           73       66      159       40       47
[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"
D6V14, binary
          cls
clus         0   1
  subtype1   3  76
  subtype2   0  64
  subtype3   3 136
  subtype4   0  58
  subtype5   1  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   76
  subtype2    0   64
  subtype3    3  136
  subtype4    0   58
  subtype5    1   60
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        0        3        0        1
  NOT HISPANIC OR LATINO       76       64      136       58       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"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  68  63
  subtype2 134  67
  subtype3 102  63
subtype1 subtype2 subtype3 
     131      201      165 
subtype1 subtype2 subtype3 
      63       67       63 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IC-A6RF 
       25.78         5.92         8.94        16.24         4.21         6.21 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D 
       33.27        20.09        20.12        18.64         0.53        17.03 
TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H 
        0.79        23.41        12.82         9.96         4.67        14.50 
TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-L5-A43C 
       44.75        68.02         3.68        41.52        42.77         3.16 
TCGA-L5-A43J TCGA-L5-A4OH TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OW 
        4.31        32.61        47.93         1.38        58.59         7.13 
TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NK TCGA-L5-A8NN 
        2.60        25.12         7.40         3.95        13.55         5.49 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
        5.92        10.45        12.66        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A6 
       15.35        12.46        12.59        12.49        12.59         0.10 
TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 
       15.52        11.54        12.33        13.22         4.47        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ 
       25.25        10.52        12.00        12.23        12.03        13.18 
TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
        0.13         5.16         8.02         5.06        14.70         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG TCGA-RE-A7BO 
        6.35         9.30        15.78         2.89        12.69         7.00 
TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU 
       20.38         3.42        18.81        19.96        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        30.71        18.18        42.87        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       11.24         9.17         3.42         2.10         2.66        19.73 
TCGA-BR-7723 TCGA-BR-8295 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A452 TCGA-BR-A4CS 
       28.73         2.20        11.54        15.81         7.53         1.48 
TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C 
       12.89         0.72         0.13         3.42         9.34        11.61 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5727 TCGA-D7-6519 TCGA-D7-A4YT TCGA-D7-A6F0 
       12.03        15.02        79.07        20.55        14.27         2.96 
TCGA-IN-8663 TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-R5-A7ZE TCGA-R5-A7ZF 
        3.39         5.56         5.56        60.56        18.21         8.52 
TCGA-RD-A8MW TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E7 TCGA-VQ-A8P5 
       37.91         5.46        13.25        35.24        34.45         7.73 
TCGA-VQ-A8PB TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A91A TCGA-VQ-A91D 
       34.29         2.70        17.85        23.41        36.69        11.70 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA69 
       52.24         9.04        21.04        11.24        28.41 

$subtype2
TCGA-2H-A9GG TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM 
       20.05        31.27        14.30        58.55         7.63        13.94 
TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A938 TCGA-JY-A93C TCGA-L5-A43E 
        3.88       122.10        60.39        25.41        23.18        30.25 
TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OP 
        8.94        24.00         4.70        19.99        18.35         7.17 
TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A4OX TCGA-L5-A88Y TCGA-L5-A893 
        3.16         4.90        29.00         7.43         0.36         3.02 
TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NR 
       55.50         2.66        12.92        16.47         7.76         8.71 
TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DQ 
       52.57        46.09        10.36        33.11         7.82         7.59 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       29.59        53.95         5.29         4.80         9.27         4.44 
TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ 
       22.82        46.19        10.16        11.70        19.56        11.01 
TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 
       34.68        13.87        32.78        19.89         8.98        30.90 
TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-8060 
       32.94        24.76        35.24        12.43        12.76        11.44 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8360 
        0.69        12.26         8.05        12.95        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 
       19.50         0.26         4.31         3.32        19.17         0.26 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8687 
        9.21        20.22         1.12        13.45         7.53         8.22 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       20.65        11.57         5.13         3.25        13.15        13.18 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10         0.10         0.13         0.10         6.58        12.20 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        8.05        14.01        36.00         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
      105.07        28.96         4.01        69.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       12.36        12.66        17.19        10.26        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A4YU 
       12.79        11.31        12.33        24.72        18.21        16.44 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
