[1] "ofn"        "-oTSARC-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/SARC-TP/19775498/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/20140640/SARC-TP.mergedcluster.txt"

nPatients in clinical file=260, in cluster file=260, common to both=260
[1]  10 260
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
70 86 74 26 
 1  2  3  4 
70 86 74 26 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6  7 
49 47 62 35 47 15  5 
 1  2  3  4  5  6  7 
49 47 62 35 47 15  5 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
59 45 61 57 
 1  2  3  4 
59 45 61 57 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
27 37 49 68 19 22 
 1  2  3  4  5  6 
27 37 49 68 19 22 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
116  78  64 
  1   2   3 
116  78  64 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
47 23 50 47 29 29 33 
 1  2  3  4  5  6  7 
47 23 50 47 29 29 33 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
109  51  98 
  1   2   3 
109  51  98 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 81  53 101  23 
  1   2   3   4 
 81  53 101  23 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
85 65 47 
 1  2  3 
85 65 47 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8 
24 33 38 24 11 22 22 23 
 1  2  3  4  5  6  7  8 
24 33 38 24 11 22 22 23 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "GENDER"                              
 [7] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
 [8] "RADIATION_THERAPY"                   
 [9] "HISTOLOGICAL_TYPE"                   
[10] "RESIDUAL_TUMOR"                      
[11] "RACE"                                
[12] "ETHNICITY"                           

Input Data has 12 rows and 260 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=91,	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=179,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=33,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'HISTOLOGICAL_TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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] "****** SUMMARY ***** "
Output Data has 260 columns, 1 survival variables, and 8 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "TUMOR_TISSUE_SITE" "GENDER"           
[4] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
[7] "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=33, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=11, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 42 28
  subtype2 59 27
  subtype3 42 32
  subtype4 19  7
subtype1 subtype2 subtype3 subtype4 
      70       86       74       26 
subtype1 subtype2 subtype3 subtype4 
      28       27       32        7 
$subtype1
TCGA-3B-A9HI TCGA-3B-A9HR TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-DX-A1KY 
       50.01        88.57        14.37        42.84        38.47        12.85 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48R 
       55.07        34.88        31.27        24.26        40.80        26.47 
TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV 
       15.95        23.44         3.06        67.20        23.54        50.50 
TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.36        15.22        17.95        61.97        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2O 
       38.17       124.37        27.95        36.69        60.66        86.10 
TCGA-DX-AB2P TCGA-DX-AB2T TCGA-HB-A3L4 TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
       12.07        77.88        34.88        12.62        33.30        52.11 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-JV-A5VE 
        9.80        80.48        26.93        19.89        13.58        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
        1.05         3.91        23.38         5.19        36.36        16.41 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DP 
       11.70        13.35        21.73         7.36         6.35        18.08 
TCGA-QC-AA9N TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G 
       17.65        18.94        22.82         8.61        13.41        10.72 
TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       72.72        22.62         9.04        26.43        29.92        18.08 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X9-A971 
       18.35        25.71        15.95        15.58 

$subtype2
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9I0 
       36.30        53.49        54.74        25.25        10.32        36.03 
TCGA-3B-A9I3 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       26.56        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3U6 TCGA-DX-A3U8 
       27.81        60.30        83.38        54.77        35.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       10.68        61.91         9.73        46.03       102.41        47.57 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BK TCGA-DX-A6Z2 TCGA-DX-A7EL 
       25.15        24.59        28.96        16.18        88.31        75.32 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BZ 
      135.48        29.49        48.20        20.05         9.34         6.58 
TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       40.60         9.21        50.40        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A76Y 
       84.66        50.89        71.31        31.13        16.60        15.48 
TCGA-FX-A8OO TCGA-IE-A4EK TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
        8.05         1.38        52.27       143.41       116.88        73.28 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-MB-A5Y9 TCGA-MB-A5YA 
      101.26        53.33       123.78        17.36         8.28         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL 
       19.73        17.98        22.39         7.46       120.20        37.55 
TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD 
       38.63        13.08         1.84        48.59        37.12       130.32 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO 
       64.77         0.72        17.52        19.63        13.22        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB 
        4.80        41.49        38.96        17.72        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF 
       13.38        15.95 

