[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/22507048/STES-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STES-TP/22555833/STES-TP.mergedcluster.txt"

nPatients in clinical file=628, in cluster file=628, common to both=628
[1]  10 628
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
151  98 182 194 
  1   2   3   4 
151  98 182 194 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
242 162 176 
  1   2   3 
242 162 176 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4 
145 137 137  64 
  1   2   3   4 
145 137 137  64 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
273 111  99 
  1   2   3 
273 111  99 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
170 275 154 
  1   2   3 
170 275 154 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
132 116  99 121 131 
  1   2   3   4   5 
132 116  99 121 131 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
167 281 172 
  1   2   3 
167 281 172 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
128 144 165  94  89 
  1   2   3   4   5 
128 144 165  94  89 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4   5 
124 156 121  47  74 
  1   2   3   4   5 
124 156 121  47  74 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 52 125 144 109  92 
  1   2   3   4   5 
 52 125 144 109  92 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"              "VITAL_STATUS"               
 [3] "DAYS_TO_DEATH"               "DAYS_TO_LAST_FOLLOWUP"      
 [5] "PATHOLOGIC_STAGE"            "PATHOLOGY_T_STAGE"          
 [7] "PATHOLOGY_N_STAGE"           "PATHOLOGY_M_STAGE"          
 [9] "GENDER"                      "RADIATION_THERAPY"          
[11] "KARNOFSKY_PERFORMANCE_SCORE" "NUMBER_PACK_YEARS_SMOKED"   
[13] "RACE"                        "ETHNICITY"                  

Input Data has 14 rows and 628 columns.

[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=217,	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=299,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 628 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "NUMBER_PACK_YEARS_SMOKED"    "RACE"                       
[11] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=56, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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  54 136 286 124 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   55   136   286   124 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  54 136 286 124 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   55   136   286   124 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
209 188  98  96 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
209 188  98  96 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
209 188  98  96 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
209 188  98  96 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=46, 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  79  65
  subtype2  52  45
  subtype3 114  63
  subtype4 109  72
subtype1 subtype2 subtype3 subtype4 
     144       97      177      181 
subtype1 subtype2 subtype3 subtype4 
      65       45       63       72 
$subtype1
TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OG TCGA-L5-A88Y TCGA-L5-A8NT TCGA-MX-A663 
       18.28         8.94         4.70         0.36        27.12         9.86 
TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IC-A6RE 
       25.78        31.27        14.30        13.94         4.21         7.69 
TCGA-JY-A6FH TCGA-JY-A93D TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4OQ 
       47.38        31.56         3.16        30.25        32.61         1.38 
TCGA-L5-A4OS TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A891 TCGA-L5-A893 TCGA-L5-A8NH 
       58.59         7.13         7.43         3.75         3.02        12.92 
TCGA-L5-A8NW TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-R6-A8W8 
       46.09         7.82        16.31         7.04         9.30         2.89 
TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-AASW TCGA-VR-A8ET TCGA-VR-AA4D 
        2.30         7.00         5.29         9.27         1.55        46.19 
TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4257 
       18.21        19.73        58.03        11.01         9.44         9.67 
TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 
        9.17         9.21        35.24        33.63        18.15        33.21 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8373 
        0.69         9.60        29.42         2.66        19.96        14.79 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 
        5.39         9.21        24.79        32.58        20.88        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF 
       13.87         7.53        34.98         0.72        13.51         1.15 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A 
       13.15        13.35        12.07        12.82        11.31        12.43 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 
        6.58        12.20        20.02         7.99        54.08         4.01 
TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 
       19.07         7.07         4.01        69.04        25.71        12.66 
TCGA-D7-6518 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 
       19.13        17.19        15.22        11.31        12.33        19.50 
TCGA-D7-A4YT TCGA-D7-A6EV TCGA-D7-A6EX TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       14.27        11.24        11.31         0.62         7.99        72.23 
TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G6 
       19.53         5.52        18.15        28.96        22.82        24.26 
TCGA-HU-A4GD TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8663 
       22.75        23.84        23.80        33.40        36.36         3.39 
TCGA-IN-A6RI TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A666 
       18.38        11.70         2.53         5.56        37.64        14.04 
TCGA-R5-A7ZE TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
       18.21         9.24         8.61         5.13        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       37.91        35.61         5.79         5.46        13.25        13.02 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH 
       21.73        37.41         7.73        46.26        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PY TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z 
        2.70        14.33        32.88         1.71         9.50        55.56 
TCGA-VQ-A922 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA6B TCGA-VQ-AA6D 
        9.04        66.81        21.04        42.54        32.94        17.13 

$subtype2
TCGA-L5-A8NG TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-VQ-A94U TCGA-2H-A9GJ 
       35.97        47.05        21.99        16.24        26.93        58.55 
TCGA-2H-A9GK TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IG-A3YA TCGA-IG-A4QS 
        7.63         8.94        16.24        32.45        20.78         3.88 
TCGA-IG-A5B8 TCGA-IG-A625 TCGA-IG-A8O2 TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OM 
        0.79        12.82         4.67        25.22        26.33        47.93 
TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OU TCGA-L5-A88Z TCGA-L5-A8NE TCGA-L5-A8NF 
       18.35         3.16        29.00         7.40        55.50         2.66 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NN TCGA-L5-A8NQ TCGA-L5-A8NR 
       13.48        16.47        13.22         5.49        21.37         8.71 
TCGA-L7-A6VZ TCGA-LN-A49L TCGA-LN-A7HV TCGA-LN-A7HX TCGA-M9-A5M8 TCGA-R6-A6DQ 
       10.36        10.45        10.52        12.23        33.11         7.59 
TCGA-R6-A6KZ TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-VR-A8EP TCGA-VR-A8EQ TCGA-VR-A8Q7 
        5.06         6.35        15.78        27.09        22.82        52.27 
TCGA-BR-4183 TCGA-BR-4255 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6709 TCGA-BR-7723 
        6.61         4.08        17.29        19.33        12.16        28.73 
TCGA-BR-8058 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8484 
       37.25        15.58         7.40        31.10        14.04        25.18 
TCGA-BR-8590 TCGA-BR-A4CS TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-CD-5803 TCGA-CD-8524 
        9.34         1.48         0.66        32.52        11.21        12.76 
TCGA-CD-8525 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-A487 TCGA-CD-A48C TCGA-CG-4437 
       12.59        12.39        11.64        12.30        11.61         8.05 
TCGA-CG-4477 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-8575 
       30.97        20.91        20.55        13.35        10.26        18.21 
TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-A9TM 
       16.44        22.29        19.96        11.38        14.07         6.21 
TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H2 TCGA-HU-A4H6 
       63.06         1.51        11.77         8.98        12.95        21.17 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-AB1V TCGA-KB-A93J TCGA-R5-A7ZR 
       18.81        12.46        19.53        15.75        36.95         6.08 
TCGA-RD-A8N1 TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91Y 
      115.69         1.87        64.57        73.41        20.81         9.73 
TCGA-VQ-A925 
        4.54 

$subtype3
TCGA-JY-A6FB TCGA-L5-A43J TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-CG-4475 
       60.39         4.31        24.00         5.16        20.02        22.98 
TCGA-CG-5727 TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-2H-A9GL TCGA-IG-A3I8 TCGA-IG-A3QL 
       79.07         0.23        27.35         5.92        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D 
        0.85         2.63        20.12        18.64         0.53        17.03 
TCGA-IG-A5S3 TCGA-IG-A6QS TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FE 
       23.41         9.96        14.50        12.16        44.75         3.68 
TCGA-JY-A93C TCGA-L5-A43H TCGA-L5-A4OO TCGA-L5-A4OP TCGA-L5-A4OT TCGA-L5-A88S 
       23.18         0.30         3.32         7.17         4.90        15.48 
TCGA-L5-A88V TCGA-L5-A8NK TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L7-A56G TCGA-LN-A49K 
        2.60        13.55        13.41        52.57        10.85         5.92 
TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S 
       12.66        12.43        13.41        12.33        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 
       15.35        12.59        13.25        12.62        12.46        12.59 
TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 TCGA-LN-A4A8 
       12.49        12.76        12.59        22.39        12.85        15.52 
TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 TCGA-LN-A5U6 TCGA-LN-A5U7 
       11.54        12.33        13.22         4.47        12.33        25.25 
TCGA-LN-A7HW TCGA-LN-A7HY TCGA-LN-A7HZ TCGA-LN-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 
       12.00        12.03        13.18        12.33        13.38        13.18 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6XG 
        0.13        12.03        12.85        12.26         8.02        38.40 
TCGA-R6-A6Y0 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-A7RE TCGA-V5-AASX 
       53.95        12.69        20.38         3.42        16.44         8.98 
TCGA-VR-A8EO TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY 
       25.81        12.43        18.31         8.12        28.11        33.70 
TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       18.18        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-6801 TCGA-BR-7716 TCGA-BR-7901 
       11.70        19.56        18.35        40.21        39.78         3.45 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-8362 TCGA-BR-8365 
       29.56        14.43        11.44         2.20        13.08        17.52 
TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       20.22         9.86         8.22        20.65        20.42        21.44 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
       13.02        13.18        12.10        12.53         7.17        12.33 
TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-A486 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4455 
       12.30        15.39         6.31         3.02        27.02        12.03 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
       18.97        12.00        36.00         1.02        12.03        15.02 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8576 
       18.84        18.54        15.98        12.79        24.72        14.66 
TCGA-D7-8578 TCGA-D7-A6F2 TCGA-FP-7735 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       21.14        15.65         3.48        17.06        13.58         0.56 
TCGA-HU-8243 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-IN-7808 
        5.92         3.25        25.81         6.58         2.10         3.45 
TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-A7NT TCGA-KB-A6F7 
       13.35         6.44         6.74         6.51        10.62        63.62 
TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E0 
       45.67         8.52         8.94         0.92        48.79        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A91A TCGA-VQ-A91N TCGA-VQ-A91V 
       43.36        17.85        13.35        39.45        18.74        42.64 
TCGA-VQ-A923 TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F 
        2.01        11.24        18.41        43.66        38.93        54.12 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$subtype4
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A4OI TCGA-L5-A88T TCGA-KB-A93G TCGA-IG-A4QT 
       15.68        34.85        19.99        22.82        20.15         9.30 
TCGA-IG-A7DP TCGA-JY-A6F8 TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A939 TCGA-JY-A93F 
       14.86       122.10        68.02        41.52        21.70        24.03 
TCGA-KH-A6WC TCGA-L5-A4OJ TCGA-L5-A88W TCGA-L5-A8NM TCGA-L5-A8NU TCGA-V5-AASV 
        6.28        21.01        25.12         7.76        83.24        15.35 
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-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
        4.08         9.34         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       15.95        13.87        13.68        39.12        26.10        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       25.61        18.05        19.89         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7957 
       44.94        21.90        36.16        35.84        15.32         9.07 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8360 TCGA-BR-8363 
       29.59        32.25         8.05         0.56         6.18         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 
       22.19         0.95        26.33         4.31         3.32        11.80 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 
       31.27         7.36        25.05         3.72         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
       27.12        28.14         6.28         7.53        26.73        31.96 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       34.13         6.08        27.55        28.57        12.89         8.98 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM 
       14.17         0.53        28.34         0.46        16.14         5.13 
TCGA-CD-5798 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 
       13.41        12.59        12.43        11.77        12.62        15.95 
TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-5717 
        1.02        14.01        29.98         0.00         9.01         6.97 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5728 
        0.99         6.02         0.99       105.07        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6818 TCGA-D7-8572 
       21.07         7.99        18.61        17.85        12.36        16.80 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       17.19        20.91         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       26.43        11.44        20.32         8.38         4.34         7.13 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HF-7132 
       14.47        21.27        22.29        59.54         5.03        77.29 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 
       52.21        30.51        26.47        24.39        22.32        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
        0.76        24.30         5.59        22.68        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
       29.98         0.10         6.51        20.25         0.26        29.00 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RS TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ 
       14.07        15.68        12.59        13.51         3.72        19.73 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       74.53         4.60        11.05        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       57.44        16.87        19.04        38.14        37.22        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       34.29        16.31         2.50         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A924 
       29.59        11.70        21.83        61.22        60.85        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA69 TCGA-VQ-AA6G TCGA-VQ-AA6I 
        6.58         5.72         2.66        28.41        26.04        16.14 
TCGA-ZA-A8F6 
       17.26 

subtype1 subtype2 subtype3 subtype4 
    0.36     0.66     0.13     0.00 
subtype1 subtype2 subtype3 subtype4 
  122.30   115.69    79.07   122.10 
subtype1 subtype2 subtype3 subtype4 
   13.30    14.04    13.08    16.87 
[1] "0.4 - 122.3 (13.3)" "0.7 - 115.7 (14.0)" "0.1 - 79.1 (13.1)" 
[4] "0.0 - 122.1 (16.9)"
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       5        2       12        8        13        24         3
  subtype2       1        6        4        8        12        10        10
  subtype3       1        3       12        7        42        24        13
  subtype4       3       10       19       10        20        29         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         27         19          6       14         0
  subtype2         14         12          8        4         3
  subtype3         22         16         15       13         1
  subtype4         32         25         17       18         0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           5        1        1        3
  STAGE IA          2        6        3       10
  STAGE IB         12        4       12       19
  STAGE II          8        8        7       10
  STAGE IIA        13       12       42       20
  STAGE IIB        24       10       24       29
  STAGE III         3       10       13        2
  STAGE IIIA       27       14       22       32
  STAGE IIIB       19       12       16       25
  STAGE IIIC        6        8       15       17
  STAGE IV         14        4       13       18
  STAGE IVA         0        3        1        0
[1] 12  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    15 33 67 26
  subtype2    13 17 50 15
  subtype3    11 46 87 29
  subtype4    16 40 79 54
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       15       13       11       16
  T2          33       17       46       40
  T3          67       50       87       79
  T4          26       15       29       54
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 41 44 29 22
  subtype2 28 34 18 13
  subtype3 71 57 20 25
  subtype4 67 52 31 36
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       41       28       71       67
  N1       44       34       57       52
  N2       29       18       20       31
  N3       22       13       25       36
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus         0   1
  subtype1 124   8
  subtype2  83   4
  subtype3 149  13
  subtype4 168  14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  124    8
  subtype2   83    4
  subtype3  149   13
  subtype4  168   14
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      124       83      149      168
  1        8        4       13       14
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  37 114
  subtype2  31  67
  subtype3  39 143
  subtype4  78 116
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37  114
  subtype2   31   67
  subtype3   39  143
  subtype4   78  116
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       37       31       39       78
  MALE        114       67      143      116
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1 111  23
  subtype2  73  20
  subtype3 118  47
  subtype4 143  29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  111   23
  subtype2   73   20
  subtype3  118   47
  subtype4  143   29
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       111       73      118      143
  YES       23       20       47       29
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, continuous
D1V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    23                         4
  subtype2    20                         1
  subtype3    57                         8
  subtype4    34                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1   102
  subtype2                                         0    62
  subtype3                                         0    96
  subtype4                                         0   132
D1V11, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           23       20       57       34
  BLACK OR AFRICAN AMERICAN                        4        1        8        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0        0
  WHITE                                          102       62       96      132
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
          cls
clus         0   1
  subtype1   3  91
  subtype2   0  59
  subtype3   5 118
  subtype4   3 136
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   91
  subtype2    0   59
  subtype3    5  118
  subtype4    3  136
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        5        3
  NOT HISPANIC OR LATINO       91       59      118      136
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2        0   1
  subtype1 149  88
  subtype2  96  64
  subtype3  97  75
subtype1 subtype2 subtype3 
     237      160      172 
subtype1 subtype2 subtype3 
      88       64       75 
$subtype1
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y 
       60.39        18.28        24.00         4.70        19.99         0.36 
TCGA-L5-A8NG TCGA-L5-A8NT TCGA-S8-A6BV TCGA-CG-5727 TCGA-FP-A8CX TCGA-VQ-A8PU 
       35.97        27.12        20.02        79.07         0.23        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GK TCGA-2H-A9GL 
       26.93        25.78        31.27        14.30         7.63         5.92 
TCGA-2H-A9GM TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A93C 
       13.94        32.45         7.69         3.88       122.10        23.18 
TCGA-JY-A93E TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON 
       25.22        30.25        26.33        32.61        21.01        18.35 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V 
        7.17         3.16         4.90         7.13         7.43         2.60 
TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L5-A8NL TCGA-L5-A8NM 
        3.02        55.50        12.92        16.47        13.22         7.76 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
        8.71        13.41        52.57        46.09        10.36        33.11 
TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A6XQ 
        7.82         8.02         7.59         5.06        38.40         6.35 
TCGA-R6-A6Y2 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE 
        9.30         2.89         2.30         7.00         5.29        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-3M-AB46 
        9.27         8.98        22.82        46.19        18.21        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TJ TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 
       26.70        11.70        11.01        34.68        13.87        19.33 
TCGA-BR-6566 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7958 
       32.78        36.16        35.84        33.63        18.15        29.56 
TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8297 
       33.21        29.59         8.05        29.42         2.66         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        6.18        31.10        13.08        26.33         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8589 
        3.32        31.27        25.05         5.39         1.12        27.12 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A44U 
       28.14         7.53        31.96        32.58         9.86        13.87 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4J8 
        7.53        34.98         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        21.44        16.14         5.13 
TCGA-CD-5799 TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8534 
       13.02        12.76        12.33        12.59        15.39        12.07 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ 
       12.82        12.43        12.43        11.61         6.58        12.62 
TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5730 
        8.05        14.01         0.99        12.03        28.96         4.01 
TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
       21.07        25.71        12.66        13.35        15.22        15.98 
TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
       12.33        19.50        18.21        14.66        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EY 
        5.92        36.43        13.78        14.76        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7829 
       20.32        19.96         0.62        14.47        21.27        19.53 
TCGA-FP-8099 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       17.06        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       52.21        30.51         1.51         5.92        24.39        22.32 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        24.26        22.68        24.20         3.25 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H0 
       29.98         8.98         0.10         6.51         6.58         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-7806 
       12.95        29.00        23.84        21.17        14.07        36.36 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.81         3.39        13.35         6.44         6.74        12.59 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A5UJ TCGA-R5-A7ZR 
       11.70         2.53        37.64        36.95        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        37.41        38.14        37.22         7.73        30.97 
TCGA-VQ-A8PB TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       34.29         9.27        23.41        29.59        14.33        73.41 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U 
       39.45        11.70        21.83        61.22        32.88         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 
       42.64        60.85         9.50         2.01        55.43         4.54 
TCGA-VQ-A928 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA69 
        5.72        66.81        42.54        11.24        43.66        28.41 
TCGA-VQ-AA6B TCGA-VQ-AA6G TCGA-VQ-AA6I 
       32.94        26.04        16.14 