        5.92        13.78        11.24        11.31        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7829 
       15.65         7.40        14.47        72.23        21.27        19.53 
TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A4BE TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 
       17.06        13.58        11.08         1.51         5.92        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD 
       12.10        10.62         5.59        11.84         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H2 
       25.81        11.77        29.98         6.51        10.19        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
       23.84        12.30         9.67         8.88         8.81         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-AB1X 
       18.81        18.38         5.19        13.08         6.44        13.51 
TCGA-IP-7968 TCGA-KB-A93G TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 
        2.53        20.15        61.25         6.08         4.60         9.24 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E0 
       16.67       122.30       115.69         5.79         0.92        18.48 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PM 
       21.73        27.88        22.19         2.50        12.79         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PS TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91E 
        9.27        13.35        26.24        27.35        64.57        11.93 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W 
       61.22        18.74        22.68         1.71        36.16         7.36 
TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D 
        9.50         2.01        55.43         4.54         6.58        64.18 
TCGA-VQ-A94U TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F 
       22.09        40.08        32.94        29.98        17.13        54.12 
TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       26.04        16.14        21.11 

$subtype3
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT 
       32.45         7.69         0.85        20.78         2.63         9.30 
TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC 
       14.86        12.16        21.70        31.56        25.22         6.28 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A88S TCGA-L5-A88T TCGA-L5-A8NG 
        0.30         3.68         3.32         6.94         8.71        35.97 
TCGA-L5-A8NI TCGA-L5-A8NL TCGA-L5-A8NQ TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NU 
       13.48        13.22        21.37        13.41        27.12        83.24 
TCGA-LN-A49N TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A4A5 TCGA-S8-A6BV TCGA-VR-A8ET 
       12.43        13.25         0.10        22.39        20.02         1.55 
TCGA-VR-AA7I TCGA-B7-5816 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-6453 TCGA-BR-6456 
       15.91        26.70         9.47         9.44        15.95        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 
       13.68        19.33        39.12        26.10         9.17        25.61 
TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
       18.05        12.16        21.11        31.20        12.82         9.21 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 
       23.93        15.42        18.15         3.45         9.07        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 
       17.49        14.43         9.60         2.66        16.31         7.40 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 
       13.08        22.19        17.52        14.04        11.80        14.79 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 
       15.85         3.72         5.39        12.79         9.34         6.28 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
        0.49        16.44         9.86        10.68        12.56         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 
       22.26        13.41        13.51         8.98        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5802 
       19.36        13.51         0.46        13.64         2.83         0.30 
TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.07         0.39         0.07         0.07         0.07         0.07 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4449 TCGA-CG-5717 
        0.13         0.16        11.31         0.10        19.07         6.97 
TCGA-CG-5719 TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        1.02        65.10        11.93        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8574 
       18.61        17.85        13.35        10.55        16.80        17.19 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A747 
       14.66        21.14        20.91        14.76        13.71         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7998 
        4.34         7.13         0.62         7.99         3.48        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GY 
       59.54         5.03         0.56        21.37         0.10         0.26 
TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-KB-A93H 
       21.21         5.36         6.51         1.81         7.82        37.64 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-RD-A7BS TCGA-RD-A7BW 
        3.72        19.73         9.86        45.67        11.05         5.13 
TCGA-RD-A8N0 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EA 
       40.64        57.44         8.94        35.61        16.87        19.04 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PQ TCGA-VQ-A8PZ 
       32.48        28.96        46.26        16.31        15.65        65.16 
TCGA-VQ-A91Q TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA64 
       20.81         9.73         5.72         2.66        42.54        18.41 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        10.62         0.79 

subtype1 subtype2 subtype3 
    0.10     0.10     0.07 
subtype1 subtype2 subtype3 
   79.07   122.30    83.24 
subtype1 subtype2 subtype3 
   12.33    12.79    13.22 
[1] "0.1 - 79.1 (12.3)"  "0.1 - 122.3 (12.8)" "0.1 - 83.2 (13.2)" 
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        2        7        3        28        19        13
  subtype2       9        8       18       13        22        30         8
  subtype3       0        2       12       14        21        26         7
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         17         13          6       10         3