$subtype3
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX 
       19.69        68.55        18.64         0.56        14.04        38.24 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LY 
       36.69        54.21        59.24         6.28         9.04        33.44 
TCGA-DX-A3M2 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A6BA 
       34.68        51.02        14.99        50.43        81.90        66.05 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
       34.55        66.31        16.87        74.10        64.21        21.30 
TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A8BH TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BT 
       34.49        15.62        14.43        35.77        14.07        35.54 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W 
       19.43         1.15        17.79        66.74       106.55       106.45 
TCGA-DX-AB2X TCGA-DX-AB3A TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT 
       13.28        32.15        21.70        20.32        19.89        48.30 
TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3K6 
       15.91         0.72        19.53         3.22        25.22        28.21 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-K1-A42W TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MJ-A68H 
        5.92        22.62        62.17        35.28        25.41        14.99 
TCGA-MO-A47R TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       10.45        81.01        20.94        46.82        18.08        35.90 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q 
      188.15       111.98        10.52        16.77        25.35        32.75 
TCGA-VT-A80J TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C4 
       26.17        38.27        65.46        63.35        36.82        16.83 
TCGA-X6-A8C6 TCGA-Z4-AAPG 
       35.08        15.98 

$subtype4
TCGA-3B-A9HO TCGA-3B-A9HS TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A2IZ 
       31.53        44.91        32.71        18.54        74.66         8.58 
TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.70        43.76        86.83       124.73        44.68        31.86 
TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-AB2F TCGA-DX-AB2G 
       24.69         9.11        17.79        21.63        12.00        15.72 
TCGA-DX-AB2H TCGA-DX-AB35 TCGA-FX-A2QS TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-LI-A67I 
       15.85        30.51        31.63         4.57        37.12        22.03 
TCGA-SG-A6Z7 TCGA-VT-AB3D 
        3.88        12.46 