$subtype2
TCGA-IC-A6RF TCGA-L5-A43J TCGA-Q9-A6FU TCGA-EQ-A4SO TCGA-2H-A9GG TCGA-2H-A9GJ 
       15.68         4.31         5.16        16.24        20.05        58.55 
TCGA-2H-A9GN TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YB 
        8.94         4.21        33.27        35.21         0.85         2.63 
TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 
       18.64         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-A6FD 
        9.96         4.67        14.50        12.16        44.75        68.02 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93F TCGA-L5-A43H TCGA-L5-A4OM 
        3.68        41.52        47.38        24.03         0.30        47.93 
TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NF TCGA-L5-A8NI 
       15.48        25.12         7.40         3.75         2.66        13.48 
TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M 
       13.55         5.49        10.85         5.92        10.45        12.66 
TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U 
       12.43        13.41        12.33        13.38        13.15        15.35 
TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 
       12.59        13.25        12.46        12.59        12.49        12.59 
TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.85        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18         0.13        12.85 
TCGA-LN-A9FR TCGA-R6-A6L4 TCGA-R6-A6Y0 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW 
       12.26        16.31        53.95        15.78        12.69        20.38 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU 
        3.42        15.35        25.81        27.09        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B 
        8.12        28.11        33.70        18.18        18.05        11.24 
TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE 
        9.17        15.91        25.08        41.23        14.37         2.10 
TCGA-Z6-A9VB TCGA-ZR-A9CJ TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-6565 TCGA-BR-6801 
        1.32        19.73        19.56         9.44         9.17        40.21 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 
        9.21        35.24        28.73         3.45        11.44         0.69 
TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-8690 
       14.79         9.21        20.22        24.79         8.22        10.68 
TCGA-BR-A4J1 TCGA-CD-5800 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH 
        0.72        13.15         7.17         6.31        12.30        12.20 
TCGA-CG-5718 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 
       36.00        15.02        20.55        18.84        17.19        10.26 
TCGA-D7-6820 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6875 
       11.31        11.31        22.29        15.65         7.99        72.23 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       13.58         0.56        28.96        22.75        25.81        11.77 
TCGA-HU-A4GX TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A7NT TCGA-R5-A7ZE 
       20.25        23.80        33.40        18.38        10.62        18.21 
TCGA-RD-A8N6 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8PE 
        8.94         5.46        13.25        13.02        43.36        22.19 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91Z 
       12.79         2.70        17.85        18.74        20.81        55.56 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6A TCGA-VQ-AA6D 
        9.04        21.04        38.93        17.13 

$subtype3
TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A88T TCGA-KB-A93G TCGA-MX-A663 TCGA-2H-A9GO 
       34.85         8.94        22.82        20.15         9.86        16.24 
TCGA-IG-A3YA TCGA-IG-A3YC TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A939 TCGA-JY-A93D 
       20.78        20.12         9.30        14.86        21.70        31.56 
TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU 
        6.28         3.16         3.32         1.38        58.59        29.00 
TCGA-L5-A8NQ TCGA-L5-A8NU TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A5 TCGA-LN-A9FP 
       21.37        83.24        12.62        12.76        22.39        12.03 
TCGA-R6-A6L6 TCGA-VR-A8ET TCGA-VR-A8Q7 TCGA-Z6-A8JD TCGA-Z6-AAPN TCGA-B7-A5TK 
        7.04         1.55        52.27         3.42         2.66         9.47 
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 
       15.95        17.29        13.68        39.12        26.10        25.61 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       18.05        19.89        12.16         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-8058 
       44.94        21.90        39.78        15.32         9.07        37.25 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
       14.43         9.60        32.25         0.56        19.96         2.20 
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-8381 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 
        7.36         3.72        25.18        12.79         9.34         6.28 
TCGA-BR-8677 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       26.73        20.88        34.13         6.08        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
        8.98        14.17        28.34         0.66        32.52         0.46 
TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 
       13.41        13.18        13.35        11.21        12.10        12.39 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-A489 
       12.59        12.53        12.30        12.39        11.64        11.31 
TCGA-CD-A4MI TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       11.77         6.97         1.02         6.02         0.99       105.07 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 
       65.10        69.04         7.99        20.91        19.13        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8572 
       18.61        17.85        12.79        12.36        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A6ET TCGA-D7-A747 TCGA-D7-A748 
       17.19        21.14        20.91        26.43         8.38         4.34 
TCGA-D7-A74B TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
        7.13        11.38         3.48        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        5.03        26.47        18.15        22.82        21.07         0.76 
TCGA-HU-A4GJ TCGA-HU-A4GY TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RJ TCGA-IN-A6RN 
       21.37         0.26        15.68         3.45        12.46        19.53 
TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
        6.51        15.75        13.51         5.56        63.62         3.72 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-RD-A7BS TCGA-RD-A7BW 
       14.04        45.67         8.52        74.53        11.05         5.13 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8E0 
       57.44        35.61        16.87         5.79         0.92        18.48 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PS 
       46.26        16.31         2.50         1.87        15.65        13.35 
TCGA-VQ-A8PX TCGA-VQ-A91Y TCGA-VQ-A927 TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-VQ-AA6F 
       64.57         9.73         6.58         2.66        18.41        54.12 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       27.55        12.43        17.26         0.79 

subtype1 subtype2 subtype3 
    0.10     0.13     0.26 
subtype1 subtype2 subtype3 
  122.10    72.23   122.30 
subtype1 subtype2 subtype3 
   14.66    13.18    15.09 
[1] "0.1 - 122.1 (14.7)" "0.1 - 72.2 (13.2)"  "0.3 - 122.3 (15.1)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       8       10       17       13        20        42        11
  subtype2       2        5       10        7        39        23        15
  subtype3       0        5       14       10        29        21         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         35         37         19       14         0
  subtype2         20         13         10        8         3
  subtype3         34         21         16       16         1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           8        2        0
  STAGE IA         10        5        5
  STAGE IB         17       10       14
  STAGE II         13        7       10
  STAGE IIA        20       39       29
  STAGE IIB        42       23       21
  STAGE III        11       15        2
  STAGE IIIA       35       20       34
  STAGE IIIB       37       13       21
  STAGE IIIC       19       10       16
  STAGE IV         14        8       16
  STAGE IVA         0        3        1
[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    33  40 110  49
  subtype2    12  44  80  21
  subtype3     8  37  84  45
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       33       12        8
  T2          40       44       37
  T3         110       80       84
  T4          49       21       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 77 69 43 41
  subtype2 65 53 20 17
  subtype3 59 48 29 33
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       77       65       59
  N1       69       53       48
  N2       43       20       29
  N3       41       17       33
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus         0   1
  subtype1 204   9
  subtype2 138   8
  subtype3 147  15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  204    9
  subtype2  138    8
  subtype3  147   15
   clus
vv  subtype1 subtype2 subtype3
  0      204      138      147
  1        9        8       15
[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  66 176
  subtype2  39 123
  subtype3  58 118
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   66  176
  subtype2   39  123
  subtype3   58  118
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       66       39       58
  MALE        176      123      118
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus         0   1
  subtype1 179  45
  subtype2 111  41
  subtype3 136  32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  179   45
  subtype2  111   41
  subtype3  136   32
     clus
vv    subtype1 subtype2 subtype3
  NO       179      111      136
  YES       45       41       32
[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"
D2V9, continuous
D2V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    43                         6
  subtype2    55                         8
  subtype3    37                         4
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1   164
  subtype2                                         0    84
  subtype3                                         0   119
D2V11, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  ASIAN                                           43       55       37
  BLACK OR AFRICAN AMERICAN                        6        8        4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                          164       84      119
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
          cls
clus         0   1
  subtype1   4 146
  subtype2   4 106
  subtype3   3 129
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  146
  subtype2    4  106
  subtype3    3  129
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        4        3
  NOT HISPANIC OR LATINO      146      106      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"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 77 54
  subtype2 89 43
  subtype3 70 63
  subtype4 38 23
subtype1 subtype2 subtype3 subtype4 
     131      132      133       61 
subtype1 subtype2 subtype3 subtype4 
      54       43       63       23 
$subtype1
TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-Q9-A6FU TCGA-EQ-A4SO TCGA-2H-A9GF 
        4.31         8.94        24.00         5.16        16.24        25.78 
TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A6FA TCGA-JY-A6FD 
        4.21        32.45         7.69         3.88        44.75        68.02 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OR TCGA-L5-A4OW 
       41.52        21.70        32.61        18.35         3.16         7.13 
TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NW TCGA-LN-A49K TCGA-LN-A49L 
       13.48        16.47        13.55        46.09         5.92        10.45 
TCGA-LN-A49M TCGA-LN-A49P TCGA-LN-A49U TCGA-LN-A49Y TCGA-LN-A4A5 TCGA-LN-A5U6 
       12.66        12.33        15.35        12.46        22.39        12.33 
TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HZ TCGA-LN-A9FR TCGA-S8-A6BW TCGA-VR-A8EP 
       25.25        12.00        13.18        12.26        20.38        27.09 
TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4253 
       41.23         2.10        19.56        11.01         9.47         4.08 
TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 
       34.68        13.87        19.89        36.16        35.24        39.78 
TCGA-BR-7723 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8381 
       28.73         8.05         2.20         4.31        31.27         7.36 
TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4IV 
        9.34        24.79        31.96         8.22        13.87        28.57 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.53         0.66        20.65        13.18        13.35 
TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        7.17        15.39        12.82        11.61         6.58        11.77 
TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 
       12.62        27.02        15.95        54.08        29.98        19.07 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
        9.01        18.97        15.02        25.71        12.66        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8575 
       18.84        18.61        13.35        10.26        12.79        18.21 
TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6F0 TCGA-F1-6875 TCGA-HF-7132 
       21.14         5.92        13.78        22.29        72.23        77.29 
TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8608 TCGA-HU-A4GQ TCGA-HU-A4GU 
       63.06        52.21        30.51        21.07         0.10         6.58 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
       20.25        12.95        33.40        36.36         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IP-7968 TCGA-VQ-A8DT 
       18.38        13.35        19.53         6.74         2.53        48.79 
TCGA-VQ-A8P2 TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91K 
       38.14         2.50         2.70        29.59        11.70        61.22 
TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A925 TCGA-VQ-A94O 
       18.74         1.71        42.64        60.85         4.54        21.04 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       28.41        38.93        32.94        54.12        16.14 

$subtype2
TCGA-JY-A6FB TCGA-L5-A4OG TCGA-L5-A4OI TCGA-VQ-A8PU TCGA-2H-A9GI TCGA-IG-A3YC 
       60.39         4.70        19.99        27.35        14.30        20.12 
TCGA-IG-A50L TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A93F TCGA-L5-A4OS 
        0.53         9.96        14.50       122.10        24.03        58.59 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NQ TCGA-L7-A6VZ TCGA-LN-A49O TCGA-LN-A49R 
        3.75        55.50        21.37        10.36        13.41        13.38 
TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4MR TCGA-LN-A7HX TCGA-LN-A8HZ 
       12.49        12.85        15.52        13.22        12.23        12.33 
TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-M9-A5M8 TCGA-RE-A7BO TCGA-VR-A8EO 
       13.18         0.13        12.03        33.11         7.00        25.81 
TCGA-VR-A8EQ TCGA-VR-A8Q7 TCGA-Z6-A8JD TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-B7-5816 
       22.82        52.27         3.42         1.32         2.66        26.70 
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6566 
       11.70         6.97        30.90         6.18         6.61        32.78 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8081 
        8.98        30.90        44.94        29.56        11.44        32.25 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
        0.56        29.42        15.58         6.18        31.10         0.26 
TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8690 
       25.05        25.18        27.12        28.14         7.53        10.68 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-8526 
       13.51         1.15        16.14         5.13        13.02        12.53 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       12.33        12.30        12.59        12.43         6.31        12.30 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4455 
       12.20        20.02         1.02         7.99         8.05        12.03 
TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5733 
        7.07        36.00       105.07        12.03        65.10        21.07 
TCGA-CG-5734 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
        7.99        15.22        15.98        11.31        12.33        24.72 
TCGA-D7-8573 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-EQ-8122 
       19.50        16.44        36.43        11.24        20.32         7.99 
TCGA-F1-6874 TCGA-F1-A448 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4GF 
       14.47        21.27        26.47        22.32         0.76        25.81 
TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-A7NT TCGA-IN-AB1X 
        6.51        29.00        23.84        23.80        10.62        13.51 
TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-SW-A7EA 
        8.61        16.67       122.30        37.91       115.69        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        0.92         5.46        18.48        21.73        37.22         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PX 
       46.26        22.19        12.79         1.87         9.27        64.57 
TCGA-VQ-A91S TCGA-VQ-A91Z TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6D 
       32.88        55.56        66.81        42.54        18.41        17.13 

$subtype3
TCGA-L5-A43I TCGA-L5-A8NT TCGA-CG-4475 TCGA-VQ-A94U TCGA-2H-A9GL TCGA-IG-A3Y9 
       18.28        27.12        22.98        26.93         5.92         0.85 
TCGA-IG-A3YA TCGA-IG-A4P3 TCGA-IG-A4QT TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 
       20.78        18.64         9.30        17.03         0.79        23.41 
TCGA-IG-A625 TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FE TCGA-JY-A93E TCGA-L5-A43C 
       12.82         4.67        12.16         3.68        25.22         3.16 
TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OT TCGA-L5-A4OX TCGA-L5-A8NF TCGA-L5-A8NL 
        0.30        26.33         4.90         7.43         2.66        13.22 
TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49N TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.41        52.57        12.43        12.59        13.25        12.62 
TCGA-LN-A4A1 TCGA-LN-A4A3 TCGA-LN-A4A4 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A7HY 
       12.59        12.76        12.59        11.54        12.33        12.03 
TCGA-LN-A8I0 TCGA-LN-A9FQ TCGA-Q9-A6FW TCGA-VR-AA7B TCGA-X8-AAAR TCGA-B7-A5TN 
       13.38        12.85         7.82        11.24        18.21         9.44 
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-6456 
        4.64         7.43         4.08         9.34         9.57        17.29 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 
       13.68        19.33        26.10        25.61        18.05        12.16 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7717 
       40.21        31.20        21.90         9.21        33.63        18.15 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       15.32         3.45         9.07        33.21        37.25        14.43 
TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 
        9.60         2.66        19.96         7.40        13.08        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       17.52         0.95        26.33        14.04         3.32        11.80 
TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 
        3.72        12.79         6.28        26.73        32.58         9.86 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4IZ 
       20.88        34.13         1.48        27.55        12.89         8.98 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 
       28.34        32.52         0.46        21.44        13.41        11.21 
TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8534 
       12.10        12.39        12.76        12.39        11.64        12.07 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-D7-6518 
       11.31        12.43        12.00         6.97         1.02        19.13 
TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-A4Z0 TCGA-D7-A6EX 
       18.54        17.85        16.80        17.19        14.76        11.31 
TCGA-D7-A6EY TCGA-D7-A748 TCGA-FP-7916 TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
       11.44         4.34        14.07        12.59         6.51        11.70 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8NB TCGA-VQ-A8E2 
        5.56        37.64         3.72         5.13        16.87        43.36 
TCGA-VQ-A8PD TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A928 
       16.31        23.41        15.65         9.73         2.01         5.72 
TCGA-VQ-A94P 
        2.66 