  subtype2         31         31         17       11         1
  subtype3         36         18         18       16         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        9        0
  STAGE IA          2        8        2
  STAGE IB          7       18       12
  STAGE II          3       13       14
  STAGE IIA        28       22       21
  STAGE IIB        19       30       26
  STAGE III        13        8        7
  STAGE IIIA       17       31       36
  STAGE IIIB       13       31       18
  STAGE IIIC        6       17       18
  STAGE IV         10       11       16
  STAGE IVA         3        1        0
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     9 30 71 13
  subtype2    29 41 97 36
  subtype3     6 34 80 50
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1        9       29        6
  T2          30       41       34
  T3          71       97       80
  T4          13       36       50
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 45 48 18 11
  subtype2 72 53 43 33
  subtype3 55 52 23 36
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       45       72       55
  N1       48       53       52
  N2       18       43       23
  N3       11       33       36
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus         0   1
  subtype1 105  11
  subtype2 179   9
  subtype3 148  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  105   11
  subtype2  179    9
  subtype3  148   11
   clus
vv  subtype1 subtype2 subtype3
  0      105      179      148
  1       11        9       11
[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  24 109
  subtype2  61 147
  subtype3  57 113
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24  109
  subtype2   61  147
  subtype3   57  113
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       24       61       57
  MALE        109      147      113
[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                                     4
  subtype2                                    17
  subtype3                                    36
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     13
  subtype2                                                     50
  subtype3                                                     52
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                11
  subtype2                                                                39
  subtype3                                                                18
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               12
  subtype2                                               44
  subtype3                                               13
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        1
  subtype2                                                        5
  subtype3                                                       13
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         1
  subtype2                                                         4
  subtype3                                                         1
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        4
  subtype3                                        5
D7V8, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  13
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  50
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 4
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   36
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  52
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 5
[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   1 132
  subtype2   3 205
  subtype3   1 169
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  132
  subtype2    3  205
  subtype3    1  169
     clus
vv    subtype1 subtype2 subtype3
  NO         1        3        1
  YES      132      205      169
[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"
D7V10, continuous
          vv
clus        R0  R1  R2
  subtype1  34   2   2
  subtype2 144   5   4
  subtype3 116   7   4
D7V11, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       34      144      116
  R1        2        5        7
  R2        2        4        4
[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"
D7V12, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    42                         3    69
  subtype2    31                         7   138
  subtype3    34                         2   128
D7V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           42       31       34
  BLACK OR AFRICAN AMERICAN        3        7        2
  WHITE                           69      138      128
[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"
D7V14, binary
          cls
clus         0   1
  subtype1   2  74
  subtype2   3 119
  subtype3   2 131
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   74
  subtype2    3  119
  subtype3    2  131
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        3        2
  NOT HISPANIC OR LATINO       74      119      131
[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_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  23  22
  subtype2  64  53
  subtype3 110  48
  subtype4  55  42
  subtype5  52  28
subtype1 subtype2 subtype3 subtype4 subtype5 
      45      117      158       97       80 
subtype1 subtype2 subtype3 subtype4 subtype5 
      22       53       48       42       28 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-L5-A4OF TCGA-L5-A4OQ 
       25.78        20.05         5.92         4.21         3.68         1.38 
TCGA-L5-A4OS TCGA-L5-A891 TCGA-L5-A8NN TCGA-R6-A6KZ TCGA-R6-A6Y2 TCGA-R6-A8WG 
       58.59         3.95         5.49         5.06         9.30        12.69 
TCGA-V5-A7RB TCGA-BR-7197 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-8373 
        5.29         9.21        28.73        11.44         2.20        14.79 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4J1 TCGA-CD-8533 
        9.21        11.54        10.68         7.53         0.72         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-5725 TCGA-D7-6822 TCGA-D7-8572 
        0.13         3.42        12.20        15.02        12.33        16.80 
TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-R5-A7ZF TCGA-SW-A7EB 
       14.27         2.96         5.56        60.56         8.52         5.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A91Z 