subtype1 subtype2 subtype3 subtype4 
    1.05     0.49     0.56     3.88 
subtype1 subtype2 subtype3 subtype4 
  124.37   143.41   188.15   124.73 
subtype1 subtype2 subtype3 subtype4 
   23.41    34.65    27.19    23.36 
[1] "1.1 - 124.4 (23.4)" "0.5 - 143.4 (34.7)" "0.6 - 188.2 (27.2)"
[4] "3.9 - 124.7 (23.4)"
D1V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  2                   0
  subtype2              1                  3                   2
  subtype3              0                  2                   0
  subtype4              0                  0                   0
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   1                             1
  subtype2                   0                             0
  subtype3                   0                             1
  subtype4                   0                             0
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                     13                    0
  subtype2                     0                      6                    2
  subtype3                     1                      9                    0
  subtype4                     0                      0                    0
          vv
clus       HEAD AND NECK - NECK HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                    0                                     0
  subtype2                    1                                     2
  subtype3                    0                                     0
  subtype4                    0                                     0
          vv
clus       LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                                0
  subtype2                                1
  subtype3                                0
  subtype4                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              0
  subtype3                                              2
  subtype4                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               3
  subtype2                               4
  subtype3                               2
  subtype4                               1
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       0                            0
  subtype2                                       2                            4
  subtype3                                       0                            0
  subtype4                                       0                            0
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       0                                7
  subtype2                       2                                2
  subtype3                       0                                8
  subtype4                       0                                0
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       4                           19
  subtype2                                       0                           10
  subtype3                                       1                           13
  subtype4                                       0                            1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       1
  subtype2                                       3
  subtype3                                       0
  subtype4                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         1
  subtype2                                         1
  subtype3                                         0
  subtype4                                         0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                0
  subtype2                                                3
  subtype3                                                1
  subtype4                                                1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        1
  subtype2                                        4
  subtype3                                        1
  subtype4                                        2
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       0
  subtype2                                                       1
  subtype3                                                       0
  subtype4                                                       1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          1
  subtype4                                          0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                 8
  subtype2                                                24
  subtype3                                                23
  subtype4                                                18
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  2
  subtype3                                                  1
  subtype4                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  1                        1
  subtype2                                  0                        2
  subtype3                                  1                        2
  subtype4                                  0                        0
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  subtype1                           2                         0
  subtype2                           1                         1
  subtype3                           1                         0
  subtype4                           0                         0
          vv
clus       UPPER EXTREMITY - SHOULDER/AXILLA UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 4                                 1
  subtype2                                 0                                 2
  subtype3                                 3                                 0
  subtype4                                 0                                 2
D1V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        1
  CHEST - CHEST WALL                                             2        3
  CHEST - LUNG/PLEURA                                            0        2
  CHEST - MEDIASTINUM                                            1        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                        13        6
  HEAD AND NECK - HEAD                                           0        2
  HEAD AND NECK - NECK                                           0        1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        2
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                3        4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        2
  LOWER EXTREMITY - FOOT/ANKLE                                   0        4
  LOWER EXTREMITY - GROIN                                        0        2
  LOWER EXTREMITY - LOWER LEG/CALF                               7        2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        4        0
  LOWER EXTREMITY - THIGH/KNEE                                  19       10
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        1        3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       1        4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              8       24
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        0
  SUPERFICIAL TRUNK - BACK                                       1        2
  SUPERFICIAL TRUNK - BUTTOCK                                    2        1
  SUPERFICIAL TRUNK - FLANK                                      0        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              4        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1        2
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             2        0
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          1        0
  GYNECOLOGICAL - UTERUS                                         9        0
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           0        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 2        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                2        1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        0
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               8        0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        0
  LOWER EXTREMITY - THIGH/KNEE                                  13        1
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               1        1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       1        2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             23       18
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             1        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        0
  SUPERFICIAL TRUNK - BACK                                       2        0
  SUPERFICIAL TRUNK - BUTTOCK                                    1        0
  SUPERFICIAL TRUNK - FLANK                                      0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              3        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        2
[1] 33  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
          cls
clus        0  1
  subtype1 46 24
  subtype2 43 43
  subtype3 42 32
  subtype4  8 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   24
  subtype2   43   43
  subtype3   42   32
  subtype4    8   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       46       43       42        8
  MALE         24       43       32       18
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1 40 28
  subtype2 68 15
  subtype3 52 20
  subtype4 20  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   28
  subtype2   68   15
  subtype3   52   20
  subtype4   20    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        40       68       52       20
  YES       28       15       20        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  subtype1                            2             0
  subtype2                           21             2
  subtype3                           14             0
  subtype4                           22             0
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        0
  subtype2                                                                        1
  subtype3                                                                        0
  subtype4                                                                        0
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                   37
  subtype2                   37
  subtype3                   28
  subtype4                    1
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                1               10
  subtype2                                                3                4
  subtype3                                                5                8
  subtype4                                                0                1
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                      13
  subtype2                                                       4
  subtype3                                                      11
  subtype4                                                       0
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        0                           0
  subtype2                                        2                           2
  subtype3                                        0                           0
  subtype4                                        0                           0
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             0
  subtype2                             6
  subtype3                             0
  subtype4                             0
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          7
  subtype2                                          4
  subtype3                                          8
  subtype4                                          2
D1V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                    2
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           37
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                               10
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      7
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   21
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                           37
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                3
  MYXOFIBROSARCOMA                                                                4
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        2
  SYNOVIAL SARCOMA - BIPHASIC                                                     2
  SYNOVIAL SARCOMA - MONOPHASIC                                                   6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      4
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                   14
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           28
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                5
  MYXOFIBROSARCOMA                                                                8
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      8
                                                                          clus
vv                                                                         subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                                   22
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                1
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      2
[1] 11  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 40 18  3  9
  subtype2 59 19  1  7
  subtype3 42 19  4  8
  subtype4 11 12  1  2
D1V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       40       59       42       11
  R1       18       19       19       12
  R2        3        1        4        1
  RX        9        7        8        2
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         8    55
  subtype2     2                         6    77
  subtype3     2                         4    65
  subtype4     0                         0    26
D1V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        2        2        0
  BLACK OR AFRICAN AMERICAN        8        6        4        0
  WHITE                           55       77       65       26
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus        0  1
  subtype1  1 62
  subtype2  2 70
  subtype3  2 62
  subtype4  0 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   62
  subtype2    2   70
  subtype3    2   62
  subtype4    0   26
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        2        0
  NOT HISPANIC OR LATINO       62       70       62       26
[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 32 17
  subtype2 35 12
  subtype3 41 21
  subtype4 16 19
  subtype5 25 22
  subtype6 12  3
  subtype7  4  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      49       47       62       35       47       15        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      17       12       21       19       22        3        1 
$subtype1
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HS TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ 
       50.01        19.69        44.91        32.71        38.24        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3LY 
       18.54        59.24         6.28         9.70       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YR 
       44.68        31.86        24.69         9.11        21.63        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 
       66.31        67.20        23.54        50.50        74.10        64.21 
TCGA-DX-A7EU TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV 
       12.20        44.68        38.17       124.37        35.54        60.66 
TCGA-DX-A8BX TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V 
       19.43        12.00        15.72        86.10        77.88       106.55 
TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ 
       30.51        84.66        32.15         4.57        19.89        37.12 
TCGA-K1-A6RU TCGA-LI-A9QH TCGA-MB-A8JK TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V9 
       23.38        13.35        21.73        20.94        17.65        46.82 
TCGA-X6-A8C6 
       35.08 