$subtype4
TCGA-IC-A6RF TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-KB-A93G 
       15.68        20.02        47.05        21.99        79.07        20.15 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3YB TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4OP 
       33.27        35.21         2.63        30.25        21.01         7.17 
TCGA-L5-A4OQ TCGA-L5-A4OU TCGA-L5-A88W TCGA-L7-A56G TCGA-LN-A49S TCGA-LN-A5U5 
        1.38        29.00        25.12        10.85        13.15         4.47 
TCGA-VR-AA4D TCGA-XP-A8T6 TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-6453 
       46.19        25.08         6.61        18.35         9.67        15.95 
TCGA-BR-6565 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A453 
        9.17         5.39         9.21        20.22         7.53         6.08 
TCGA-BR-A4CQ TCGA-BR-A4J2 TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-8525 TCGA-CG-4301 
       34.98        14.17        20.42        13.15        12.59         3.02 
TCGA-CG-4477 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 
       30.97         0.99         6.02        28.96         4.01        69.04 
TCGA-D7-5579 TCGA-D7-6818 TCGA-D7-A4YT TCGA-F1-A72C TCGA-FP-7998 TCGA-HU-A4GY 
       20.91        12.36        14.27        11.38        22.29         0.26 
TCGA-IN-8462 TCGA-IN-AB1V TCGA-RD-A7BS TCGA-RD-A8N0 TCGA-SW-A7EB TCGA-VQ-A8E7 
       18.81        15.75        11.05        40.64         5.79        37.41 
TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91X TCGA-VQ-AA6G TCGA-VQ-AA6K 
       17.85        13.35        73.41         9.50        26.04        12.43 
TCGA-ZA-A8F6 
       17.26 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.13     0.30     0.26 
subtype1 subtype2 subtype3 subtype4 
   77.29   122.30    52.57    79.07 
subtype1 subtype2 subtype3 subtype4 
  15.950   14.485   12.590   15.750 
[1] "0.1 - 77.3 (15.9)"  "0.1 - 122.3 (14.5)" "0.3 - 52.6 (12.6)" 
[4] "0.3 - 79.1 (15.8)" 
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       3        6       13        8        19        20         5
  subtype2       3        2       15        8        27        19         4
  subtype3       0        1        3       11        20        23        10
  subtype4       2        5        5        3         8         5         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         25         18         12        6         0
  subtype2         21         18          8        6         0
  subtype3         17         18         11       14         1
  subtype4         16          4          3       10         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           3        3        0        2
  STAGE IA          6        2        1        5
  STAGE IB         13       15        3        5
  STAGE II          8        8       11        3
  STAGE IIA        19       27       20        8
  STAGE IIB        20       19       23        5
  STAGE III         5        4       10        0
  STAGE IIIA       25       21       17       16
  STAGE IIIB       18       18       18        4
  STAGE IIIC       12        8       11        3
  STAGE IV          6        6       14       10
  STAGE IVA         0        0        1        0
[1] 12  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    13 40 60 29
  subtype2     6 40 66 23
  subtype3     5 16 75 37
  subtype4     8 15 24 14
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       13        6        5        8
  T2          40       40       16       15
  T3          60       66       75       24
  T4          29       23       37       14
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 46 43 28 20
  subtype2 58 36 20 19
  subtype3 43 46 16 27
  subtype4 24 20 10  8
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       46       58       43       24
  N1       43       36       46       20
  N2       28       20       16       10
  N3       20       19       27        8
[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"
D3V6, binary
          cls
clus         0   1
  subtype1 130   4
  subtype2 128   3
  subtype3 121  10
  subtype4  48   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  130    4
  subtype2  128    3
  subtype3  121   10
  subtype4   48    8
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      130      128      121       48
  1        4        3       10        8
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1  36 109
  subtype2  46  91
  subtype3  38  99
  subtype4  19  45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36  109
  subtype2   46   91
  subtype3   38   99
  subtype4   19   45
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       36       46       38       19
  MALE        109       91       99       45
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus         0   1
  subtype1  97  29
  subtype2  96  28
  subtype3 113  18
  subtype4  43  14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   97   29
  subtype2   96   28
  subtype3  113   18
  subtype4   43   14
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        97       96      113       43
  YES       29       28       18       14
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, continuous
D3V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    35                         3
  subtype2    29                         2
  subtype3    36                         0
  subtype4     9                         2
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    82
  subtype2                                         1    89
  subtype3                                         0    93
  subtype4                                         0    41
D3V11, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           35       29       36        9
  BLACK OR AFRICAN AMERICAN                        3        2        0        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0        0
  WHITE                                           82       89       93       41
[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"
D3V12, binary
          cls
clus         0   1
  subtype1   1  92
  subtype2   1  91
  subtype3   0 105
  subtype4   2  35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   92
  subtype2    1   91
  subtype3    0  105
  subtype4    2   35
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        0        2
  NOT HISPANIC OR LATINO       92       91      105       35
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2        0   1
  subtype1 151 103
  subtype2  70  37
  subtype3  53  43
subtype1 subtype2 subtype3 
     254      107       96 
subtype1 subtype2 subtype3 
     103       37       43 
$subtype1
TCGA-L5-A43I TCGA-L5-A43J TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OI TCGA-Q9-A6FU 
       18.28         4.31         8.94        24.00        19.99         5.16 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A8PU 
       20.02        47.05        21.99        22.98        16.24        27.35 
TCGA-VQ-A94U TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-2H-A9GR TCGA-IC-A6RE 
       26.93        25.78         5.92         4.21        32.45         7.69 
TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A4QS TCGA-IG-A51D TCGA-IG-A5B8 
       33.27        35.21         0.85         3.88        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A8O2 TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
       23.41         4.67        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A939 TCGA-L5-A43E TCGA-L5-A43H TCGA-L5-A4OH TCGA-L5-A4OJ 
       41.52        21.70        30.25         0.30        32.61        21.01 
TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88W 
       18.35         7.17         3.16         7.13         7.43        25.12 
TCGA-L5-A8NF TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NK TCGA-L5-A8NL TCGA-L5-A8NW 
        2.66        13.48        16.47        13.55        13.22        46.09 
TCGA-L7-A6VZ TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.36         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49Y 
       12.33        13.38        13.15        15.35        12.59        12.46 
TCGA-LN-A4A1 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4MQ TCGA-LN-A4MR TCGA-LN-A5U5 
       12.59        12.59        22.39        12.33        13.22         4.47 
TCGA-LN-A5U6 TCGA-LN-A5U7 TCGA-LN-A7HW TCGA-LN-A7HX TCGA-LN-A7HZ TCGA-LN-A8HZ 
       12.33        25.25        12.00        12.23        13.18        12.33 
TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FR TCGA-S8-A6BW TCGA-VR-A8EP TCGA-VR-A8Q7 
        0.13        12.03        12.26        20.38        27.09        52.27 
TCGA-VR-AA4D TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-Z6-A8JE TCGA-B7-A5TI TCGA-B7-A5TJ 
       46.19        25.08        41.23         2.10        19.56        11.01 
TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4253 TCGA-BR-4280 
        9.47         6.61         6.97        18.35         4.08         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6566 
       34.68        15.95        13.87        19.33         9.17        32.78 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 
       18.05        19.89        12.16        36.16        35.24        33.63 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8295 
       39.78        18.15        28.73         8.05        29.42         2.20 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8372 
       15.58         6.18        31.10         0.95         4.31        31.27 
TCGA-BR-8381 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        7.36        25.18         9.21        20.22        27.12         9.34 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A453 
       24.79        31.96        20.88         8.22        13.87         6.08 
TCGA-BR-A4CQ TCGA-BR-A4IV TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J8 
       34.98        28.57         0.72        14.17         0.53        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.65        20.42        16.14         5.13        13.02        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18        13.35        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        7.17        12.30        12.59        11.64        15.39        12.82 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
       12.43         6.31        11.61         6.58        12.20        11.77 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4438 TCGA-CG-4443 
       12.62         3.02        27.02        15.95        54.08        29.98 
TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5720 
       19.07         9.01        18.97         7.07        30.97         0.99 
TCGA-CG-5721 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
        6.02        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       69.04         7.99        25.71        12.66        20.91        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       18.84        18.61        13.35        10.26        15.22        12.79 
TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YY TCGA-D7-A6F0 
       12.36        24.72        18.21        21.14        13.78        22.29 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-HF-7132 TCGA-HF-7133 
       72.23        11.38        14.07        22.29        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4GQ TCGA-HU-A4GT 
       52.21        30.51        22.32        21.07         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-7806 
        6.58        20.25         0.26        12.95        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.45         3.39        18.38        13.35        19.53         6.74 
TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IP-7968 TCGA-RD-A7BS TCGA-RD-A8N0 TCGA-SW-A7EB 
       10.62        15.75         2.53        11.05        40.64         5.79 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
       48.79         5.46        43.36        21.73        37.41        38.14 
TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PS 
        2.50         2.70        17.85         1.87         9.27        13.35 
TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91U 
       29.59        73.41        11.70        61.22        18.74         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-A94O 
       42.64        60.85         9.50        55.56         4.54        21.04 
TCGA-VQ-AA64 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        28.41        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6K 
       16.14        12.43 

$subtype2
TCGA-JY-A6FB TCGA-L5-A4OG TCGA-CG-5727 TCGA-KB-A93G TCGA-2H-A9GI TCGA-IG-A3YC 
       60.39         4.70        79.07        20.15        14.30        20.12 
TCGA-IG-A4QT TCGA-IG-A50L TCGA-IG-A6QS TCGA-IG-A97H TCGA-JY-A6F8 TCGA-JY-A93F 
        9.30         0.53         9.96        14.50       122.10        24.03 
TCGA-L5-A43C TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A891 TCGA-L5-A8NE 
        3.16         1.38        58.59        29.00         3.75        55.50 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A4A2 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A8I1 
       21.37        10.85        12.49        12.85        15.52        13.18 
TCGA-M9-A5M8 TCGA-RE-A7BO TCGA-VR-A8EO TCGA-VR-A8EQ TCGA-Z6-A8JD TCGA-Z6-A9VB 
       33.11         7.00        25.81        22.82         3.42         1.32 
TCGA-Z6-AAPN TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TN TCGA-BR-4201 TCGA-BR-4257 
        2.66        26.70        11.70         9.44        30.90         9.67 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8060 
        6.18         9.57         8.98        30.90        44.94        11.44 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8382 TCGA-BR-8483 
       32.25         0.56        19.96         7.40        25.05         5.39 
TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4IZ 
       28.14         7.53        26.73        10.68         7.53         8.98 
TCGA-BR-A4PF TCGA-CD-5813 TCGA-CD-8528 TCGA-CD-8534 TCGA-CD-A487 TCGA-CG-4300 
        1.15        12.39        12.33        12.07        12.30        20.02 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4455 TCGA-CG-5718 TCGA-CG-5723 
        1.02         7.99         8.05        12.03        36.00       105.07 
TCGA-CG-5733 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8574 
       21.07        15.98        11.31        12.33        19.50        17.19 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A748 
       14.27        16.44        36.43        11.24        20.32         4.34 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-HJ-7597 TCGA-HU-8610 TCGA-HU-A4GF 
        7.99        14.47        21.27        26.47         0.76        25.81 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-AB1X TCGA-RD-A7BT TCGA-RD-A7C1 
       29.00        23.84        23.80        13.51         8.61        16.67 
TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8P3 
      122.30       115.69        19.04         0.92        18.48        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PX 
        7.73        46.26        16.31        22.19        12.79        64.57 
TCGA-VQ-A91S TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA6D TCGA-ZA-A8F6 
       32.88        66.81        42.54        17.13        17.26 

$subtype3
TCGA-IC-A6RF TCGA-L5-A8NT TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4P3 TCGA-IG-A625 
       15.68        27.12        20.78         2.63        18.64        12.82 
TCGA-JY-A93E TCGA-L5-A4OF TCGA-L5-A4OT TCGA-L5-A8NS TCGA-L5-A8NV TCGA-LN-A49W 
       25.22        26.33         4.90        13.41        52.57        13.25 
TCGA-LN-A49X TCGA-LN-A4A3 TCGA-LN-A4A9 TCGA-LN-A7HY TCGA-LN-A8I0 TCGA-LN-A9FQ 
       12.62        12.76        11.54        12.03        13.38        12.85 
TCGA-Q9-A6FW TCGA-VR-AA7B TCGA-X8-AAAR TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4255 
        7.82        11.24        18.21         4.64         7.43         4.08 
TCGA-BR-4256 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6801 
        9.34        17.29        13.68        26.10        25.61        40.21 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 
       31.20        21.90         9.21        15.32         3.45         9.07 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8289 
       29.56        33.21        37.25        14.43         9.60         2.66 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 
       13.08         0.26        22.19        17.52        26.33        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8682 
        3.32        11.80         3.72        12.79         6.28        32.58 
TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4J5 
        9.86        34.13         1.48        27.55        12.89        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 
        0.66        32.52         0.46        21.44        13.41        11.21 
TCGA-CD-8530 TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 
       12.39        11.31        12.43        12.00         6.97         1.02 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-8572 TCGA-D7-A4YV TCGA-D7-A4Z0 
       19.13        18.54        17.85        16.80         5.92        14.76 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-IN-8462 TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU 
       11.31        11.44        18.81        12.59         6.51        11.70 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8NB 
        5.56        37.64         3.72         5.13        37.91        16.87 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A94P 
       23.41        15.65         9.73         2.01         5.72         2.66 