        5.46        13.25        35.24        22.19        12.79        52.24 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6B 
        9.04        21.04        29.98 

$subtype2
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63        13.94         8.94 
TCGA-2H-A9GO TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FB TCGA-JY-A93C TCGA-L5-A43E 
       16.24         3.88       122.10        60.39        23.18        30.25 
TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OH TCGA-L5-A4OI TCGA-L5-A4ON TCGA-L5-A4OP 
       24.00         4.70        32.61        19.99        18.35         7.17 
TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A88Y TCGA-L5-A8NE 
        3.16         7.13         7.43         2.60         0.36        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NW TCGA-L7-A6VZ 
        2.66        12.92        16.47         7.76        46.09        10.36 
TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG 
       33.11         8.02         7.59        14.70         7.04        29.59 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-S8-A6BV 
        6.35        53.95        15.78         2.89         7.00        20.02 
TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-BR-8077 
        4.80         9.27         4.44        22.82        46.19         0.69 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-A4CS 
        6.18        19.50         4.31        20.22         1.12         1.48 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5727 TCGA-D7-6527 
       20.65        11.57        36.00         0.99        79.07        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A74A 
       15.22        15.98        11.31        18.21        11.24         7.40 
TCGA-F1-6874 TCGA-FP-8099 TCGA-FP-A4BE TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-A4G3 
       14.47        17.06        11.08         5.92        11.41         5.59 
TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GX 
       11.84        22.75        25.81        11.77         6.51        10.19 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-IN-7808 TCGA-IN-A6RI TCGA-KB-A93G 
       12.95        12.30         8.88         3.45        18.38        20.15 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-VQ-A8DL 
       18.21        61.25         6.08         9.24        16.67         0.92 
TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PB TCGA-VQ-A8PJ 
       18.48        21.73        34.45        27.88        34.29         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91D 
       17.85         9.27        26.24        27.35        64.57        11.70 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       11.93        18.74        22.68         1.71        36.16         9.50 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        4.54        64.18        11.24        40.08        32.94        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       54.12        26.04        16.14 

$subtype3
TCGA-2H-A9GR TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6FE TCGA-JY-A6FH TCGA-JY-A938 
       32.45         9.30        14.86         3.68        42.77        25.41 
TCGA-JY-A939 TCGA-JY-A93E TCGA-L5-A43C TCGA-L5-A43M TCGA-L5-A4OO TCGA-L5-A4OT 
       21.70        25.22         3.16         8.94         3.32         4.90 
TCGA-L5-A4OU TCGA-L5-A88T TCGA-L5-A893 TCGA-L5-A8NG TCGA-L5-A8NI TCGA-L5-A8NR 
       29.00         8.71         3.02        35.97        13.48         8.71 
TCGA-L5-A8NS TCGA-L5-A8NT TCGA-L5-A8NV TCGA-Q9-A6FW TCGA-X8-AAAR TCGA-B7-5816 
       13.41        27.12        52.57         7.82        10.16        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-6452 
       11.70        19.56        11.01         9.47         9.44        34.68 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 
       13.87        19.33         9.17        32.78        19.89        12.16 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        8.98        30.90        32.94        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 
       15.42        18.15        12.43        12.76        17.49        12.26 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8370 TCGA-BR-8372 
        8.05        12.95        15.58         0.26         3.32        19.17 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-A4CQ 
        0.26        15.85        13.45         7.53        15.81        22.26 
TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       13.64         5.13         3.25        13.15        13.18         0.30 
TCGA-CD-5813 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG 
        0.39         0.10         0.10         0.10        11.61         6.58 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5722 
        8.05        14.01        19.07         6.97         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
      105.07        12.03        28.96         4.01        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-D7-8570 TCGA-D7-8576 TCGA-D7-A4YU 
       17.19        12.79        10.55        24.72        14.66        16.44 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
        5.92        13.78        14.76        11.31        11.44         9.76 
TCGA-D7-A6F2 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       15.65        72.23        21.27         3.48        19.53        22.29 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4GC 
       13.58         0.56         1.51        12.10        10.62         3.25 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-IN-7806 
       21.37        29.98        23.84         9.67         8.81        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39         5.36         5.19        13.08         6.44 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-R5-A804 
        6.51         1.81         7.82        13.51         2.53         4.60 
TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-SW-A7EA TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       11.05       122.30       115.69        19.04        32.48         7.73 
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-A8PZ TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W 
       15.65        13.35        65.16        61.22        20.81         7.36 
TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94U TCGA-VQ-AA64 TCGA-VQ-AA69 
        2.01        55.43         6.58        22.09        18.41        28.41 
TCGA-VQ-AA6J TCGA-VQ-AA6K 
       21.11        12.43 

$subtype4