$subtype2
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-3B-A9HT TCGA-DX-A1KU TCGA-DX-A1L1 TCGA-DX-A1L3 
       36.30        31.53        54.74        14.04        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       42.54         5.26        83.38        54.77         9.04        86.83 
TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BK 
       34.68        35.77         4.54        28.96        17.79        16.18 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BO 
       20.05        15.22        17.95        14.43        61.97        35.77 
TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-HB-A2OT 
       14.07        51.91         9.21        50.40       101.98        48.30 
TCGA-IE-A4EJ TCGA-K1-A3PO TCGA-K1-A6RT TCGA-MB-A5Y9 TCGA-QQ-A5V2 TCGA-QQ-A5VA 
        3.22        53.33        17.36         8.28         1.84        18.08 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71P TCGA-UE-A6QT 
       64.77         0.72        16.77        17.52        25.35        13.22 
TCGA-UE-A6QU TCGA-VT-A80J TCGA-VT-AB3D TCGA-WK-A8XO TCGA-X9-A973 
       13.41        26.17        12.46        11.93        36.43 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       53.49        68.55        88.57        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A3U7 TCGA-DX-A3U9 
       38.47        36.03        18.64        26.56        51.02        14.99 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       55.07        50.43        34.88        81.90         9.73        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       40.80        46.03        26.47       102.41        47.57        25.15 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       66.05        23.44        88.31        75.32        48.36        15.62 
TCGA-FX-A3NJ TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       31.13        12.62        33.30         9.80        80.48        26.93 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-JV-A5VE 
       19.53         1.38        25.22        52.27        28.21        16.41 
TCGA-K1-A3PN TCGA-K1-A42W TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5YA TCGA-MJ-A68H 
      101.26        62.17        16.41        35.28         0.49        14.99 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-WK-A8XS TCGA-WK-A8XX 
      120.20        37.55        81.01        18.08        72.72        38.27 
TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       65.46        56.61         9.04        29.92        18.08        18.35 
TCGA-X6-A8C5 TCGA-X9-A971 
       38.96        15.58 

$subtype4
TCGA-3B-A9HV TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3UA TCGA-DX-A7EI 
       14.37        12.85        74.66         8.58        10.68        34.49 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 
      135.48        29.49        48.20        15.85        40.60        22.85 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3RE TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N8 
       50.89        71.31        21.70         8.05        34.88         0.72 
TCGA-IW-A3M5 TCGA-JV-A75J TCGA-LI-A67I TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R 
        5.92         3.91        22.03        19.73        22.39        10.45 
TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8C 
       38.63        20.52        10.52         3.88        32.75        19.63 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.80        41.49        17.72        13.38        15.95 

$subtype5
TCGA-3R-A8YX TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LT TCGA-DX-A48K TCGA-DX-A6B8 
        0.56        76.41        60.30        43.76        31.27        15.95 
TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BS 
        3.06        16.87        21.30         9.34        33.07        27.95 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2P TCGA-DX-AB2Q 
       36.69         6.58         1.15        17.79        12.07        66.74 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB36 TCGA-FX-A3TO TCGA-IS-A3K7 TCGA-JV-A5VF 
      106.45        13.28        60.00        20.32       143.41         1.05 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-N1-A6IA TCGA-PC-A5DM 
        5.19        36.36        11.70        25.41         7.36         6.35 
TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-SG-A6Z4 
       13.08        48.59        35.90       130.32       111.98        18.94 
TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC 
       22.82         8.61        10.72        22.62        26.43        36.82 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-Z4-A8JB TCGA-Z4-AAPG 
       25.71        15.95        16.83         4.37        15.98 

$subtype6
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A3UB TCGA-DX-A6B9 TCGA-FX-A3NK TCGA-FX-A48G 
       66.87        27.81        61.91        24.59        16.60        19.89 
TCGA-FX-A76Y TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-K1-A42X TCGA-MJ-A68J 
       15.48       116.88        73.28        22.62       123.78        17.98 
TCGA-MO-A47P TCGA-QQ-A5VD TCGA-X2-A95T 
        7.46        37.12        63.35 