subtype1 subtype2 subtype3 
    0.10     0.53     0.26 
subtype1 subtype2 subtype3 
   77.29   122.30    52.57 
subtype1 subtype2 subtype3 
  13.825   15.520   12.835 
[1] "0.1 - 77.3 (13.8)"  "0.5 - 122.3 (15.5)" "0.3 - 52.6 (12.8)" 
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       5       10       20       15        42        33        13
  subtype2       3        2       14        9        17        18         2
  subtype3       0        2        2        6        15        16         4
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         49         31         20       20         1
  subtype2         16         13          6        4         0
  subtype3         14         14          8       12         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           5        3        0
  STAGE IA         10        2        2
  STAGE IB         20       14        2
  STAGE II         15        9        6
  STAGE IIA        42       17       15
  STAGE IIB        33       18       16
  STAGE III        13        2        4
  STAGE IIIA       49       16       14
  STAGE IIIB       31       13       14
  STAGE IIIC       20        6        8
  STAGE IV         20        4       12
  STAGE IVA         1        0        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    22  63 128  55
  subtype2     6  36  45  20
  subtype3     4  12  52  28
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       22        6        4
  T2          63       36       12
  T3         128       45       52
  T4          55       20       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 96 89 42 37
  subtype2 44 25 18 17
  subtype3 31 31 14 20
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       96       44       31
  N1       89       25       31
  N2       42       18       14
  N3       37       17       20
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus         0   1
  subtype1 237  14
  subtype2 102   3
  subtype3  88   8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  237   14
  subtype2  102    3
  subtype3   88    8
   clus
vv  subtype1 subtype2 subtype3
  0      237      102       88
  1       14        3        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus         0   1
  subtype1  75 198
  subtype2  31  80
  subtype3  33  66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   75  198
  subtype2   31   80
  subtype3   33   66
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       75       31       33
  MALE        198       80       66
[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"
D4V8, binary
          cls
clus         0   1
  subtype1 183  58
  subtype2  83  19
  subtype3  83  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  183   58
  subtype2   83   19
  subtype3   83   12
     clus
vv    subtype1 subtype2 subtype3
  NO       183       83       83
  YES       58       19       12
[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"
D4V9, continuous
D4V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    71                         4
  subtype2    17                         3
  subtype3    21                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0   157
  subtype2                                         1    76
  subtype3                                         0    72
D4V11, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  ASIAN                                           71       17       21
  BLACK OR AFRICAN AMERICAN                        4        3        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                          157       76       72
[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"
D4V12, binary
          cls
clus         0   1
  subtype1   3 173
  subtype2   1  71
  subtype3   0  79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  173
  subtype2    1   71
  subtype3    0   79
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        0
  NOT HISPANIC OR LATINO      173       71       79
[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(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1 104  64
  subtype2 155 106
  subtype3  79  65
subtype1 subtype2 subtype3 
     168      261      144 
subtype1 subtype2 subtype3 
      64      106       65 
$subtype1
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T 
       15.68        34.85         4.31        24.00         4.70        22.82 
TCGA-L5-A88Y TCGA-Q9-A6FU TCGA-2H-A9GF TCGA-2H-A9GM TCGA-2H-A9GQ TCGA-IG-A3I8 
        0.36         5.16        25.78        13.94         4.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3Y9 TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 
       35.21         0.85        20.78         2.63        20.12        18.64 
TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS 
        0.53        17.03         0.79        23.41        12.82         9.96 
TCGA-IG-A8O2 TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FE 
        4.67        14.50        12.16        44.75        68.02         3.68 
TCGA-JY-A6FG TCGA-JY-A6FH TCGA-JY-A93F TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OM 
       41.52        47.38        24.03         6.28         0.30        47.93 
TCGA-L5-A4OS TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 
       58.59        15.48         2.60        25.12         7.40         3.75 
TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A56G 
        3.02        13.55        21.37         8.71        46.09        10.85 
TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
        5.92        10.45        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49V TCGA-LN-A49W TCGA-LN-A49X 
       13.38        13.15        15.35        12.59        13.25        12.62 
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 
       12.85        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ 
       13.18        12.33        13.38        13.18         0.13        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6DN TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.26        33.11         7.82         8.02        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-R6-A8WG 
        6.35        53.95         9.30        15.78         2.89        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        25.81        27.09 
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        33.70 
TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       18.18        52.27        18.05        11.24         9.17        15.91 
TCGA-X8-AAAR TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB 
       18.21        25.08        14.37         3.42         2.10         1.32 
TCGA-Z6-AAPN TCGA-ZR-A9CJ TCGA-BR-8295 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-A4IY 
        2.66        19.73         2.20        24.79        31.96        12.89 
TCGA-BR-A4J4 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A486 TCGA-CG-4443 
        0.53        12.59         7.17        12.82         6.31        29.98 
TCGA-CG-4449 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
       19.07        30.97         6.97       105.07        12.03        15.02 
TCGA-D7-6519 TCGA-D7-6525 TCGA-D7-6822 TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-F1-6875 
       20.55        13.35        12.33        20.32        22.29        72.23 
TCGA-HU-8602 TCGA-HU-A4H5 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
       22.32        23.80        18.81         3.39        12.46        19.53 
TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X 
       12.59         6.51        10.62        11.70        15.75        13.51 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A7BS TCGA-SW-A7EA TCGA-VQ-A8E3 TCGA-VQ-A8P5 
       18.21         8.52        11.05        19.04        21.73         7.73 
TCGA-VQ-A8PP TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6D 
       23.41        55.56         9.04        11.24        28.41        17.13 

$subtype2
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-L5-A4OI TCGA-L5-A8NG TCGA-S8-A6BV 
       60.39        18.28         8.94        19.99        35.97        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-2H-A9GG 
       47.05        21.99        16.24         0.23        27.35        20.05 
TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GN 
       31.27        14.30        58.55         7.63         5.92         8.94 
TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A93C 
       16.24        32.45         7.69         3.88       122.10        23.18 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OJ TCGA-L5-A4ON 
        3.16        30.25        26.33        32.61        21.01        18.35 
TCGA-L5-A4OP TCGA-L5-A4OQ TCGA-L5-A4OR TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A8NE 
        7.17         1.38         3.16         7.13         7.43        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NN 
        2.66        12.92        13.48        16.47         7.76         5.49 
TCGA-L5-A8NV TCGA-L7-A6VZ TCGA-R6-A6DQ TCGA-R6-A6KZ TCGA-R6-A6XG TCGA-R6-A8WC 
       52.57        10.36         7.59         5.06        38.40         2.30 
TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D 
        7.00        16.44         9.27         8.98        22.82        46.19 
TCGA-3M-AB46 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4191 
       58.03        11.70        19.56        11.01         9.44        18.35 
TCGA-BR-4253 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 
        4.08         9.67         6.18         6.61        34.68        32.78 
TCGA-BR-6802 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
       30.90        36.16        35.24        35.84        39.78        18.15 
TCGA-BR-7722 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 
       15.32         0.69        29.42        31.10         4.31        31.27 
TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       14.79        25.05         5.39        25.18         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44U 
        1.12        27.12        28.14         9.86         8.22        13.87 
TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        7.53         1.48         0.72        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       21.44        16.14         5.13        13.02        13.15        13.18 
TCGA-CD-5804 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
       12.10        12.33        12.30        11.64        15.39        12.43 
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-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5718 
       14.01         0.00         9.01        18.97         7.07        36.00 
TCGA-CG-5720 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        0.99        28.96        69.04         7.99        25.71        12.66 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YT 
       11.31        19.50        18.21        14.66        21.14        14.27 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-D7-A748 
       36.43        13.78        14.76        11.24        15.65         4.34 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       19.96         7.99        14.47        21.27        11.38         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF 
       19.53        17.06        13.58         0.56        11.08         5.52 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 
        6.21        77.29        63.06        52.21        30.51        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
        1.51         5.92        24.39        28.96        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        11.77        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51         6.58        20.25         2.10        12.95        29.00 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       23.84        21.17        14.07        15.68        33.40        36.36 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H 
       18.38        13.35         6.74         2.53        63.62        37.64 
TCGA-KB-A93J TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZI TCGA-R5-A7ZR 
       36.95        19.73        14.04        45.67        74.53         6.08 
TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-SW-A7EB TCGA-VQ-A8DT 
        9.24         8.61       122.30        57.44         5.79        48.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E7 TCGA-VQ-A8P2 
        5.46        13.25        13.02        18.48        37.41        38.14 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PE 
       37.22        30.97        34.29        46.26        16.31        22.19 
TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
        2.50        12.79         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N 
       64.57        39.45        11.70        21.83        61.22        18.74 
TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       20.81        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A923 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
        2.01         4.54         6.58        66.81        21.04        42.54 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       43.66        38.93        32.94        54.12        26.04        16.14 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$subtype3
TCGA-L5-A8NT TCGA-CG-4475 TCGA-KB-A93G TCGA-MX-A663 TCGA-VQ-A94U TCGA-IG-A4QT 
       27.12        22.98        20.15         9.86        26.93         9.30 
TCGA-IG-A7DP TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-L5-A4OO TCGA-L5-A4OT 
       14.86        21.70        31.56        25.22         3.32         4.90 
TCGA-L5-A4OU TCGA-L5-A8NL TCGA-L5-A8NS TCGA-L5-A8NU TCGA-LN-A9FP TCGA-B7-5816 
       29.00        13.22        13.41        83.24        12.03        26.70 
TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 
        9.47         4.64        30.90         4.08         9.34         9.57 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.87        17.29        13.68        19.33        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       26.10         9.17        25.61        18.05        19.89        12.16 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 
       40.21        31.20        44.94        21.90         9.21        33.63 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       28.73         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
       14.43        11.44        29.59         9.60        32.25         8.05 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 
        2.66        19.96        15.58         7.40        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
       22.19        17.52         0.95        26.33        14.04        11.80 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        7.36         3.72        12.79         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 
       26.73        32.58        20.88        10.68        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       27.55        28.57         8.98        14.17        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-5813 
       32.52        13.51         0.46        13.41        11.21        12.39 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-A487 
       12.76        12.53        12.39        12.59        12.07        12.30 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5721 
       11.31        12.43        11.77        12.00         1.02         6.02 
TCGA-CG-5722 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6818 
        0.99        19.13        18.84        18.54        18.61        12.36 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
       24.72        16.80        17.19        20.91        16.44         5.92 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       11.31        11.44         8.38        14.07        22.29        59.54 
TCGA-FP-8210 TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-IN-7808 TCGA-MX-A5UG 
        5.03        21.37         0.10         0.26         3.45         3.72 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        5.13        16.67        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8E2 TCGA-VQ-A8PQ 
       71.38         8.94        35.61        16.87        43.36        15.65 
TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA64 TCGA-ZA-A8F6 
        9.73        55.43         5.72         2.66        18.41        17.26 

subtype1 subtype2 subtype3 
    0.13     0.00     0.10 
subtype1 subtype2 subtype3 
  105.07   122.30   116.38 
subtype1 subtype2 subtype3 
  12.850   15.950   14.055 
[1] "0.1 - 105.1 (12.8)" "0.0 - 122.3 (15.9)" "0.1 - 116.4 (14.1)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       2        8       13        5        45        24        15
  subtype2       8       13       24       15        20        36        12
  subtype3       0        0        8       10        19        27         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         18         10          3        9         2
  subtype2         46         31         23       25         2
  subtype3         24         25         18       12         0
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        8        0
  STAGE IA          8       13        0
  STAGE IB         13       24        8
  STAGE II          5       15       10
  STAGE IIA        45       20       19
  STAGE IIB        24       36       27
  STAGE III        15       12        2
  STAGE IIIA       18       46       24
  STAGE IIIB       10       31       25
  STAGE IIIC        3       23       18
  STAGE IV          9       25       12
  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    19  51  77  13
  subtype2    34  54 115  59
  subtype3     1  25  77  48
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       19       34        1
  T2          51       54       25
  T3          77      115       77
  T4          13       59       48
[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 77 57 17  7
  subtype2 74 86 51 48
  subtype3 48 38 24 35
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       77       74       48
  N1       57       86       38
  N2       17       51       24
  N3        7       48       35
[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 138   9
  subtype2 226  18
  subtype3 138   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  138    9
  subtype2  226   18
  subtype3  138    9
   clus
vv  subtype1 subtype2 subtype3
  0      138      226      138
  1        9       18        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus         0   1
  subtype1  33 137
  subtype2  81 194
  subtype3  59  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33  137
  subtype2   81  194
  subtype3   59   95
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       33       81       59
  MALE        137      194       95
[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"
D5V8, binary
          cls
clus         0   1
  subtype1 118  39
  subtype2 187  54
  subtype3 121  22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  118   39
  subtype2  187   54
  subtype3  121   22
     clus
vv    subtype1 subtype2 subtype3
  NO       118      187      121
  YES       39       54       22
[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"
D5V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
      61        5        1 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [7] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[19] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[25] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[31] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[37] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[43] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[49] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[55] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[61] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
D5V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    53                         7
  subtype2    50                        10
  subtype3    30                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    89
  subtype2                                         1   167
  subtype3                                         0   117
D5V11, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  ASIAN                                           53       50       30
  BLACK OR AFRICAN AMERICAN                        7       10        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0
  WHITE                                           89      167      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"
D5V12, binary
          cls
clus         0   1
  subtype1   5 105
  subtype2   4 157
  subtype3   1 128
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  105
  subtype2    4  157
  subtype3    1  128
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        4        1
  NOT HISPANIC OR LATINO      105      157      128
[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 = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 62 61
  subtype2 71 41
  subtype3 60 30
  subtype4 79 42
  subtype5 66 61
subtype1 subtype2 subtype3 subtype4 subtype5 
     123      112       90      121      127 
subtype1 subtype2 subtype3 subtype4 subtype5 
      61       41       30       42       61 
$subtype1
TCGA-JY-A938 TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4460 TCGA-CG-4475 TCGA-MX-A663 
       34.85        35.97        27.12        21.99        22.98         9.86 
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        47.38 
TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A4OU TCGA-L5-A4OW 
       26.33         3.32         1.38        58.59        29.00         7.13 
TCGA-L5-A891 TCGA-L5-A8NI TCGA-L5-A8NN TCGA-L5-A8NR TCGA-L5-A8NS TCGA-LN-A49L 
        3.75        13.48         5.49         8.71        13.41        10.45 
TCGA-LN-A49V TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG 
       12.59         8.02         5.06         9.30        15.78        12.69 
TCGA-VR-A8EO TCGA-VR-A8Q7 TCGA-X8-AAAR TCGA-ZR-A9CJ TCGA-3M-AB46 TCGA-B7-A5TN 
       25.81        52.27        18.21        19.73        58.03         9.44 
TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       12.16         9.21        35.24        33.63        39.78        18.15 
TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8295 TCGA-BR-8373 
       28.73         3.45        11.44         0.69         2.20        14.79 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4IY 
        9.21        24.79         8.22         7.53         1.48        12.89 
TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-CD-5800 TCGA-CD-5804 TCGA-CD-8525 TCGA-CD-8526 
        0.72         0.66        13.15        12.10        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        7.17        15.39        12.82         6.31        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5718 
       12.20         4.01        29.98        19.07        18.97        36.00 
TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6818 
       12.03        15.02        20.55        18.84        13.35        12.36 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-A4YT TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-F1-6875 
       12.33        16.80        14.27        11.31        22.29        72.23 
TCGA-FP-7735 TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4H5 
        3.48        17.06         0.56        26.47         5.92        23.80 
TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H 
       33.40         3.39        11.70         2.53        63.62        37.64 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-RD-A7C1 TCGA-RD-A8MW 
       14.04        45.67         8.52        74.53        16.67        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        8.94         5.79         5.46        13.25        13.02        43.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PK TCGA-VQ-A91Q 
       37.22         7.73        22.19        12.79        17.85        20.81 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 
       55.56         9.04         5.72        21.04        11.24        18.41 
TCGA-VQ-AA6D TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       17.13        12.43         0.79 

$subtype2
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A43M TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-VQ-A8PU 
       60.39        18.28         8.94        16.24         0.23        27.35 
TCGA-2H-A9GH TCGA-2H-A9GJ TCGA-2H-A9GK TCGA-2H-A9GO TCGA-2H-A9GR TCGA-IC-A6RE 
       31.27        58.55         7.63        16.24        32.45         7.69 
TCGA-JY-A6F8 TCGA-JY-A939 TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A8NE 
      122.10        21.70        30.25        21.01        18.35        55.50 
TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NJ TCGA-L7-A6VZ TCGA-R6-A6DQ TCGA-R6-A6XG 
        2.66        12.92        16.47        10.36         7.59        38.40 
TCGA-V5-A7RE TCGA-V5-AASX TCGA-VR-A8EQ TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4267 
       16.44         8.98        22.82        19.56        18.35         6.18 
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7722 TCGA-BR-8058 TCGA-BR-8286 TCGA-BR-8296 
       34.68        30.90        15.32        37.25        29.42        15.58 
TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-8529 TCGA-CD-8532 
       25.18        12.79        20.65        20.42        12.30        11.64 
TCGA-CD-8536 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4462 
       12.43         3.02        15.95         1.02         8.05         0.00 
TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6527 
       28.96        69.04         7.99        18.54        17.85        10.26 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4Z0 
       12.79        11.31        18.21        14.66        21.14        14.76 
TCGA-D7-A6EV TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 
       11.24        19.96        11.38        13.58         6.21        77.29 
TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       63.06         1.51         0.76         5.59        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4H2 
        3.25        11.77        21.37         8.98        20.25        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RI TCGA-IN-A6RL 
       23.84        21.17        14.07        15.68        18.38        13.35 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-KB-A93J TCGA-MX-A5UJ TCGA-R5-A7ZR TCGA-R5-A805 
       19.53         6.74        36.95        19.73         6.08         9.24 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-VQ-A8DT TCGA-VQ-A8E0 TCGA-VQ-A8P8 
      122.30        40.64       115.69        48.79        18.48        30.97 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91E 
       46.26        16.31         2.70         1.87        64.57        21.83 
TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6A 
       18.74        42.64         4.54         6.58        43.66        38.93 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       54.12        26.04        16.14        27.55 