TCGA-IC-A6RE TCGA-JY-A93D TCGA-L5-A8NL TCGA-L5-A8NU TCGA-ZR-A9CJ TCGA-BR-6453 
        7.69        31.56        13.22        83.24        19.73        15.95 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
       17.29        13.68        39.12        26.10        25.61        18.05 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 
       21.11        31.20        12.82         3.45         9.07        18.71 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 
       14.43         9.60         2.66        16.31         7.40        13.08 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8483 
       22.19        17.52        14.04        11.80         3.72         5.39 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
       12.79         9.34         6.28         0.49        16.44         9.86 
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-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 
       12.82         0.66        19.36        13.51         0.46         2.83 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-5719 TCGA-CG-5728 
        0.16         9.34        11.31         0.10         1.02        65.10 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8574 
       11.93        19.13        18.84        18.61        17.85        17.19 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A6ET TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       21.14        20.91        13.71         8.38         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ TCGA-HU-A4GY 
        0.62         7.99        59.54         5.03         0.10         0.26 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-R5-A7O7 TCGA-RD-A7BW 
       37.64         3.72        19.73         9.86        45.67         5.13 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
       37.91        40.64        57.44         8.94        35.61        16.87 
TCGA-VQ-A91A TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-ZA-A8F6 
       36.69         9.73         5.72         2.66        42.54        10.62 
TCGA-ZQ-A9CR 
        0.79 

$subtype5
TCGA-IC-A6RF TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB 
        6.21        33.27        20.09         0.85        20.78         2.63 
TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.12        18.64         0.53        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA 
       12.82         9.96         4.67        14.50        12.16        44.75 
TCGA-JY-A6FD TCGA-JY-A6FG TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A43J TCGA-L5-A4OM 
       68.02        41.52         6.28         0.30         4.31        47.93 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-LN-A49K 
        6.94        25.12         7.40        13.55        21.37         5.92 
TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49R TCGA-LN-A49S 
       10.45        12.66        12.43        13.41         0.10        13.15 
TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 
       15.35        13.25         0.10        12.46        12.59        12.49 
TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ 
       12.59        22.39         0.10        15.52        11.54        12.33 
TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HV TCGA-LN-A7HW 
       13.22         4.47        12.33        25.25        10.52        12.00 
TCGA-LN-A7HX TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A9FO TCGA-Q9-A6FU TCGA-S8-A6BW 
       12.23        12.03        13.18         0.13         5.16        20.38 
TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU 
        3.42        18.81        19.96        12.43         1.55        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G 
        8.12        28.11        30.71        18.18        42.87        15.06 
TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-AAPN 
       11.24         9.17        15.91         3.42         2.10         2.66 
TCGA-BR-A4IY TCGA-IN-A7NT 
       12.89         5.56 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.13     0.36     0.10     0.07     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
   60.56   122.10   122.30    83.24    68.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
   9.300   14.300   13.265   12.560   12.475 
[1] "0.1 - 60.6 (9.3)"   "0.4 - 122.1 (14.3)" "0.1 - 122.3 (13.3)"
[4] "0.1 - 83.2 (12.6)"  "0.1 - 68.0 (12.5)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        0        6        2         2         5         5
  subtype2       9        5       13        4        10        18         8
  subtype3       1        4        8       15        16        27         4
  subtype4       0        0        7        8        11        13         2
  subtype5       0        3        3        1        32        12         9
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         12          5          3        2         0
  subtype2         11         14          9        5         3
  subtype3         33         22         14       15         0
  subtype4         19         15         13       12         0
  subtype5          9          6          2        3         1
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        9        1        0        0
  STAGE IA          0        5        4        0        3
  STAGE IB          6       13        8        7        3
  STAGE II          2        4       15        8        1
  STAGE IIA         2       10       16       11       32
  STAGE IIB         5       18       27       13       12
  STAGE III         5        8        4        2        9
  STAGE IIIA       12       11       33       19        9
  STAGE IIIB        5       14       22       15        6
  STAGE IIIC        3        9       14       13        2
  STAGE IV          2        5       15       12        3
  STAGE IVA         0        3        0        0        1
[1] 12  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     3 10 22  9
  subtype2    24 20 46 20
  subtype3     9 33 85 34
  subtype4     1 18 50 31
  subtype5     7 24 45  5
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        3       24        9        1        7
  T2          10       20       33       18       24
  T3          22       46       85       50       45
  T4           9       20       34       31        5
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 10 18  8  8
  subtype2 43 35 19 12
  subtype3 47 46 33 32
  subtype4 26 29 18 25
  subtype5 46 25  6  3