$subtype7
TCGA-FX-A2QS TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IS-A3KA TCGA-QQ-A8VB 
       31.63        15.91        52.11        13.58       188.15 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    4.57     0.72     0.49     0.72     0.56     7.46    13.58 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  124.73   101.98   120.20   135.48   143.41   123.78   188.15 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   34.55    20.05    35.08    19.73    20.32    27.81    31.63 
[1] "4.6 - 124.7 (34.5)"  "0.7 - 102.0 (20.1)"  "0.5 - 120.2 (35.1)" 
[4] "0.7 - 135.5 (19.7)"  "0.6 - 143.4 (20.3)"  "7.5 - 123.8 (27.8)" 
[7] "13.6 - 188.2 (31.6)"
D2V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  2                   0
  subtype2              0                  1                   0
  subtype3              0                  0                   0
  subtype4              1                  1                   2
  subtype5              0                  3                   0
  subtype6              0                  0                   0
  subtype7              0                  0                   0
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             0
  subtype2                   0                             0
  subtype3                   1                             1
  subtype4                   0                             1
  subtype5                   0                             0
  subtype6                   0                             0
  subtype7                   0                             0
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                      0                    0
  subtype2                     0                      0                    1
  subtype3                     0                      9                    0
  subtype4                     1                      6                    0
  subtype5                     0                      4                    1
  subtype6                     0                      7                    0
  subtype7                     0                      3                    0
          vv
clus       HEAD AND NECK - NECK HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                    0                                     0
  subtype2                    0                                     2
  subtype3                    0                                     0
  subtype4                    1                                     0
  subtype5                    0                                     0
  subtype6                    0                                     0
  subtype7                    0                                     0
          vv
clus       LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                                0
  subtype2                                1
  subtype3                                0
  subtype4                                0
  subtype5                                0
  subtype6                                0
  subtype7                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              0
  subtype3                                              2
  subtype4                                              0
  subtype5                                              0
  subtype6                                              0
  subtype7                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               3
  subtype2                               2
  subtype3                               3
  subtype4                               1
  subtype5                               2
  subtype6                               0
  subtype7                               0
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       0                            0
  subtype2                                       1                            0
  subtype3                                       0                            0
  subtype4                                       0                            3
  subtype5                                       1                            0
  subtype6                                       0                            1
  subtype7                                       0                            0
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       0                                2
  subtype2                       1                                3
  subtype3                       0                                3
  subtype4                       0                                0
  subtype5                       1                                8
  subtype6                       0                                1
  subtype7                       0                                0
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       1                           12
  subtype2                                       0                            8
  subtype3                                       0                            6
  subtype4                                       0                            6
  subtype5                                       4                           12
  subtype6                                       0                            0
  subtype7                                       0                            0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       0
  subtype3                                       3
  subtype4                                       0
  subtype5                                       0
  subtype6                                       1
  subtype7                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         0
  subtype2                                         0
  subtype3                                         1
  subtype4                                         0
  subtype5                                         0
  subtype6                                         1
  subtype7                                         0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                0
  subtype2                                                2
  subtype3                                                0
  subtype4                                                2
  subtype5                                                1
  subtype6                                                0
  subtype7                                                0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        1
  subtype2                                        0
  subtype3                                        4
  subtype4                                        2
  subtype5                                        0
  subtype6                                        1
  subtype7                                        0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       0
  subtype2                                                       0
  subtype3                                                       1
  subtype4                                                       0
  subtype5                                                       0
  subtype6                                                       0
  subtype7                                                       1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          1
  subtype4                                          0
  subtype5                                          0
  subtype6                                          0
  subtype7                                          0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                22
  subtype2                                                16
  subtype3                                                23
  subtype4                                                 6
  subtype5                                                 5
  subtype6                                                 2
  subtype7                                                 0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  2
  subtype4                                                  0
  subtype5                                                  0
  subtype6                                                  1
  subtype7                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  0                        2
  subtype2                                  2                        2
  subtype3                                  0                        1
  subtype4                                  0                        0
  subtype5                                  0                        0
  subtype6                                  0                        0
  subtype7                                  0                        0
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  subtype1                           2                         0
  subtype2                           0                         0
  subtype3                           0                         0
  subtype4                           0                         1
  subtype5                           1                         0
  subtype6                           0                         0
  subtype7                           1                         0
          vv
clus       UPPER EXTREMITY - SHOULDER/AXILLA UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 1                                 1
  subtype2                                 2                                 2
  subtype3                                 1                                 0
  subtype4                                 0                                 1
  subtype5                                 3                                 1
  subtype6                                 0                                 0
  subtype7                                 0                                 0
D2V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             2        1
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         0        0
  HEAD AND NECK - HEAD                                           0        1
  HEAD AND NECK - NECK                                           0        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        2
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                3        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        1
  LOWER EXTREMITY - FOOT/ANKLE                                   0        0
  LOWER EXTREMITY - GROIN                                        0        1
  LOWER EXTREMITY - LOWER LEG/CALF                               2        3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        0
  LOWER EXTREMITY - THIGH/KNEE                                  12        8
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       1        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             22       16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        2
  SUPERFICIAL TRUNK - BACK                                       2        2
  SUPERFICIAL TRUNK - BUTTOCK                                    2        0
  SUPERFICIAL TRUNK - FLANK                                      0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        2
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1        2
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 0        1
  CHEST - CHEST WALL                                             0        1
  CHEST - LUNG/PLEURA                                            0        2
  CHEST - MEDIASTINUM                                            1        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        1
  GYNECOLOGICAL - OVARY                                          0        1
  GYNECOLOGICAL - UTERUS                                         9        6
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           0        1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 2        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                3        1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        3
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               3        0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        0
  LOWER EXTREMITY - THIGH/KNEE                                   6        6
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        3        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       4        2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             23        6
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             2        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       1        0
  SUPERFICIAL TRUNK - BUTTOCK                                    0        0
  SUPERFICIAL TRUNK - FLANK                                      0        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        1
                                                         clus
vv                                                        subtype5 subtype6
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             3        0
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         4        7
  HEAD AND NECK - HEAD                                           1        0
  HEAD AND NECK - NECK                                           0        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                2        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        1