$subtype3
TCGA-L5-A4OI TCGA-CG-4444 TCGA-2H-A9GI TCGA-2H-A9GN TCGA-JY-A93C TCGA-L5-A4OH 
       19.99        47.05        14.30         8.94        23.18        32.61 
TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OX TCGA-L5-A8NM TCGA-R6-A8WC TCGA-RE-A7BO 
        7.17         3.16         7.43         7.76         2.30         7.00 
TCGA-V5-AASW TCGA-VR-AA4D TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-6565 
        9.27        46.19        11.01         9.67         6.61         9.17 
TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 
       32.78        40.21        44.94        36.16        35.84        29.59 
TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8483 
       32.25        31.10         4.31        31.27        25.05         5.39 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8690 
       20.22         1.12        28.14        31.96         9.86        10.68 
TCGA-BR-A44U TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 
       13.87         1.15        21.44        16.14         5.13        13.02 
TCGA-CD-8528 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 
       12.33         6.58        12.62        27.02         7.99        54.08 
TCGA-CG-4441 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5720 TCGA-D7-5578 TCGA-D7-6526 
       14.01         9.01         7.07         0.99        12.66        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A4YY TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6874 
       15.22        15.98        13.78        15.65         7.99        14.47 
TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7134 TCGA-HF-A5NB 
       21.27        19.53        11.08         5.52        52.21        30.51 
TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF 
       24.39        28.96        22.32        22.82        22.75        25.81 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-RD-A7BT TCGA-SW-A7EA 
       29.98         6.51         6.58        29.00         8.61        19.04 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8PB TCGA-VQ-A8PO TCGA-VQ-A91D TCGA-VQ-A91K 
       21.73        38.14        34.29         9.27        11.70        61.22 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A92D TCGA-VQ-AA6B 
       32.88         1.71         9.50        55.43        66.81        32.94 

$subtype4
TCGA-IC-A6RF TCGA-L5-A43J TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A88T TCGA-L5-A88Y 
       15.68         4.31        24.00         4.70        22.82         0.36 
TCGA-Q9-A6FU TCGA-S8-A6BV TCGA-2H-A9GM TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
        5.16        20.02        13.94        33.27        35.21         0.85 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A4QS TCGA-IG-A50L 
       20.78         2.63        20.12        18.64         3.88         0.53 
TCGA-IG-A51D TCGA-IG-A5B8 TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 
       17.03         0.79        23.41        12.82         9.96         4.67 
TCGA-IG-A97H TCGA-IG-A97I TCGA-JY-A6FA TCGA-JY-A6FD TCGA-JY-A6FG TCGA-JY-A93F 
       14.50        12.16        44.75        68.02        41.52        24.03 
TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88V TCGA-L5-A88W 
        6.28         0.30        47.93        15.48         2.60        25.12 
TCGA-L5-A88Z TCGA-L5-A893 TCGA-L5-A8NK TCGA-L5-A8NQ TCGA-L5-A8NV TCGA-L5-A8NW 
        7.40         3.02        13.55        21.37        52.57        46.09 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O TCGA-LN-A49P 
       10.85         5.92        12.66        12.43        13.41        12.33 
TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X TCGA-LN-A49Y 
       13.38        13.15        15.35        13.25        12.62        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        12.85 
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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-M9-A5M8 TCGA-Q9-A6FW TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XQ 
       12.26        33.11         7.82        16.31         7.04         6.35 
TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-S8-A6BW TCGA-V5-A7RB TCGA-V5-A7RC TCGA-V5-AASV 
       53.95         2.89        20.38         5.29         3.42        15.35 
TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       27.09        12.43         1.55        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I 
       33.70        18.18        18.05        11.24         9.17        15.91 
TCGA-XP-A8T6 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       25.08        14.37         3.42         2.10         1.32         2.66 
TCGA-CG-4477 TCGA-CG-5717 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RS 
       30.97         6.97        36.36        18.81        12.46        12.59 
TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-AB1V TCGA-IN-AB1X TCGA-R5-A7ZE TCGA-RD-A7BS 
        6.51        10.62        15.75        13.51        18.21        11.05 
TCGA-VQ-A8E7 
       37.41 

$subtype5
TCGA-KB-A93G TCGA-VQ-A94U TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A93D TCGA-JY-A93E 
       20.15        26.93         9.30        14.86        31.56        25.22 
TCGA-L5-A43C TCGA-L5-A4OT TCGA-L5-A8NL TCGA-L5-A8NU TCGA-B7-5816 TCGA-B7-5818 
        3.16         4.90        13.22        83.24        26.70        11.70 
TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 
        9.47         4.64        30.90         4.08         4.08         9.34 
TCGA-BR-4279 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        9.57        15.95        13.87        17.29        13.68        19.33 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6803 
       39.12        26.10        25.61        18.05        19.89        31.20 
TCGA-BR-7196 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8080 
       21.90         9.07        29.56        33.21        14.43         9.60 
TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 
        8.05         2.66        19.96         7.40        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
       22.19        17.52         0.95        26.33        14.04        11.80 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8676 
        7.36         3.72        27.12         9.34         6.28         7.53 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       26.73        32.58        20.88        34.13         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       28.57         8.98        14.17         0.53        28.34        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-5813 
       13.51         0.46        13.41        13.18        11.21        12.39 
TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-A487 TCGA-CD-A489 
       12.76        12.39        12.59        12.07        12.30        11.31 
TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       11.77        12.00         1.02         6.02         0.99       105.07 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 
       25.71        19.13        18.61        24.72        19.50        17.19 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6EY TCGA-D7-A6EZ 
       20.91        16.44         5.92        36.43        11.44        20.32 
TCGA-D7-A747 TCGA-D7-A748 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        8.38         4.34        14.07        22.29        59.54         5.03 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 
       21.07        24.30        24.26         0.10         0.26         2.10 
TCGA-IN-7808 TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        3.45         3.72         5.13       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8PF TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A91A 
       35.61        16.87         2.50        23.41        15.65        39.45 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-VQ-AA69 
       60.85         9.73         2.01         2.66        42.54        28.41 
TCGA-ZA-A8F6 
       17.26 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.56     0.00     0.99     0.13     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
   74.53   122.30    66.81    68.02   116.38 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.020   18.245   15.815   12.760   14.070 
[1] "0.6 - 74.5 (13.0)"  "0.0 - 122.3 (18.2)" "1.0 - 66.8 (15.8)" 
[4] "0.1 - 68.0 (12.8)"  "0.1 - 116.4 (14.1)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        2       12        7        14        18         9
  subtype2       6        5        6        9         6        18         4
  subtype3       2        7       13        3        12        16         3
  subtype4       2        6        6        2        40        18        11
  subtype5       0        1        8        9        12        17         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         22         12         10       11         1
  subtype2         16         14         10       11         2
  subtype3         13         11          8        6         0
  subtype4         11          8          2        5         1
  subtype5         26         21         14       13         0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        6        2        2        0
  STAGE IA          2        5        7        6        1
  STAGE IB         12        6       13        6        8
  STAGE II          7        9        3        2        9
  STAGE IIA        14        6       12       40       12
  STAGE IIB        18       18       16       18       17
  STAGE III         9        4        3       11        2
  STAGE IIIA       22       16       13       11       26
  STAGE IIIB       12       14       11        8       21
  STAGE IIIC       10       10        8        2       14
  STAGE IV         11       11        6        5       13
  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     4 31 67 23
  subtype2    22 23 42 25
  subtype3    11 22 38 24
  subtype4    16 35 59  4
  subtype5     1 19 63 44
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        4       22       11       16        1
  T2          31       23       22       35       19
  T3          67       42       38       59       63
  T4          23       25       24        4       44
[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 35 46 18 22
  subtype2 30 33 29 19
  subtype3 42 19 19 14
  subtype4 60 39 10  4
  subtype5 32 44 16 31
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       35       30       42       60       32
  N1       46       33       19       39       44
  N2       18       29       19       10       16
  N3       22       19       14        4       31
[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 106   8
  subtype2  96   9
  subtype3  89   3
  subtype4  97   6
  subtype5 114  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  106    8
  subtype2   96    9
  subtype3   89    3
  subtype4   97    6
  subtype5  114   10
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      106       96       89       97      114
  1        8        9        3        6       10
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  37  95
  subtype2  35  81
  subtype3  37  62
  subtype4  21 100
  subtype5  43  88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   95
  subtype2   35   81
  subtype3   37   62
  subtype4   21  100
  subtype5   43   88
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       37       35       37       21       43
  MALE         95       81       62      100       88
[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"
D6V8, binary
          cls
clus         0   1
  subtype1  94  22
  subtype2  76  26
  subtype3  69  16
  subtype4  82  32
  subtype5 105  19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94   22
  subtype2   76   26
  subtype3   69   16
  subtype4   82   32
  subtype5  105   19
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        94       76       69       82      105
  YES       22       26       16       32       19
[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"
D6V9, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       4        3        2       57        1 
 [1] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype1" "subtype4"
[13] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[19] "subtype1" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[25] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[37] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[43] "subtype2" "subtype4" "subtype2" "subtype1" "subtype4" "subtype2"
[49] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[55] "subtype4" "subtype1" "subtype4" "subtype4" "subtype4" "subtype4"
[61] "subtype4" "subtype4" "subtype4" "subtype4"
D6V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    21                         5
  subtype2    19                         4
  subtype3    19                         3
  subtype4    43                         5
  subtype5    31                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    85
  subtype2                                         0    69
  subtype3                                         1    61
  subtype4                                         0    65
  subtype5                                         0    93
D6V11, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           21       19       19       43
  BLACK OR AFRICAN AMERICAN                        5        4        3        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1        0
  WHITE                                           85       69       61       65
                                           clus
vv                                          subtype5
  ASIAN                                           31
  BLACK OR AFRICAN AMERICAN                        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0
  WHITE                                           93
[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"
D6V12, binary
          cls
clus         0   1
  subtype1   5  75
  subtype2   0  64
  subtype3   1  64
  subtype4   3  80
  subtype5   1 107
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   75
  subtype2    0   64
  subtype3    1   64
  subtype4    3   80
  subtype5    1  107
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            5        0        1        3        1
  NOT HISPANIC OR LATINO       75       64       64       80      107
[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_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  98  67
  subtype2 152 110
  subtype3 100  67
subtype1 subtype2 subtype3 
     165      262      167 
subtype1 subtype2 subtype3 
      67      110       67 
$subtype1
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43J TCGA-Q9-A6FU TCGA-CG-4460 TCGA-EQ-A4SO 
       15.68        34.85         4.31         5.16        21.99        16.24 
TCGA-2H-A9GF TCGA-2H-A9GL TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3I8 TCGA-IG-A3QL 
       25.78         5.92        16.24         4.21        33.27        35.21 
TCGA-IG-A3Y9 TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
        0.85        20.12        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        47.38        24.03 
TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A88V TCGA-L5-A88W TCGA-L5-A88Z 
       47.93         1.38        58.59         2.60        25.12         7.40 
TCGA-L5-A891 TCGA-L5-A8NE TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L7-A56G TCGA-LN-A49K 
        3.75        55.50        13.55         5.49        10.85         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        13.38        13.15 
TCGA-LN-A49U TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 
       15.35        12.62        12.46        12.59        12.49        12.76 
TCGA-LN-A4A4 TCGA-LN-A4A6 TCGA-LN-A4A8 TCGA-LN-A4A9 TCGA-LN-A4MQ TCGA-LN-A4MR 
       12.59        12.85        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-R6-A6DN TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6L6 
       12.85        12.26         8.02         5.06        16.31         7.04 
TCGA-R6-A6XQ TCGA-R6-A6Y2 TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW TCGA-V5-A7RB 
        6.35         9.30        15.78        12.69        20.38         5.29 
TCGA-V5-A7RC TCGA-V5-AASV TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8ET 
        3.42        15.35        25.81        27.09        12.43         1.55 
TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 
       18.31         8.12        28.11        33.70        18.18        52.27 
TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 
       18.05        11.24         9.17        15.91        25.08        41.23 
TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-ZR-A9CJ 
       14.37         3.42         2.10         1.32         2.66        19.73 
TCGA-BR-6709 TCGA-BR-7723 TCGA-BR-8295 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-A452 
       12.16        28.73         2.20         7.53        24.79         7.53 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8526 
        1.48        12.89         0.72        13.15        13.35        12.53 
TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CG-4449 TCGA-CG-5724 
       12.59        12.82         6.31        12.30        19.07        12.03 
TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YV 
       15.02        20.55        12.33        24.72        19.50         5.92 
TCGA-D7-A6F0 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4GH 
       22.29        18.15        22.32        24.26        25.81        11.77 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI 
        2.10        29.00        23.80        33.40         3.39        18.38 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
       12.59        10.62        63.62        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 
        8.52        37.91        13.25        13.02        43.36         7.73 
TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A91Z TCGA-VQ-A922 
       12.79         2.70        17.85        23.41        55.56         9.04 
TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6D 
       11.24        28.41        17.13 

$subtype2
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y 
       60.39        18.28        24.00         4.70        19.99         0.36 
TCGA-S8-A6BV TCGA-CG-4444 TCGA-CG-5727 TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-VQ-A94U 
       20.02        47.05        79.07         0.23        27.35        26.93 
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-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OH 
        8.94         3.88       122.10        23.18        30.25        32.61 
TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT TCGA-L5-A4OW 
       21.01        18.35         7.17         3.16         4.90         7.13 
TCGA-L5-A4OX TCGA-L5-A8NF TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ TCGA-L5-A8NL 
        7.43         2.66        12.92        13.48        16.47        13.22 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DQ 
        7.76         8.71        46.09        10.36        33.11         7.59 
TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC TCGA-RE-A7BO TCGA-V5-A7RE 
       38.40        53.95         2.89         2.30         7.00        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-3M-AB46 
        9.27         8.98        22.82        46.19        18.21        58.03 
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-4253 TCGA-BR-4257 TCGA-BR-4267 
        6.97        18.35        30.90         4.08         9.67         6.18 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 
        6.61        34.68        15.95        13.87        19.33        32.78 
TCGA-BR-6707 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       19.89        30.90        44.94        36.16        35.24        35.84 
TCGA-BR-7722 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       15.32        29.56         0.69        29.59        32.25         8.05 
TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
       29.42        15.58         6.18        31.10        13.08         0.26 
TCGA-BR-8368 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        4.31        31.27        25.05         5.39        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-8687 TCGA-BR-8690 
       20.22         1.12        27.12        31.96         8.22        10.68 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       13.87        34.98        20.65        20.42         1.15        16.14 
TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8528 TCGA-CD-8533 
        5.13        13.02        13.18        12.39        12.33        15.39 
TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MJ TCGA-CG-4300 
       12.43        11.61         6.58        12.20        12.62        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 
       54.08         4.01        14.01        29.98        12.03         0.00 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5726 
        9.01        18.97         7.07        36.00         0.99        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6524 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-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT 
       12.79        11.31        17.19        18.21        14.66        14.27 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A 
       36.43        13.78        11.24        20.32        15.65        19.96 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 
       14.47        72.23        21.27        19.53        17.06        13.58 
TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
        0.56        11.08         5.52         6.21        77.29        63.06 
TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
       52.21        30.51        26.47         1.51         5.92        24.39 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       28.96        22.82        21.07         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GN TCGA-HU-A4GP 
       22.68        24.20         3.25        22.75        29.98         8.98 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
        6.51         6.58        20.25        12.95        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RP 
       14.07        15.68         3.45        18.81        13.35         6.44 
TCGA-IN-A6RR TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93J TCGA-R5-A7ZI 
        6.74        13.51         2.53         5.56        36.95        74.53 
TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-SW-A7EA 
        6.08         4.60         9.24        16.67       122.30        19.04 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E3 
        5.79         0.92        48.79         5.46        18.48        21.73 
TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       37.41        38.14        37.22        34.29        46.26        16.31 
TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PX 
       22.19         2.50         1.87         9.27        15.65        64.57 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q 
       39.45        11.70        21.83        61.22        18.74        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 
       32.88         1.71        42.64        60.85         9.50         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94R 
       55.43         4.54         6.58        66.81        21.04        42.54 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        38.93        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       16.14        27.55        12.43         0.79 