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       10       43       47       26       46
  N1       18       35       46       29       25
  N2        8       19       33       18        6
  N3        8       12       32       25        3
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus         0   1
  subtype1  40   1
  subtype2  90   8
  subtype3 144   9
  subtype4  86   9
  subtype5  72   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    1
  subtype2   90    8
  subtype3  144    9
  subtype4   86    9
  subtype5   72    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       40       90      144       86       72
  1        1        8        9        9        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"
D8V7, binary
          cls
clus         0   1
  subtype1  12  35
  subtype2  34  86
  subtype3  44 118
  subtype4  40  60
  subtype5  12  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   35
  subtype2   34   86
  subtype3   44  118
  subtype4   40   60
  subtype5   12   70
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       12       34       44       40       12
  MALE         35       86      118       60       70
[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                                     0
  subtype2                                     7
  subtype3                                    23
  subtype4                                    27
  subtype5                                     0
          vv
clus       STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     16
  subtype2                                                     14
  subtype3                                                     53
  subtype4                                                     30
  subtype5                                                      2
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 7
  subtype2                                                                19
  subtype3                                                                27
  subtype4                                                                15
  subtype5                                                                 0
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  subtype1                                               10
  subtype2                                               27
  subtype3                                               23
  subtype4                                                9
  subtype5                                                0
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  subtype1                                                        1
  subtype2                                                        1
  subtype3                                                        6
  subtype4                                                       11
  subtype5                                                        0
          vv
clus       STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  subtype1                                                         0
  subtype2                                                         3
  subtype3                                                         2
  subtype4                                                         1
  subtype5                                                         0
          vv
clus       STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  subtype1                                        0
  subtype2                                        2
  subtype3                                        5
  subtype4                                        2
  subtype5                                        0
D8V8, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      34       73      139       95        2 
  [1] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
  [7] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
 [13] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype4"
 [19] "subtype4" "subtype3" "subtype3" "subtype3" "subtype4" "subtype3"
 [25] "subtype4" "subtype3" "subtype4" "subtype1" "subtype3" "subtype3"
 [31] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype4"
 [37] "subtype4" "subtype3" "subtype4" "subtype3" "subtype4" "subtype1"
 [43] "subtype2" "subtype3" "subtype4" "subtype3" "subtype3" "subtype4"
 [49] "subtype4" "subtype1" "subtype3" "subtype4" "subtype2" "subtype2"
 [55] "subtype4" "subtype3" "subtype4" "subtype4" "subtype2" "subtype4"
 [61] "subtype3" "subtype4" "subtype3" "subtype1" "subtype4" "subtype3"
 [67] "subtype3" "subtype4" "subtype4" "subtype1" "subtype2" "subtype2"
 [73] "subtype4" "subtype4" "subtype3" "subtype4" "subtype3" "subtype4"
 [79] "subtype1" "subtype4" "subtype3" "subtype4" "subtype4" "subtype4"
 [85] "subtype1" "subtype4" "subtype1" "subtype4" "subtype3" "subtype1"
 [91] "subtype2" "subtype4" "subtype4" "subtype4" "subtype1" "subtype4"
 [97] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype3"
[103] "subtype2" "subtype3" "subtype4" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype4" "subtype3" "subtype3" "subtype4" "subtype4"
[115] "subtype4" "subtype4" "subtype4" "subtype4" "subtype3" "subtype3"
[121] "subtype1" "subtype4" "subtype1" "subtype3" "subtype1" "subtype4"
[127] "subtype4" "subtype3" "subtype3" "subtype1" "subtype4" "subtype3"
[133] "subtype3" "subtype3" "subtype3" "subtype3" "subtype2" "subtype4"
[139] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[145] "subtype3" "subtype2" "subtype4" "subtype3" "subtype3" "subtype3"
[151] "subtype3" "subtype3" "subtype3" "subtype4" "subtype4" "subtype3"
[157] "subtype4" "subtype3" "subtype4" "subtype4" "subtype3" "subtype3"
[163] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[169] "subtype1" "subtype3" "subtype1" "subtype4" "subtype2" "subtype3"
[175] "subtype4" "subtype4" "subtype1" "subtype3" "subtype3" "subtype3"
[181] "subtype3" "subtype4" "subtype2" "subtype3" "subtype3" "subtype3"
[187] "subtype1" "subtype3" "subtype4" "subtype4" "subtype2" "subtype4"
[193] "subtype4" "subtype4" "subtype2" "subtype2" "subtype3" "subtype3"
[199] "subtype3" "subtype3" "subtype3" "subtype2" "subtype4" "subtype4"
[205] "subtype3" "subtype3" "subtype2" "subtype2" "subtype3" "subtype2"
[211] "subtype1" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[217] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[223] "subtype3" "subtype3" "subtype4" "subtype2" "subtype2" "subtype4"