  LOWER EXTREMITY - GROIN                                        1        0
  LOWER EXTREMITY - LOWER LEG/CALF                               8        1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        4        0
  LOWER EXTREMITY - THIGH/KNEE                                  12        0
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               1        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              5        2
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       0        0
  SUPERFICIAL TRUNK - BUTTOCK                                    1        0
  SUPERFICIAL TRUNK - FLANK                                      0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              3        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1        0
                                                         clus
vv                                                        subtype7
  CHEST - BREAST                                                 0
  CHEST - CHEST WALL                                             0
  CHEST - LUNG/PLEURA                                            0
  CHEST - MEDIASTINUM                                            0
  CHEST - OTHER (PLEASE SPECIFY                                  0
  GYNECOLOGICAL - OVARY                                          0
  GYNECOLOGICAL - UTERUS                                         3
  HEAD AND NECK - HEAD                                           0
  HEAD AND NECK - NECK                                           0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0
  LOWER ABDOMINAL/PELVIC - PELVIC                                0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0
  LOWER EXTREMITY - GROIN                                        0
  LOWER EXTREMITY - LOWER LEG/CALF                               0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0
  LOWER EXTREMITY - THIGH/KNEE                                   0
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              0
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0
  SUPERFICIAL TRUNK - BACK                                       0
  SUPERFICIAL TRUNK - BUTTOCK                                    1
  SUPERFICIAL TRUNK - FLANK                                      0
  UPPER EXTREMITY - SHOULDER/AXILLA                              0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0
[1] 33  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
          cls
clus        0  1
  subtype1 18 31
  subtype2 19 28
  subtype3 40 22
  subtype4 27  8
  subtype5 22 25
  subtype6 11  4
  subtype7  5  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   31
  subtype2   19   28
  subtype3   40   22
  subtype4   27    8
  subtype5   22   25
  subtype6   11    4
  subtype7    5    0
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       18       19       40       27       22       11        5
  MALE         31       28       22        8       25        4        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus        0  1
  subtype1 32 17
  subtype2 32 13
  subtype3 49  9
  subtype4 26  9
  subtype5 25 21
  subtype6 14  1
  subtype7  4  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   17
  subtype2   32   13
  subtype3   49    9
  subtype4   26    9
  subtype5   25   21
  subtype6   14    1
  subtype7    4    1
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        32       32       49       26       25       14        4
  YES       17       13        9        9       21        1        1
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  subtype1                           22             0
  subtype2                           19             0
  subtype3                            0             0
  subtype4                            8             0
  subtype5                            5             2
  subtype6                            4             0
  subtype7                            1             0
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        0
  subtype2                                                                        1
  subtype3                                                                        0
  subtype4                                                                        0
  subtype5                                                                        0
  subtype6                                                                        0
  subtype7                                                                        0
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                    1
  subtype2                    4
  subtype3                   62
  subtype4                   11
  subtype5                   14
  subtype6                   10
  subtype7                    3
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                0               13
  subtype2                                                4                3
  subtype3                                                0                0
  subtype4                                                3                2
  subtype5                                                1                5
  subtype6                                                0                1
  subtype7                                                1                0
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       9
  subtype2                                                       7
  subtype3                                                       0
  subtype4                                                       1
  subtype5                                                      12
  subtype6                                                       0
  subtype7                                                       0
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        0                           0
  subtype2                                        0                           0
  subtype3                                        0                           0
  subtype4                                        2                           2
  subtype5                                        0                           0
  subtype6                                        0                           0
  subtype7                                        0                           0
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             0
  subtype2                             0
  subtype3                             0
  subtype4                             6
  subtype5                             0
  subtype6                             0
  subtype7                             0
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          4
  subtype2                                          9
  subtype3                                          0
  subtype4                                          0
  subtype5                                          8
  subtype6                                          0
  subtype7                                          0
D2V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   22
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                               13
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      4
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   19
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                            4
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                4
  MYXOFIBROSARCOMA                                                                3
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      9
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    0
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           62
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      0
                                                                          clus
vv                                                                         subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                                    8
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           11
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                3
  MYXOFIBROSARCOMA                                                                2
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        2
  SYNOVIAL SARCOMA - BIPHASIC                                                     2
  SYNOVIAL SARCOMA - MONOPHASIC                                                   6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      0
                                                                          clus
vv                                                                         subtype5
  DEDIFFERENTIATED LIPOSARCOMA                                                    5
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           14
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                                5
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      8
                                                                          clus
vv                                                                         subtype6
  DEDIFFERENTIATED LIPOSARCOMA                                                    4
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           10
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                1
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      0
                                                                          clus
vv                                                                         subtype7
  DEDIFFERENTIATED LIPOSARCOMA                                                    1
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            3
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      0
[1] 11  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 27 18  2  2
  subtype2 26 14  1  5
  subtype3 44 13  1  4
  subtype4 19  7  3  6
  subtype5 24 14  2  7
  subtype6 11  3  0  1
  subtype7  4  0  0  1
D2V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       27       26       44       19       24       11        4
  R1       18       14       13        7       14        3        0
  R2        2        1        1        3        2        0        0
  RX        2        5        4        6        7        1        1
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    47
  subtype2     2                         2    42
  subtype3     0                         7    52
  subtype4     1                         1    32
  subtype5     1                         4    39
  subtype6     2                         2    11
  subtype7     0                         0     4
D2V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        2        0        1        1
  BLACK OR AFRICAN AMERICAN        2        2        7        1        4
  WHITE                           47       42       52       32       39
                           clus
vv                          subtype6 subtype7
  ASIAN                            2        0
  BLACK OR AFRICAN AMERICAN        2        0
  WHITE                           11        4
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus        0  1
  subtype1  1 46
  subtype2  1 43
  subtype3  0 55
  subtype4  2 25
  subtype5  1 40
  subtype6  0 11
  subtype7  0  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   46
  subtype2    1   43
  subtype3    0   55
  subtype4    2   25
  subtype5    1   40
  subtype6    0   11
  subtype7    0    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        1        0        2        1        0
  NOT HISPANIC OR LATINO       46       43       55       25       40       11
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO        3
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 43 16
  subtype2 19 26
  subtype3 45 16
  subtype4 34 23
subtype1 subtype2 subtype3 subtype4 
      59       45       61       57 
subtype1 subtype2 subtype3 subtype4 
      16       26       16       23 
$subtype1
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       50.01        36.30        14.04        32.71        38.24        18.54 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       59.24        33.53        74.66        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY 
       60.30         8.58        54.77        43.76       124.73        33.44 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       34.68        31.86        24.69        28.96        17.79        21.63 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 
       66.31        67.20        23.54        50.50        74.10        64.21 
TCGA-DX-A7ES TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F 
       20.05        12.20        17.95        60.66        19.43        12.00 
TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
       15.85        86.10         9.21        77.88       106.55       106.45 
TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A3TO TCGA-IE-A6BZ TCGA-K1-A6RT 
       22.85        30.51        32.15        20.32        19.89        17.36 
TCGA-K1-A6RU TCGA-MB-A8JK TCGA-PC-A5DN TCGA-PT-A8TR TCGA-SI-A71Q TCGA-SI-AA8B 
       23.38        21.73        38.63        20.52        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-X6-A8C4 TCGA-Z4-A9VC TCGA-Z4-AAPF 
       19.63        13.22        16.83        13.38        15.95 