$subtype3
TCGA-L5-A43M TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4475 TCGA-MX-A663 
        8.94        22.82        35.97        27.12        22.98         9.86 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A7DP 
       32.45         7.69        20.78         2.63         9.30        14.86 
TCGA-JY-A939 TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43C TCGA-L5-A43H 
       21.70        31.56        25.22         6.28         3.16         0.30 
TCGA-L5-A4OF TCGA-L5-A4OO TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A893 TCGA-L5-A8NQ 
       26.33         3.32        29.00        15.48         3.02        21.37 
TCGA-L5-A8NS TCGA-L5-A8NU TCGA-L5-A8NV TCGA-LN-A49P TCGA-LN-A49W TCGA-LN-A4A5 
       13.41        83.24        52.57        12.33        13.25        22.39 
TCGA-LN-A9FP TCGA-Q9-A6FW TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4255 
       12.03         7.82         9.47         4.64         7.43         4.08 
TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        9.34         9.57        17.29        13.68        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
        9.17        25.61        18.05         8.98        40.21        31.20 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 
       21.90         9.21        33.63        39.78        18.15         3.45 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 
        9.07        33.21        37.25        14.43        11.44         9.60 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 
        0.56         2.66        19.96         7.40        22.19        17.52 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 
        0.95        26.33        14.04         3.32        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        7.36         3.72        12.79         9.34        28.14         6.28 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 
       26.73        32.58         9.86        20.88        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       27.55        28.57         8.98        14.17         0.53        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 
        0.66        32.52        13.51         0.46        21.44        13.41 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 
       11.21        12.10        12.76        12.59         7.17        12.30 
TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI 
       12.39        11.64        12.07        11.31        12.43        11.77 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5722 
       12.00        30.97         6.97         1.02         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5728 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
      105.07        65.10        20.91        19.13        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6818 TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       18.61        12.36        16.80        21.14        20.91        16.44 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 
       14.76        26.43        11.31        11.44         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
        7.13         0.62         7.99        11.38         3.48        14.07 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GY 
       22.29        59.54         5.03        21.37         0.10         0.26 
TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
       36.36        12.46        19.53         6.51        11.70        15.75 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 
        3.72        19.73        11.05         5.13        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-VQ-A8P8 TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P TCGA-ZA-A8F6 
       30.97         9.73         5.72         2.66        17.26 

subtype1 subtype2 subtype3 
    0.13     0.00     0.10 
subtype1 subtype2 subtype3 
   68.02   122.30   116.38 
subtype1 subtype2 subtype3 
   12.85    16.06    13.25 
[1] "0.1 - 68.0 (12.8)"  "0.0 - 122.3 (16.1)" "0.1 - 116.4 (13.2)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        5       10        4        42        24        14
  subtype2       8       13       25       17        21        36        11
  subtype3       1        3       11       12        24        26         4
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         18         15          6       11         3
  subtype2         48         33         24       21         1
  subtype3         28         22         16       16         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        8        1
  STAGE IA          5       13        3
  STAGE IB         10       25       11
  STAGE II          4       17       12
  STAGE IIA        42       21       24
  STAGE IIB        24       36       26
  STAGE III        14       11        4
  STAGE IIIA       18       48       28
  STAGE IIIB       15       33       22
  STAGE IIIC        6       24       16
  STAGE IV         11       21       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    13  44  82  19
  subtype2    34  61 117  56
  subtype3     8  30  81  48
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       13       34        8
  T2          44       61       30
  T3          82      117       81
  T4          19       56       48
[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 67 57 15 15
  subtype2 83 81 54 46
  subtype3 55 48 28 34
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       67       83       55
  N1       57       81       48
  N2       15       54       28
  N3       15       46       34
[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 134  12
  subtype2 235  16
  subtype3 150  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  134   12
  subtype2  235   16
  subtype3  150   11
   clus
vv  subtype1 subtype2 subtype3
  0      134      235      150
  1       12       16       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  32 135
  subtype2  89 192
  subtype3  61 111
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32  135
  subtype2   89  192
  subtype3   61  111
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       32       89       61
  MALE        135      192      111
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus         0   1
  subtype1 117  38
  subtype2 192  50
  subtype3 134  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  117   38
  subtype2  192   50
  subtype3  134   28
     clus
vv    subtype1 subtype2 subtype3
  NO       117      192      134
  YES       38       50       28
[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"
D7V9, continuous
D7V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    60                         7    82
  subtype2    37                         9   184
  subtype3    36                         2   121
D7V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           60       37       36
  BLACK OR AFRICAN AMERICAN        7        9        2
  WHITE                           82      184      121
[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, binary
          cls
clus         0   1
  subtype1   7 106
  subtype2   3 162
  subtype3   1 136
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  106
  subtype2    3  162
  subtype3    1  136
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        3        1
  NOT HISPANIC OR LATINO      106      162      136
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 64 57
  subtype2 80 56
  subtype3 96 59
  subtype4 65 29
  subtype5 45 43
subtype1 subtype2 subtype3 subtype4 subtype5 
     121      136      155       94       88 
subtype1 subtype2 subtype3 subtype4 subtype5 
      57       56       59       29       43 
$subtype1
TCGA-L5-A43I TCGA-CG-4460 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-2H-A9GF 
       18.28        21.99        79.07         0.23         9.86        25.78 
TCGA-2H-A9GG TCGA-2H-A9GJ TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A4QS TCGA-JY-A6FH 
       20.05        58.55        16.24         4.21         3.88        47.38 
TCGA-L5-A4OF TCGA-L5-A4OH TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A891 TCGA-L5-A8NE 
       26.33        32.61         1.38        58.59         3.75        55.50 
TCGA-L5-A8NF TCGA-L5-A8NN TCGA-L7-A6VZ TCGA-R6-A6KZ TCGA-R6-A6Y2 TCGA-R6-A8W5 
        2.66         5.49        10.36         5.06         9.30        15.78 
TCGA-R6-A8WG TCGA-ZR-A9CJ TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7197 
       12.69        19.73         9.44        17.29         9.17         9.21 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       39.78        28.73         3.45        14.43        11.44         0.69 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 
        2.66         2.20         7.40        14.79         5.39         9.21 
TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4J1 
        9.34        24.79         8.22        10.68         7.53         0.72 
TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       20.65        13.15        13.35        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 
        7.17        12.30        12.39        12.82         6.31        12.30 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4306 TCGA-CG-4438 TCGA-CG-4449 TCGA-CG-4466 
       12.20        20.02         1.02        54.08        19.07        18.97 
TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6520 TCGA-D7-6526 
       36.00        15.02         4.01        69.04        18.84        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       10.26        15.98        12.36        11.31        12.33        16.80 
TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8631 
       21.14         5.92        22.29         7.99        17.06         0.56 
TCGA-HF-7133 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H2 
       63.06        28.96        22.75        25.81        11.77        12.95 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RL TCGA-KB-A6F5 TCGA-KB-A6F7 
       23.80        33.40        18.38        13.35         5.56        63.62 
TCGA-KB-A93J TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-RD-A8MW 
       36.95        19.73        14.04        45.67         8.52        37.91 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 
        8.94         5.79         5.46        13.25        13.02        18.48 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       43.36         7.73        22.19        12.79         2.70        17.85 
TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6A TCGA-VQ-AA6D 
       18.74        55.56         9.04        21.04        38.93        17.13 
TCGA-ZQ-A9CR 
        0.79 

$subtype2
TCGA-JY-A6FB TCGA-JY-A938 TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y 
       60.39        34.85        24.00         4.70        19.99         0.36 
TCGA-S8-A6BV TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI 
       20.02        16.24        27.35        26.93        31.27        14.30 
TCGA-2H-A9GK TCGA-2H-A9GL TCGA-2H-A9GM TCGA-2H-A9GN TCGA-JY-A6F8 TCGA-JY-A93C 
        7.63         5.92        13.94         8.94       122.10        23.18 
TCGA-L5-A43C TCGA-L5-A43E TCGA-L5-A4OJ TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
        3.16        30.25        21.01        18.35         7.17         3.16 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A8NH TCGA-L5-A8NI TCGA-L5-A8NJ 
        7.13         7.43         2.60        12.92        13.48        16.47 
TCGA-L5-A8NM TCGA-L5-A8NR TCGA-L5-A8NW TCGA-M9-A5M8 TCGA-R6-A6DN TCGA-R6-A6L4 
        7.76         8.71        46.09        33.11         8.02        16.31 
TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-R6-A8WC 
        7.04        38.40         6.35        53.95         2.89         2.30 
TCGA-RE-A7BO TCGA-V5-A7RB TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ 
        7.00         5.29        16.44         9.27         8.98        22.82 
TCGA-VR-AA4D TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-BR-4257 TCGA-BR-4280 TCGA-BR-7704 
       46.19        58.03        11.01         9.67         6.61        35.24 
TCGA-BR-7707 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 
       35.84        29.42         6.18        31.10         4.31         1.12 
TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4PE TCGA-BR-A4PF 
       31.96        13.87        34.98         1.48        20.42         1.15 
TCGA-BR-A4QL TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG 
       16.14        12.33        15.39        12.43        11.61         6.58 
TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4465 TCGA-CG-4469 
       12.62        15.95         7.99         4.01         9.01         7.07 
TCGA-D7-5578 TCGA-D7-6528 TCGA-D7-A4YT TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-D7-A74A 
       12.66        15.22        14.27        11.24        15.65        19.96 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-HF-7134 
       14.47        72.23        19.53        11.08         5.52        52.21 
TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       30.51         5.92        24.39        18.15        22.32        22.82 
TCGA-HU-8610 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GT 
        0.76        22.68        24.20         3.25        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H8 TCGA-IN-A6RP TCGA-IN-A6RR 
        6.58        29.00        23.84        14.07         6.44         6.74 
TCGA-IN-A6RS TCGA-IP-7968 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 
       12.59         2.53        18.21         6.08         9.24        16.67 
TCGA-RD-A8N5 TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       57.44        48.79        21.73        37.41        38.14        37.22 
TCGA-VQ-A8PB TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91Q 
       34.29         1.87         9.27        39.45        11.70        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X TCGA-VQ-A92D TCGA-VQ-A94R 
       32.88         1.71        42.64         9.50        66.81        42.54 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6B TCGA-VQ-AA6K 
       11.24        18.41        32.94        12.43 

$subtype3
TCGA-L5-A43M TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-CG-4444 TCGA-CG-4475 
        8.94        22.82        35.97        27.12        47.05        22.98 
TCGA-2H-A9GR TCGA-IC-A6RE TCGA-IG-A4QT TCGA-JY-A6FE TCGA-JY-A939 TCGA-L5-A4OO 
       32.45         7.69         9.30         3.68        21.70         3.32 
TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NL TCGA-L5-A8NU TCGA-L5-A8NV 
        4.90        29.00         3.02        13.22        83.24        52.57 
TCGA-Q9-A6FW TCGA-R6-A6DQ TCGA-VR-A8ET TCGA-X8-AAAR TCGA-B7-5816 TCGA-B7-5818 
        7.82         7.59         1.55        18.21        26.70        11.70 
TCGA-B7-A5TI TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 
       19.56         6.61         6.97        18.35        30.90         4.08 
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 
        6.18        34.68        15.95        13.87        19.33        32.78 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 
       19.89        12.16         8.98        30.90        44.94        36.16 
TCGA-BR-7722 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 
       15.32        29.56        37.25        29.59        32.25         8.05 
TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8372 
        0.56        19.96        15.58         0.26         0.95        31.27 
TCGA-BR-8381 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 
        7.36        25.18        20.22        27.12        28.14         7.53 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5813 
        0.53         0.66         5.13        13.02        13.18        12.39 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 TCGA-CG-4441 
       12.59        11.64         3.02        27.02         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 
       29.98        12.03         0.00        30.97         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5733 
        6.02         0.99       105.07        12.03        28.96        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6525 
        7.99        25.71        20.55        18.54        17.85        13.35 
TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.79        24.72        19.50        17.19        18.21        14.66 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EZ TCGA-F1-A448 TCGA-F1-A72C 
       36.43        13.78        14.76        20.32        21.27        11.38 
TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8608 
       13.58         6.21        77.29        26.47         1.51        21.07 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX 
       24.30         5.59        24.26        21.37         8.98        20.25 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
        0.26         2.10        21.17        15.68        36.36         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NR TCGA-IN-A7NU 
       18.81         3.39        12.46        19.53         6.51        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8MV 
       15.75        13.51        74.53         4.60        11.05       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8PC TCGA-VQ-A8PD 
       40.64       115.69        19.04         0.92        46.26        16.31 
TCGA-VQ-A8PF TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PX TCGA-VQ-A91E TCGA-VQ-A91K 
        2.50        23.41        15.65        64.57        21.83        61.22 
TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA68 
       60.85         2.01        55.43         4.54         6.58        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       28.41        54.12        26.04        16.14        27.55 

$subtype4
TCGA-IC-A6RF TCGA-L5-A43J TCGA-Q9-A6FU TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       15.68         4.31         5.16        33.27        35.21         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-A6FG TCGA-JY-A93F TCGA-KH-A6WC 
       12.16        44.75        68.02        41.52        24.03         6.28 
TCGA-L5-A43H TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK 
        0.30        47.93        15.48        25.12         7.40        13.55 
TCGA-L5-A8NQ TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N 
       21.37        10.85         5.92        10.45        12.66        12.43 
TCGA-LN-A49O TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W 
       13.41        12.33        13.38        13.15        15.35        13.25 
TCGA-LN-A49X TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A3 TCGA-LN-A4A4 
       12.62        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        12.85        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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO 
       12.03        13.18        12.33        13.38        13.18         0.13 
TCGA-LN-A9FP TCGA-LN-A9FQ TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-V5-AASV 
       12.03        12.85        12.26        20.38         3.42        15.35 
TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU TCGA-VR-A8EW TCGA-VR-A8EX 
       25.81        27.09        12.43        18.31         8.12        28.11 
TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D 
       33.70        18.18        52.27        18.05        11.24         9.17 
TCGA-VR-AA7I TCGA-XP-A8T6 TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE 
       15.91        25.08        41.23        14.37         3.42         2.10 
TCGA-Z6-A9VB TCGA-Z6-AAPN TCGA-BR-A4IY TCGA-IN-A7NT 
        1.32         2.66        12.89        10.62 