[229] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[235] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[241] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[247] "subtype3" "subtype3" "subtype1" "subtype1" "subtype2" "subtype4"
[253] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype1"
[259] "subtype2" "subtype2" "subtype3" "subtype2" "subtype3" "subtype4"
[265] "subtype2" "subtype3" "subtype4" "subtype4" "subtype3" "subtype4"
[271] "subtype4" "subtype4" "subtype4" "subtype3" "subtype1" "subtype2"
[277] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[283] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype3"
[289] "subtype3" "subtype1" "subtype3" "subtype1" "subtype2" "subtype2"
[295] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype2"
[301] "subtype2" "subtype2" "subtype3" "subtype4" "subtype2" "subtype2"
[307] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[313] "subtype3" "subtype2" "subtype4" "subtype1" "subtype1" "subtype3"
[319] "subtype3" "subtype2" "subtype3" "subtype4" "subtype2" "subtype1"
[325] "subtype4" "subtype4" "subtype2" "subtype3" "subtype3" "subtype2"
[331] "subtype3" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[337] "subtype2" "subtype3" "subtype3" "subtype4" "subtype4"
                                                                   clus
vv                                                                  subtype1
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    0
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 0
                                                                   clus
vv                                                                  subtype2
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                    7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  14
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 2
                                                                   clus
vv                                                                  subtype3
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   23
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  53
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                        23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                 5
                                                                   clus
vv                                                                  subtype4
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                   27
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                  30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                         9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                1
  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   1  46
  subtype2   1 119
  subtype3   3 159
  subtype4   0 100
  subtype5   0  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   46
  subtype2    1  119
  subtype3    3  159
  subtype4    0  100
  subtype5    0   82
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         1        1        3        0        0
  YES       46      119      159      100       82
[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"
D8V10, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       4       21       15        1       47 
 [1] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
 [7] "subtype3" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[13] "subtype5" "subtype3" "subtype5" "subtype3" "subtype5" "subtype3"
[19] "subtype2" "subtype5" "subtype5" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype5" "subtype2" "subtype3" "subtype2" "subtype1"
[31] "subtype3" "subtype3" "subtype2" "subtype2" "subtype5" "subtype3"
[37] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype3"
[43] "subtype5" "subtype1" "subtype5" "subtype3" "subtype3" "subtype3"
[49] "subtype2" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[55] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[61] "subtype5" "subtype5" "subtype5" "subtype2" "subtype5" "subtype3"
[67] "subtype2" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
[73] "subtype2" "subtype1" "subtype5" "subtype5" "subtype5" "subtype5"
[79] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[85] "subtype5" "subtype3" "subtype5"
          vv
clus        R0  R1  R2
  subtype1  29   2   0
  subtype2  66   0   2
  subtype3 118   6   5
  subtype4  79   6   3
  subtype5   2   0   0
D8V11, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      31       68      129       88        2 
  [1] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
  [7] "subtype4" "subtype4" "subtype3" "subtype4" "subtype4" "subtype3"
 [13] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype3"
 [19] "subtype4" "subtype3" "subtype4" "subtype3" "subtype4" "subtype1"
 [25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [31] "subtype3" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
 [37] "subtype4" "subtype1" "subtype2" "subtype3" "subtype4" "subtype3"
 [43] "subtype3" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
 [49] "subtype2" "subtype2" "subtype4" "subtype3" "subtype4" "subtype4"
 [55] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype1"
 [61] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype1"
 [67] "subtype2" "subtype2" "subtype4" "subtype4" "subtype3" "subtype4"
 [73] "subtype3" "subtype4" "subtype1" "subtype4" "subtype3" "subtype4"
 [79] "subtype4" "subtype4" "subtype1" "subtype4" "subtype1" "subtype4"
 [85] "subtype3" "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
 [91] "subtype1" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [97] "subtype2" "subtype3" "subtype2" "subtype3" "subtype3" "subtype3"
[103] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[109] "subtype4" "subtype3" "subtype3" "subtype1" "subtype4" "subtype1"
[115] "subtype3" "subtype4" "subtype3" "subtype3" "subtype3" "subtype3"
[121] "subtype3" "subtype2" "subtype4" "subtype2" "subtype3" "subtype3"
[127] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype4"
[133] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[139] "subtype4" "subtype4" "subtype3" "subtype4" "subtype3" "subtype4"
[145] "subtype4" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[151] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[157] "subtype4" "subtype2" "subtype3" "subtype4" "subtype4" "subtype1"
[163] "subtype3" "subtype3" "subtype3" "subtype3" "subtype4" "subtype2"
[169] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype4"
[175] "subtype4" "subtype2" "subtype4" "subtype4" "subtype2" "subtype2"