$subtype2
TCGA-3B-A9HL TCGA-3B-A9I1 TCGA-DX-A1KY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48K 
       19.69        18.64        12.85        44.68        10.68        31.27 
TCGA-DX-A6B8 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BJ 
       15.95        21.30        34.49        29.49        48.20         9.34 
TCGA-DX-A8BN TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q 
       38.17        36.69         1.15        40.60        12.07        66.74 
TCGA-DX-AB36 TCGA-DX-AB3C TCGA-FX-A2QS TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N9 
       60.00        71.31        31.63        34.88         4.57        52.11 
TCGA-IE-A4EJ TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH 
        3.22         5.92         1.05         5.19        22.03        13.35 
TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QC-AA9N TCGA-QQ-A5VC 
       19.73        10.45         7.36         6.35        17.65        35.90 
TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-VT-A80G 
      111.98        10.52        18.94         3.88        22.82        10.72 
TCGA-X6-A7WC TCGA-X6-A8C6 TCGA-X6-A8C7 
       36.82        35.08        17.72 

$subtype3
TCGA-3B-A9HV TCGA-3B-A9I3 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       14.37        26.56        51.02        14.99        61.91        55.07 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O 
       50.43        34.88        81.90         9.73        24.26        40.80 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       46.03        26.47       102.41        47.57        25.15        24.59 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       66.05        23.44        88.31        75.32        48.36        15.62 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA 
       31.13        21.70        15.91        12.62        33.30         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IS-A3K6 TCGA-IS-A3K8 
       80.48        26.93        19.53         1.38        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28        22.62        16.41       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-KF-A41W TCGA-MB-A5YA TCGA-MO-A47P TCGA-PC-A5DK 
       62.17       123.78        11.70         0.49         7.46       120.20 
TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A8VB TCGA-RN-A68Q 
       37.55        81.01        18.08        13.08       188.15         0.72 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 
       38.27         9.04        29.92        18.08        18.35        38.96 
TCGA-X9-A971 
       15.58 