$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-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-6457 TCGA-BR-6563 
        7.43         4.08         9.34         9.57        13.68        39.12 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 
       26.10        25.61        18.05        40.21        31.20        21.90 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8362 
       33.63        18.15         9.07        33.21         9.60        13.08 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       22.19        17.52        26.33        14.04         3.32        11.80 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 
       25.05         3.72        12.79         6.28        26.73        32.58 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        9.86        20.88        34.13         6.08        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        8.98        14.17        28.34        32.52        13.51         0.46 
TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8534 TCGA-CD-A489 
       21.44        13.41        11.21        12.10        12.07        11.31 
TCGA-CD-A48A TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5728 TCGA-D7-5579 
       12.43        11.77        12.00         1.02        65.10        20.91 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET TCGA-D7-A6EX 
       19.13        18.61        20.91        16.44        26.43        11.31 
TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-FP-7735 
       11.44         8.38         4.34         7.13         0.62         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ TCGA-MX-A5UG 
       14.07        22.29        59.54         5.03         0.10         3.72 
TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8P8 
        5.13       116.38        71.38        35.61        16.87        30.97 
TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P TCGA-ZA-A8F6 
        9.73         5.72         2.66        17.26 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.23     0.36     0.00     0.13     0.10 
subtype1 subtype2 subtype3 subtype4 subtype5 
   79.07   122.10   122.30    68.02   116.38 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.150   14.385   16.310   12.835   13.860 
[1] "0.2 - 79.1 (13.2)"  "0.4 - 122.1 (14.4)" "0.0 - 122.3 (16.3)"
[4] "0.1 - 68.0 (12.8)"  "0.1 - 116.4 (13.9)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       3        1        9       11         7        19         5
  subtype2       6        9       17        6        10        19        11
  subtype3       1        8        9       10        21        24         3
  subtype4       0        3        4        1        39        15        10
  subtype5       0        0        7        5        10         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         25         11         12       14         3
  subtype2         15         16          9        8         0
  subtype3         28         22         12       14         0
  subtype4          9          5          2        3         1
  subtype5         17         16         11        9         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           3        6        1        0        0
  STAGE IA          1        9        8        3        0
  STAGE IB          9       17        9        4        7
  STAGE II         11        6       10        1        5
  STAGE IIA         7       10       21       39       10
  STAGE IIB        19       19       24       15        9
  STAGE III         5       11        3       10        0
  STAGE IIIA       25       15       28        9       17
  STAGE IIIB       11       16       22        5       16
  STAGE IIIC       12        9       12        2       11
  STAGE IV         14        8       14        3        9
  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 30 57 29
  subtype2    26 26 55 24
  subtype3    14 36 78 33
  subtype4     8 31 48  5
  subtype5     0 12 42 32
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        7       26       14        8        0
  T2          30       26       36       31       12
  T3          57       55       78       48       42
  T4          29       24       33        5       32
[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 29 43 25 22
  subtype2 50 40 21 17
  subtype3 47 52 35 27
  subtype4 53 29  6  3
  subtype5 26 22 10 26
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       29       50       47       53       26
  N1       43       40       52       29       22
  N2       25       21       35        6       10
  N3       22       17       27        3       26
[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 101  12
  subtype2 114   5
  subtype3 145  12
  subtype4  82   4
  subtype5  77   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  101   12
  subtype2  114    5
  subtype3  145   12
  subtype4   82    4
  subtype5   77    6
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      101      114      145       82       77
  1       12        5       12        4        6
[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  37  91
  subtype2  40 104
  subtype3  54 111
  subtype4  16  78
  subtype5  35  54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   91
  subtype2   40  104
  subtype3   54  111
  subtype4   16   78
  subtype5   35   54
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       37       40       54       16       35
  MALE         91      104      111       78       54
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus         0   1
  subtype1  93  21
  subtype2  99  28
  subtype3 118  25
  subtype4  56  32
  subtype5  77  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93   21
  subtype2   99   28
  subtype3  118   25
  subtype4   56   32
  subtype5   77   10
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        93       99      118       56       77
  YES       21       28       25       32       10
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype5"              
clus
subtype2 subtype3 subtype4 subtype5 
       6        1       59        1 
 [1] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
 [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[13] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[19] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[25] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[31] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[37] "subtype4" "subtype4" "subtype4" "subtype2" "subtype4" "subtype2"
[43] "subtype4" "subtype2" "subtype2" "subtype4" "subtype4" "subtype2"
[49] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[55] "subtype4" "subtype2" "subtype4" "subtype4" "subtype4" "subtype4"
[61] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
D8V10, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       9       21       12       54        1 
 [1] "subtype4" "subtype1" "subtype4" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype4" "subtype3"
[13] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype3"
[19] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[25] "subtype3" "subtype4" "subtype1" "subtype4" "subtype2" "subtype2"
[31] "subtype4" "subtype1" "subtype4" "subtype2" "subtype3" "subtype2"
[37] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
[43] "subtype2" "subtype3" "subtype1" "subtype1" "subtype4" "subtype1"
[49] "subtype4" "subtype2" "subtype2" "subtype4" "subtype4" "subtype4"
[55] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[61] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[67] "subtype4" "subtype4" "subtype2" "subtype3" "subtype2" "subtype2"
[73] "subtype2" "subtype1" "subtype1" "subtype2" "subtype2" "subtype2"
[79] "subtype2" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[85] "subtype4" "subtype4" "subtype4" "subtype4" "subtype4" "subtype4"
[91] "subtype4" "subtype3" "subtype4" "subtype4" "subtype4" "subtype4"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    22                         4    77
  subtype2    25                         5    91
  subtype3    19                         2   116
  subtype4    45                         5    41
  subtype5    22                         2    62
D8V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           22       25       19       45       22
  BLACK OR AFRICAN AMERICAN        4        5        2        5        2
  WHITE                           77       91      116       41       62
[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"
D8V12, binary
          cls
clus         0   1
  subtype1   3  77
  subtype2   2  78
  subtype3   2 106
  subtype4   3  65
  subtype5   1  78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   77
  subtype2    2   78
  subtype3    2  106
  subtype4    3   65
  subtype5    1   78
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        2        2        3        1
  NOT HISPANIC OR LATINO       77       78      106       65       78
[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(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 67 55
  subtype2 94 61
  subtype3 72 48
  subtype4 25 20
  subtype5 41 29
subtype1 subtype2 subtype3 subtype4 subtype5 
     122      155      120       45       70 
subtype1 subtype2 subtype3 subtype4 subtype5 
      55       61       48       20       29 
$subtype1
TCGA-IC-A6RF TCGA-JY-A938 TCGA-L5-A43I TCGA-L5-A43J TCGA-Q9-A6FU TCGA-2H-A9GF 
       15.68        34.85        18.28         4.31         5.16        25.78 
TCGA-2H-A9GG TCGA-2H-A9GL TCGA-2H-A9GN TCGA-2H-A9GO TCGA-2H-A9GQ TCGA-IG-A3I8 
       20.05         5.92         8.94        16.24         4.21        33.27 
TCGA-IG-A3QL TCGA-IG-A3YC TCGA-IG-A4P3 TCGA-IG-A50L TCGA-IG-A51D TCGA-IG-A5B8 
       35.21        20.12        18.64         0.53        17.03         0.79 
TCGA-IG-A5S3 TCGA-IG-A625 TCGA-IG-A6QS TCGA-IG-A8O2 TCGA-IG-A97H TCGA-JY-A6FA 
       23.41        12.82         9.96         4.67        14.50        44.75 
TCGA-JY-A6FE TCGA-JY-A6FG TCGA-L5-A4OM TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A88V 
        3.68        41.52        47.93         1.38        58.59         2.60 
TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A891 TCGA-L5-A8NK TCGA-L5-A8NN TCGA-L7-A56G 
       25.12         7.40         3.75        13.55         5.49        10.85 
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        13.38        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        12.85 
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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FQ TCGA-R6-A6DN 
       12.33        13.38        13.18         0.13        12.85         8.02 
TCGA-R6-A6KZ TCGA-R6-A6L4 TCGA-R6-A6XQ TCGA-R6-A8W5 TCGA-R6-A8WG TCGA-S8-A6BW 
        5.06        16.31         6.35        15.78        12.69        20.38 
TCGA-V5-A7RB TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER TCGA-VR-A8EU 
        5.29         3.42        25.81        27.09        12.43        18.31 
TCGA-VR-A8EW TCGA-VR-A8EX TCGA-VR-A8EY TCGA-VR-A8EZ TCGA-VR-A8Q7 TCGA-VR-AA7B 
        8.12        28.11        33.70        18.18        52.27        11.24 
TCGA-VR-AA7D TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
        9.17        41.23        14.37         2.10         1.32         2.66 
TCGA-BR-8295 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 
        2.20         7.53        24.79         7.53         1.48         0.72 
TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-D7-A4YT TCGA-D7-A6F0 
       12.59        12.82         6.31        12.30        14.27        22.29 
TCGA-HU-A4GH TCGA-HU-A4H5 TCGA-IN-8663 TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A666 
       11.77        23.80         3.39        10.62        63.62        14.04 
TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8PH 
       18.21         8.52        37.91        13.25        43.36        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94T 
        2.70        17.85        55.56         9.04        21.04        11.24 
TCGA-VQ-AA69 TCGA-VQ-AA6D 
       28.41        17.13 

$subtype2
TCGA-JY-A6FB TCGA-L5-A43M TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y 
       60.39         8.94        24.00         4.70        19.99         0.36 
TCGA-S8-A6BV TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        27.35        26.93        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-IG-A4QS TCGA-JY-A6F8 TCGA-JY-A6FH TCGA-JY-A93C 
        7.63        13.94         3.88       122.10        47.38        23.18 
TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR TCGA-L5-A4OT 
       30.25        32.61        18.35         7.17         3.16         4.90 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A893 TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.13         7.43         3.02        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NV TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 
       16.47         7.76        52.57        46.09        10.36        33.11 
TCGA-R6-A6DQ TCGA-R6-A6XG TCGA-R6-A6Y0 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RE 
        7.59        38.40        53.95         2.89         7.00        16.44 
TCGA-V5-AASW TCGA-V5-AASX TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-X8-AAAR TCGA-3M-AB46 
        9.27         8.98        22.82        46.19        18.21        58.03 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 
       19.56        11.01        36.16        35.24        35.84        18.15 
TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8485 TCGA-BR-8486 
        0.69        29.42        31.10         4.31         9.21        20.22 
TCGA-BR-8487 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-8533 TCGA-CD-8536 
        1.12        20.65        16.14         5.13        15.39        12.43 
TCGA-CD-A4MH TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-D7-A6EV 
       12.20        18.21        14.66         5.92        14.76        11.24 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
       20.32        15.65        19.96        72.23        21.27         3.48 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BE TCGA-FP-A9TM 
       19.53        17.06        13.58         0.56        11.08         6.21 
TCGA-HF-7132 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8604 
       77.29        52.21         1.51         5.92        22.32        22.82 
TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       21.07         5.59        22.68         3.25        22.75        25.81 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
       29.98         6.51        20.25        12.95        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN 
       14.07        15.68         3.45        18.38        13.35        19.53 
TCGA-IN-A6RP TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A93J TCGA-R5-A7ZI TCGA-R5-A7ZR 
        6.44        13.51         2.53        36.95        74.53         6.08 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-SW-A7EB 
        4.60         9.24        16.67       122.30       115.69         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8PB 
        0.92         5.46        18.48        21.73        38.14        34.29 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PX 
       46.26        22.19         2.50         1.87         9.27        64.57 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S 
       11.70        21.83        61.22        18.74        20.81        32.88 
TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 TCGA-VQ-A925 
        1.71        42.64        60.85         9.50         2.01         4.54 
TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
        6.58        66.81        18.41        43.66        38.93        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       54.12        26.04        16.14        27.55        12.43 

$subtype3
TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-MX-A663 TCGA-2H-A9GR TCGA-IC-A6RE 
       22.82        35.97        27.12         9.86        32.45         7.69 
TCGA-IG-A3YA TCGA-IG-A3YB TCGA-IG-A4QT TCGA-IG-A7DP TCGA-IG-A97I TCGA-JY-A939 
       20.78         2.63         9.30        14.86        12.16        21.70 
TCGA-JY-A93D TCGA-JY-A93E TCGA-KH-A6WC TCGA-L5-A43H TCGA-L5-A4OF TCGA-L5-A4OO 
       31.56        25.22         6.28         0.30        26.33         3.32 
TCGA-L5-A4OU TCGA-L5-A88S TCGA-L5-A8NQ TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NU 
       29.00        15.48        21.37         8.71        13.41        83.24 
TCGA-LN-A49N TCGA-LN-A49P TCGA-LN-A49W TCGA-LN-A4A5 TCGA-LN-A9FP TCGA-Q9-A6FW 
       12.43        12.33        13.25        22.39        12.03         7.82 
TCGA-XP-A8T6 TCGA-B7-A5TK TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       25.08         9.47        17.29        13.68        39.12        26.10 
TCGA-BR-6705 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7901 TCGA-BR-7957 
       25.61        31.20        21.90         9.21         3.45         9.07 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8297 
       33.21        37.25        11.44         9.60         2.66         7.40 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
       13.08        22.19        17.52        14.04         3.32        11.80 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        3.72         5.39        12.79         9.34        28.14         6.28 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       32.58         9.86         8.22        34.13         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       28.57        28.34         0.66        32.52        13.51         0.46 
TCGA-BR-A4QI TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       21.44        11.21        12.10        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-A489 
        7.17        12.30        12.39        11.64        12.07        11.31 
TCGA-CD-A4MI TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-8572 TCGA-D7-8579 
       11.77        19.13        18.54        18.61        16.80        20.91 
TCGA-D7-A4YU TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-D7-A74B 
       16.44        26.43        11.31        11.44         8.38         7.13 
TCGA-EQ-8122 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GJ TCGA-HU-A4GQ 
        7.99        22.29        59.54         5.03        21.37         0.10 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG 
       36.36        18.81        12.46         6.51        15.75         3.72 
TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N6 
       19.73        45.67        11.05         5.13        40.64         8.94 
TCGA-RD-A8NB TCGA-VQ-A8P8 TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A94P TCGA-ZA-A8F6 
       16.87        30.97        15.65         9.73         2.66        17.26 

$subtype4
TCGA-IG-A3Y9 TCGA-JY-A6FD TCGA-L5-A43C TCGA-L5-A8NI TCGA-L5-A8NL TCGA-LN-A49X 
        0.85        68.02         3.16        13.48        13.22        12.62 
TCGA-LN-A9FR TCGA-R6-A6L6 TCGA-R6-A6Y2 TCGA-VR-A8ET TCGA-VR-AA4G TCGA-VR-AA7I 
       12.26         7.04         9.30         1.55        18.05        15.91 
TCGA-Z6-A8JD TCGA-ZR-A9CJ TCGA-B7-A5TN TCGA-BR-6453 TCGA-BR-7715 TCGA-BR-7723 
        3.42        19.73         9.44        15.95        33.63        28.73 
TCGA-BR-8059 TCGA-BR-8291 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-A4CQ TCGA-BR-A4IY 
       14.43        19.96        26.73        31.96        34.98        12.89 
TCGA-BR-A4IZ TCGA-CD-A48C TCGA-CD-A4MG TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-A4YY 
        8.98        11.61         6.58        17.19        21.14        13.78 
TCGA-D7-A748 TCGA-HU-A4GY TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-RD-A8N5 TCGA-RD-A8N9 
        4.34         0.26        11.70         5.56        57.44        35.61 
TCGA-SW-A7EA TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A91A 
       19.04        37.41        37.22         7.73        16.31        39.45 
TCGA-VQ-A928 TCGA-VQ-A94R TCGA-ZQ-A9CR 
        5.72        42.54         0.79 

$subtype5
TCGA-CG-5727 TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 
       79.07        26.70        11.70        34.68        13.87        19.33 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8284 
       40.21        30.90        44.94        29.56        29.59         8.05 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8381 
       15.58         6.18         0.26        31.27        14.79         7.36 
TCGA-BR-8382 TCGA-BR-8690 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       25.05        10.68        13.41        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5813 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-5717 
       13.35        12.39         8.05        14.01        19.07         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       36.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       21.07         7.99        25.71        12.66        20.91        20.55 
TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.84        17.85        13.35        17.19        10.26        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.98        12.79        12.36        11.31        12.33        24.72 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-VQ-A8PP TCGA-VQ-A924 
        0.62        14.47        23.41        55.43 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.13     0.36     0.10     0.26     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
   63.62   122.30    83.24    68.02   105.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  12.740   18.210   12.935   13.780   14.630 
[1] "0.1 - 63.6 (12.7)"  "0.4 - 122.3 (18.2)" "0.1 - 83.2 (12.9)" 
[4] "0.3 - 68.0 (13.8)"  "0.3 - 105.1 (14.6)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        3        7        1        34        14        14
  subtype2       8        7       11        7        15        26         5
  subtype3       0        3        5        7        18        22         4
  subtype4       0        0        3        1         7         6         4
  subtype5       1        1        9       14         7         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         17         11          5        6         3
  subtype2         20         24         12        8         1
  subtype3         21         15         15        8         0
  subtype4          8          7          3        4         0
  subtype5         15          4          4        9         0
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        8        0        0        1
  STAGE IA          3        7        3        0        1
  STAGE IB          7       11        5        3        9
  STAGE II          1        7        7        1       14
  STAGE IIA        34       15       18        7        7
  STAGE IIB        14       26       22        6        9
  STAGE III        14        5        4        4        0
  STAGE IIIA       17       20       21        8       15
  STAGE IIIB       11       24       15        7        4
  STAGE IIIC        5       12       15        3        4
  STAGE IV          6        8        8        4        9
  STAGE IVA         3        1        0        0        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    10 31 65 11
  subtype2    28 24 72 26
  subtype3     6 21 62 32
  subtype4     0  9 21 14
  subtype5     2 29 28 15
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       10       28        6        0        2
  T2          31       24       21        9       29
  T3          65       72       62       21       28
  T4          11       26       32       14       15
[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 45 47 13 10
  subtype2 50 41 36 21
  subtype3 39 34 19 25
  subtype4 13 13  6 11
  subtype5 29 21 12 12
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       45       50       39       13       29
  N1       47       41       34       13       21
  N2       13       36       19        6       12
  N3       10       21       25       11       12
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus         0   1
  subtype1 100   8
  subtype2 127   6
  subtype3 106   8
  subtype4  38   3
  subtype5  67   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  100    8
  subtype2  127    6
  subtype3  106    8
  subtype4   38    3
  subtype5   67    6
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0      100      127      106       38       67
  1        8        6        8        3        6
[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"
D9V7, binary
          cls
clus         0   1
  subtype1  22 102
  subtype2  43 113
  subtype3  41  80
  subtype4  11  36
  subtype5  26  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22  102
  subtype2   43  113
  subtype3   41   80
  subtype4   11   36
  subtype5   26   48
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       22       43       41       11       26
  MALE        102      113       80       36       48
[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"
D9V8, binary
          cls
clus         0   1
  subtype1  84  31
  subtype2 109  37
  subtype3  99  20
  subtype4  35  11
  subtype5  59   5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   84   31
  subtype2  109   37
  subtype3   99   20
  subtype4   35   11
  subtype5   59    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        84      109       99       35       59
  YES       31       37       20       11        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, continuous
D9V10, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    44                         5    59
  subtype2    23                         8   109
  subtype3    28                         2    89
  subtype4    10                         0    36
  subtype5     6                         1    45
D9V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           44       23       28       10        6
  BLACK OR AFRICAN AMERICAN        5        8        2        0        1
  WHITE                           59      109       89       36       45
[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"
D9V12, binary
          cls
clus        0  1
  subtype1  4 75
  subtype2  3 79
  subtype3  3 97
  subtype4  1 31
  subtype5  0 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   75
  subtype2    3   79
  subtype3    3   97
  subtype4    1   31
  subtype5    0   52
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            4        3        3        1        0
  NOT HISPANIC OR LATINO       75       79       97       31       52
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 26 24
  subtype2 66 57
  subtype3 89 52
  subtype4 56 50
  subtype5 62 30
subtype1 subtype2 subtype3 subtype4 subtype5 
      50      123      141      106       92 
subtype1 subtype2 subtype3 subtype4 subtype5 
      24       57       52       50       30 
$subtype1
TCGA-2H-A9GF TCGA-2H-A9GG TCGA-2H-A9GL TCGA-2H-A9GQ TCGA-JY-A6FH TCGA-L5-A4OF 
       25.78        20.05         5.92         4.21        47.38        26.33 
TCGA-L5-A4OQ TCGA-L5-A4OS TCGA-L5-A891 TCGA-L5-A8NN TCGA-R6-A6KZ TCGA-R6-A6Y2 
        1.38        58.59         3.75         5.49         5.06         9.30 
TCGA-R6-A8WG TCGA-V5-A7RB TCGA-B7-A5TN TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 
       12.69         5.29         9.44        28.73        11.44         0.69 
TCGA-BR-8295 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8690 TCGA-BR-A452 
        2.20         9.21        24.79        31.96        10.68         7.53 
TCGA-BR-A4J1 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-5725 
        0.72        15.39        12.82         6.31        12.20        15.02 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-FP-8099 TCGA-FP-8631 
       12.33        16.80        14.27        22.29        17.06         0.56 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A666 TCGA-R5-A7ZF TCGA-SW-A7EB TCGA-VQ-A8DU 
        5.56        63.62        14.04         8.52         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A91Z TCGA-VQ-A922 
       13.25        43.36        22.19        12.79        55.56         9.04 
TCGA-VQ-A94O TCGA-VQ-AA6B 
       21.04        32.94 