[181] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype2"
[187] "subtype4" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[193] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
[199] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[205] "subtype3" "subtype3" "subtype4" "subtype2" "subtype2" "subtype4"
[211] "subtype2" "subtype3" "subtype2" "subtype3" "subtype2" "subtype3"
[217] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[223] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[229] "subtype3" "subtype1" "subtype1" "subtype2" "subtype4" "subtype4"
[235] "subtype4" "subtype4" "subtype2" "subtype3" "subtype4" "subtype2"
[241] "subtype3" "subtype4" "subtype4" "subtype3" "subtype4" "subtype4"
[247] "subtype4" "subtype4" "subtype3" "subtype1" "subtype2" "subtype1"
[253] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[259] "subtype3" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[265] "subtype1" "subtype3" "subtype1" "subtype2" "subtype2" "subtype3"
[271] "subtype2" "subtype3" "subtype3" "subtype3" "subtype2" "subtype2"
[277] "subtype2" "subtype3" "subtype4" "subtype2" "subtype2" "subtype3"
[283] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[289] "subtype2" "subtype4" "subtype1" "subtype1" "subtype3" "subtype3"
[295] "subtype2" "subtype3" "subtype4" "subtype2" "subtype1" "subtype4"
[301] "subtype4" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[307] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype2"
[313] "subtype3" "subtype3" "subtype4" "subtype4"
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       29       66      118       79
  R1        2        0        6        6
  R2        0        2        5        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
      30       70      124       83        2 
  [1] "subtype3" "subtype3" "subtype3" "subtype4" "subtype3" "subtype3"
  [7] "subtype4" "subtype4" "subtype3" "subtype4" "subtype4" "subtype3"
 [13] "subtype3" "subtype4" "subtype4" "subtype3" "subtype3" "subtype3"
 [19] "subtype4" "subtype3" "subtype4" "subtype3" "subtype4" "subtype1"
 [25] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
 [31] "subtype3" "subtype4" "subtype4" "subtype3" "subtype4" "subtype3"
 [37] "subtype4" "subtype1" "subtype2" "subtype3" "subtype4" "subtype3"
 [43] "subtype3" "subtype4" "subtype4" "subtype1" "subtype3" "subtype4"
 [49] "subtype2" "subtype2" "subtype4" "subtype3" "subtype4" "subtype4"
 [55] "subtype2" "subtype4" "subtype3" "subtype4" "subtype3" "subtype1"
 [61] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype1"
 [67] "subtype2" "subtype2" "subtype4" "subtype4" "subtype3" "subtype4"
 [73] "subtype3" "subtype4" "subtype1" "subtype4" "subtype3" "subtype4"
 [79] "subtype4" "subtype4" "subtype1" "subtype4" "subtype1" "subtype4"
 [85] "subtype3" "subtype1" "subtype2" "subtype4" "subtype4" "subtype4"
 [91] "subtype1" "subtype4" "subtype4" "subtype4" "subtype4" "subtype2"
 [97] "subtype3" "subtype2" "subtype3" "subtype3" "subtype4" "subtype4"
[103] "subtype3" "subtype1" "subtype4" "subtype3" "subtype3" "subtype3"
[109] "subtype3" "subtype2" "subtype4" "subtype2" "subtype3" "subtype3"
[115] "subtype3" "subtype3" "subtype1" "subtype3" "subtype2" "subtype4"
[121] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[127] "subtype4" "subtype4" "subtype3" "subtype4" "subtype3" "subtype4"
[133] "subtype4" "subtype3" "subtype3" "subtype2" "subtype2" "subtype2"
[139] "subtype3" "subtype3" "subtype2" "subtype1" "subtype3" "subtype1"
[145] "subtype4" "subtype2" "subtype3" "subtype4" "subtype4" "subtype1"
[151] "subtype3" "subtype3" "subtype3" "subtype3" "subtype4" "subtype2"
[157] "subtype3" "subtype3" "subtype3" "subtype1" "subtype3" "subtype4"
[163] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype2"
[169] "subtype2" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
[175] "subtype2" "subtype4" "subtype4" "subtype3" "subtype3" "subtype2"
[181] "subtype2" "subtype3" "subtype2" "subtype1" "subtype3" "subtype2"
[187] "subtype2" "subtype3" "subtype3" "subtype2" "subtype2" "subtype3"
[193] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype4"
[199] "subtype2" "subtype2" "subtype4" "subtype2" "subtype3" "subtype2"
[205] "subtype3" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3"
[211] "subtype3" "subtype2" "subtype3" "subtype3" "subtype3" "subtype3"
[217] "subtype3" "subtype3" "subtype3" "subtype3" "subtype3" "subtype1"
[223] "subtype1" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
[229] "subtype2" "subtype3" "subtype4" "subtype2" "subtype3" "subtype4"
[235] "subtype4" "subtype3" "subtype4" "subtype4" "subtype4" "subtype4"
[241] "subtype3" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[247] "subtype1" "subtype2" "subtype2" "subtype2" "subtype3" "subtype3"
[253] "subtype3" "subtype2" "subtype3" "subtype3" "subtype1" "subtype3"
[259] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[265] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[271] "subtype4" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
[277] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype4"
[283] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[289] "subtype4" "subtype2" "subtype1" "subtype4" "subtype2" "subtype3"
[295] "subtype3" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
[301] "subtype2" "subtype2" "subtype2" "subtype3" "subtype3" "subtype4"
[307] "subtype4"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     7                         2    28
  subtype2    14                         5    81
  subtype3    21                         4   115
  subtype4    26                         0    72
  subtype5    39                         1    39
D8V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            7       14       21       26       39
  BLACK OR AFRICAN AMERICAN        2        5        4        0        1
  WHITE                           28       81      115       72       39
[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"
D8V14, binary
          cls
clus         0   1
  subtype1   3  22
  subtype2   1  54
  subtype3   2 104
  subtype4   1  88
  subtype5   0  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   22
  subtype2    1   54
  subtype3    2  104
  subtype4    1   88
  subtype5    0   56
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        1        2        1        0
  NOT HISPANIC OR LATINO       22       54      104       88       56
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