$subtype2
TCGA-JY-A6FB TCGA-L5-A43I TCGA-L5-A4OE TCGA-L5-A4OG TCGA-L5-A4OI TCGA-L5-A88Y 
       60.39        18.28        24.00         4.70        19.99         0.36 
TCGA-S8-A6BV TCGA-CG-5727 TCGA-VQ-A8PU TCGA-2H-A9GH TCGA-2H-A9GI TCGA-2H-A9GJ 
       20.02        79.07        27.35        31.27        14.30        58.55 
TCGA-2H-A9GK TCGA-2H-A9GM TCGA-2H-A9GN TCGA-2H-A9GO TCGA-IG-A4QS TCGA-JY-A6F8 
        7.63        13.94         8.94        16.24         3.88       122.10 
TCGA-JY-A93C TCGA-L5-A43E TCGA-L5-A4OH TCGA-L5-A4ON TCGA-L5-A4OP TCGA-L5-A4OR 
       23.18        30.25        32.61        18.35         7.17         3.16 
TCGA-L5-A4OW TCGA-L5-A4OX TCGA-L5-A88V TCGA-L5-A8NE TCGA-L5-A8NF TCGA-L5-A8NH 
        7.13         7.43         2.60        55.50         2.66        12.92 
TCGA-L5-A8NJ TCGA-L5-A8NM TCGA-L5-A8NW TCGA-L7-A6VZ TCGA-M9-A5M8 TCGA-R6-A6DN 
       16.47         7.76        46.09        10.36        33.11         8.02 
TCGA-R6-A6DQ TCGA-R6-A6L4 TCGA-R6-A6L6 TCGA-R6-A6XG TCGA-R6-A6XQ TCGA-R6-A6Y0 
        7.59        16.31         7.04        38.40         6.35        53.95 
TCGA-R6-A8W5 TCGA-R6-A8W8 TCGA-RE-A7BO TCGA-V5-A7RE TCGA-V5-AASW TCGA-V5-AASX 
       15.78         2.89         7.00        16.44         9.27         8.98 
TCGA-VR-A8EQ TCGA-VR-AA4D TCGA-3M-AB46 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 
       22.82        46.19        58.03         6.18        31.10         4.31 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-A4CS TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-A4MG 
       20.22         1.12         1.48        20.65        16.14         6.58 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5730 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       36.00         0.99         4.01        10.26        15.22        15.98 
TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A74A TCGA-F1-6874 TCGA-FP-A4BE 
       11.31        18.21        11.24        19.96        14.47        11.08 
TCGA-HF-7134 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 
       52.21         5.92        22.32        21.07         5.59        22.68 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX 
       22.75        25.81        11.77        29.98         6.51        20.25 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-IN-A6RI TCGA-KB-A93J 
       12.95        23.84        23.80        14.07        18.38        36.95 
TCGA-R5-A7ZE TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7C1 TCGA-RD-A8MV 
       18.21        74.53         6.08         9.24        16.67       122.30 
TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
        0.92        18.48        21.73        37.41        38.14         7.73 
TCGA-VQ-A8PB TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PX TCGA-VQ-A91D 
       34.29         2.70        17.85         9.27        64.57        11.70 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       21.83        18.74        32.88         1.71        42.64         9.50 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6D 
        4.54        66.81        11.24        43.66        38.93        17.13 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
       54.12        26.04        16.14 

$subtype3
TCGA-JY-A938 TCGA-L5-A43M TCGA-L5-A88T TCGA-L5-A8NG TCGA-L5-A8NT TCGA-VQ-A94U 
       34.85         8.94        22.82        35.97        27.12        26.93 
TCGA-2H-A9GR TCGA-IG-A4QT TCGA-IG-A7DP TCGA-JY-A6FE TCGA-JY-A939 TCGA-JY-A93E 
       32.45         9.30        14.86         3.68        21.70        25.22 
TCGA-L5-A43C TCGA-L5-A4OO TCGA-L5-A4OT TCGA-L5-A4OU TCGA-L5-A893 TCGA-L5-A8NI 
        3.16         3.32         4.90        29.00         3.02        13.48 
TCGA-L5-A8NR TCGA-L5-A8NS TCGA-L5-A8NV TCGA-Q9-A6FW TCGA-X8-AAAR TCGA-B7-5816 
        8.71        13.41        52.57         7.82        18.21        26.70 
TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-6452 TCGA-BR-6455 
       11.70        19.56        11.01         9.47        34.68        13.87 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
        9.17        32.78        19.89        12.16         8.98        30.90 
TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7958 TCGA-BR-8058 
       44.94        36.16        35.24        35.84        29.56        37.25 
TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8372 
       29.59         8.05        29.42        15.58         0.26        31.27 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-A4CQ TCGA-BR-A4J6 
        7.36        25.05        28.14         7.53        34.98         0.66 
TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8531 TCGA-CD-8532 
        5.13        13.02        13.15        13.18        12.59        11.64 
TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A48C TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-5717 
       12.07        12.43        11.61         8.05        14.01         6.97 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5732 
        6.02         0.99       105.07        12.03        28.96        69.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6521 
       21.07         7.99        25.71        12.66        20.55        18.54 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8576 
       17.85        13.35        17.19        12.79        24.72        14.66 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       16.44         5.92        13.78        11.44        20.32        15.65 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8211 
       72.23        21.27         3.48        19.53        22.29        13.58 
TCGA-FP-A9TM TCGA-HF-7132 TCGA-HU-8238 TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GJ 
        6.21        77.29         1.51        22.82         3.25        21.37 
TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ 
       21.17        15.68         3.45        18.81         3.39        12.46 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V 
       13.35        19.53         6.44         6.51        11.70        15.75 
TCGA-IN-AB1X TCGA-IP-7968 TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8N1 TCGA-RD-A8N5 
       13.51         2.53         4.60        11.05       115.69        57.44 
TCGA-SW-A7EA TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       19.04        37.22        30.97        46.26        16.31         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91Q 
        1.87        23.41        15.65        39.45        61.22        20.81 
TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA64 TCGA-VQ-AA69 
       60.85         2.01        55.43         6.58        18.41        28.41 
TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       27.55        12.43         0.79 

$subtype4
TCGA-MX-A663 TCGA-IC-A6RE TCGA-JY-A93D TCGA-L5-A8NL TCGA-L5-A8NU TCGA-ZR-A9CJ 
        9.86         7.69        31.56        13.22        83.24        19.73 
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
       25.61        18.05        40.21        31.20        21.90         9.21 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8059 
       33.63        18.15         3.45         9.07        33.21        14.43 
TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 
        9.60         2.66        19.96         7.40        13.08        22.19 
TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8384 
       17.52        14.04         3.32        11.80        14.79         3.72 
TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 
        5.39        12.79         9.34         6.28        26.73        32.58 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
        9.86         8.22        34.13         6.08        27.55        28.57 
TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI 
        8.98        28.34        32.52        13.51         0.46        21.44 
TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-5813 TCGA-CD-8524 
       13.41        13.35        11.21        12.10        12.39        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-A487 
       12.59        12.53         7.17        12.30        12.39        12.30 
TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4449 TCGA-CG-5719 TCGA-CG-5728 TCGA-D7-5579 
       11.31        11.77        19.07         1.02        65.10        20.91 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6818 TCGA-D7-8574 TCGA-D7-8578 
       19.13        18.84        18.61        12.36        17.19        21.14 
TCGA-D7-8579 TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A747 TCGA-D7-A748 
       20.91        14.76        26.43        11.31         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ 
        7.13         0.62         7.99        59.54         5.03         0.10 
TCGA-HU-A4GY TCGA-IN-7806 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-R5-A7O7 TCGA-RD-A7BW 
        0.26        36.36         3.72        19.73        45.67         5.13 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A91Y 
       37.91        40.64         8.94        35.61        16.87         9.73 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-ZA-A8F6 
        5.72         2.66        42.54        17.26 

$subtype5
TCGA-IC-A6RF TCGA-L5-A43J TCGA-Q9-A6FU TCGA-IG-A3I8 TCGA-IG-A3QL TCGA-IG-A3Y9 
       15.68         4.31         5.16        33.27        35.21         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-A6FG TCGA-KH-A6WC TCGA-L5-A43H 
       12.16        44.75        68.02        41.52         6.28         0.30 
TCGA-L5-A4OM TCGA-L5-A88S TCGA-L5-A88W TCGA-L5-A88Z TCGA-L5-A8NK TCGA-L5-A8NQ 
       47.93        15.48        25.12         7.40        13.55        21.37 
TCGA-L7-A56G TCGA-LN-A49K TCGA-LN-A49L TCGA-LN-A49M TCGA-LN-A49N TCGA-LN-A49O 
       10.85         5.92        10.45        12.66        12.43        13.41 
TCGA-LN-A49P TCGA-LN-A49R TCGA-LN-A49S TCGA-LN-A49U TCGA-LN-A49W TCGA-LN-A49X 
       12.33        13.38        13.15        15.35        13.25        12.62 
TCGA-LN-A49Y TCGA-LN-A4A1 TCGA-LN-A4A2 TCGA-LN-A4A4 TCGA-LN-A4A5 TCGA-LN-A4A6 
       12.46        12.59        12.49        12.59        22.39        12.85 
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-A8HZ TCGA-LN-A8I0 TCGA-LN-A8I1 TCGA-LN-A9FO TCGA-LN-A9FP TCGA-LN-A9FQ 
       12.33        13.38        13.18         0.13        12.03        12.85 
TCGA-LN-A9FR TCGA-S8-A6BW TCGA-V5-A7RC TCGA-VR-A8EO TCGA-VR-A8EP TCGA-VR-A8ER 
       12.26        20.38         3.42        25.81        27.09        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        33.70        18.18 
TCGA-VR-A8Q7 TCGA-VR-AA4G TCGA-VR-AA7B TCGA-VR-AA7D TCGA-VR-AA7I TCGA-XP-A8T6 
       52.27        18.05        11.24         9.17        15.91        25.08 
TCGA-XP-A8T7 TCGA-XP-A8T8 TCGA-Z6-A8JD TCGA-Z6-A8JE TCGA-Z6-A9VB TCGA-Z6-AAPN 
       41.23        14.37         3.42         2.10         1.32         2.66 
TCGA-BR-A4IY TCGA-IN-A7NT 
       12.89        10.62 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.56     0.36     0.26     0.10     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 
   63.62   122.30   115.69    83.24    68.02 
subtype1 subtype2 subtype3 subtype4 subtype5 
   12.51    16.47    15.65    13.46    12.74 
[1] "0.6 - 63.6 (12.5)"  "0.4 - 122.3 (16.5)" "0.3 - 115.7 (15.7)"
[4] "0.1 - 83.2 (13.5)"  "0.1 - 68.0 (12.7)" 
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        0        6        1         4         7         5
  subtype2       8        6       12        5        12        20         7
  subtype3       1        5        7       13        13        21         4
  subtype4       0        0        7       10        12        15         2
  subtype5       0        3        3        1        40        14         9
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  subtype1         11          7          3        3         0
  subtype2         12         14          9        6         3
  subtype3         27         20         13       12         0
  subtype4         22         15         12       11         0
  subtype5          9          5          2        3         1
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        8        1        0        0
  STAGE IA          0        6        5        0        3
  STAGE IB          6       12        7        7        3
  STAGE II          1        5       13       10        1
  STAGE IIA         4       12       13       12       40
  STAGE IIB         7       20       21       15       14
  STAGE III         5        7        4        2        9
  STAGE IIIA       11       12       27       22        9
  STAGE IIIB        7       14       20       15        5
  STAGE IIIC        3        9       13       12        2
  STAGE IV          3        6       12       11        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 12 23 11
  subtype2    24 24 48 19
  subtype3    10 27 75 31
  subtype4     1 20 56 32
  subtype5     8 31 46  5
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        3       24       10        1        8
  T2          12       24       27       20       31
  T3          23       48       75       56       46
  T4          11       19       31       32        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 19 10  8
  subtype2 43 38 22 11
  subtype3 42 39 27 32
  subtype4 29 32 21 25
  subtype5 52 28  6  3
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       10       43       42       29       52
  N1       19       38       39       32       28
  N2       10       22       27       21        6
  N3        8       11       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"
D10V6, binary
          cls
clus         0   1
  subtype1  41   2
  subtype2  94   8
  subtype3 127   8
  subtype4  95   9
  subtype5  81   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41    2
  subtype2   94    8
  subtype3  127    8
  subtype4   95    9
  subtype5   81    4
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       41       94      127       95       81
  1        2        8        8        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"
D10V7, binary
          cls
clus         0   1
  subtype1  12  40
  subtype2  35  90
  subtype3  39 105
  subtype4  42  67
  subtype5  15  77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   40
  subtype2   35   90
  subtype3   39  105
  subtype4   42   67
  subtype5   15   77
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       12       35       39       42       15
  MALE         40       90      105       67       77
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus         0   1
  subtype1  42   6
  subtype2  90  25
  subtype3 111  25
  subtype4  87  18
  subtype5  56  30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42    6
  subtype2   90   25
  subtype3  111   25
  subtype4   87   18
  subtype5   56   30
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        42       90      111       87       56
  YES        6       25       25       18       30
[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"
D10V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 subtype5 
       1        5        1       58 
 [1] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
 [7] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[13] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[19] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[25] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[31] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[37] "subtype5" "subtype5" "subtype5" "subtype2" "subtype2" "subtype2"
[43] "subtype5" "subtype5" "subtype2" "subtype5" "subtype5" "subtype5"
[49] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype2"
[55] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[61] "subtype5" "subtype5" "subtype5"
D10V10, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       5       22       14        1       52 
 [1] "subtype5" "subtype2" "subtype5" "subtype2" "subtype2" "subtype2"
 [7] "subtype3" "subtype2" "subtype3" "subtype3" "subtype5" "subtype5"
[13] "subtype5" "subtype5" "subtype5" "subtype5" "subtype3" "subtype5"
[19] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype3"
[25] "subtype5" "subtype1" "subtype5" "subtype3" "subtype2" "subtype5"
[31] "subtype2" "subtype5" "subtype2" "subtype3" "subtype2" "subtype1"
[37] "subtype3" "subtype3" "subtype2" "subtype2" "subtype5" "subtype2"
[43] "subtype3" "subtype2" "subtype2" "subtype5" "subtype1" "subtype5"
[49] "subtype3" "subtype3" "subtype2" "subtype5" "subtype5" "subtype5"
[55] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[61] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[67] "subtype5" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[73] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype5"
[79] "subtype5" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[85] "subtype5" "subtype5" "subtype5" "subtype5" "subtype3" "subtype5"
[91] "subtype5" "subtype5" "subtype5"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     8                         2    32
  subtype2    18                         5    81
  subtype3    14                         5   105
  subtype4    27                         0    79
  subtype5    44                         4    41
D10V11, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            8       18       14       27       44
  BLACK OR AFRICAN AMERICAN        2        5        5        0        4
  WHITE                           32       81      105       79       41
[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"
D10V12, binary
          cls
clus        0  1
  subtype1  3 26
  subtype2  2 56
  subtype3  2 91
  subtype4  1 98
  subtype5  3 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   26
  subtype2    2   56
  subtype3    2   91
  subtype4    1   98
  subtype5    3   63
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        2        2        1        3
  NOT HISPANIC OR LATINO       26       56       91       98       63
[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"