$subtype4
TCGA-3R-A8YX TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23Y 
        0.56        36.69        54.21        42.54         5.26         6.28 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U8 
        9.70        83.38         9.04        86.83        35.77         4.54 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7ET TCGA-DX-A8BH 
        9.11        16.18         3.06        16.87        15.22        14.43 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ 
       61.97        33.07        44.68        35.77        14.07        51.91 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G 
      124.37        27.95        35.54         6.58        17.79        15.72 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-HS-A5N8 
       13.28        50.40       101.98        84.66        50.89         0.72 
TCGA-IS-A3K7 TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QQ-A5V2 TCGA-QQ-A5V9 
      143.41        25.41         8.28        20.94         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SG-A849 
       18.08        48.59        37.12        64.77        16.77        17.52 
TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C2 
       25.35        13.41        26.17        22.62        26.43        25.71 
TCGA-X6-A8C3 TCGA-X9-A973 TCGA-Z4-AAPG 
       15.95        36.43        15.98 

subtype1 subtype2 subtype3 subtype4 
    8.58     1.05     0.49     0.56 
subtype1 subtype2 subtype3 subtype4 
  124.73   111.98   188.15   143.41 
subtype1 subtype2 subtype3 subtype4 
   30.51    19.69    28.21    25.35 
[1] "8.6 - 124.7 (30.5)" "1.1 - 112.0 (19.7)" "0.5 - 188.2 (28.2)"
[4] "0.6 - 143.4 (25.4)"
D3V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  2                   0
  subtype2              1                  2                   1
  subtype3              0                  0                   0
  subtype4              0                  2                   0
          vv
clus       CHEST - OTHER (PLEASE SPECIFY GYNECOLOGICAL - OVARY
  subtype1                             0                     0
  subtype2                             1                     0
  subtype3                             1                     1
  subtype4                             0                     0
          vv
clus       GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                      1                    1
  subtype2                      5                    0
  subtype3                     14                    1
  subtype4                      2                    0
          vv
clus       HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                                     0
  subtype2                                     0
  subtype3                                     1
  subtype4                                     0
          vv
clus       LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                                0
  subtype2                                0
  subtype3                                1
  subtype4                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              0
  subtype3                                              1
  subtype4                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               4
  subtype2                               2
  subtype3                               3
  subtype4                               2
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       1                            0
  subtype2                                       0                            2
  subtype3                                       0                            0
  subtype4                                       1                            2
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       1                                2
  subtype2                       0                                4
  subtype3                       0                                2
  subtype4                       1                                7
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       1                           14
  subtype2                                       3                           13
  subtype3                                       0                            3
  subtype4                                       1                           10
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       0
  subtype3                                       3
  subtype4                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                1
  subtype2                                                1
  subtype3                                                0
  subtype4                                                0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        0
  subtype2                                        2
  subtype3                                        5
  subtype4                                        0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       0
  subtype2                                                       1
  subtype3                                                       1
  subtype4                                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          1
  subtype4                                          0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                25
  subtype2                                                 5
  subtype3                                                18
  subtype4                                                17
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  2
  subtype4                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  0                        2
  subtype2                                  0                        0
  subtype3                                  0                        1
  subtype4                                  2                        2
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK UPPER EXTREMITY - SHOULDER/AXILLA
  subtype1                           1                                 0
  subtype2                           1                                 1
  subtype3                           1                                 1
  subtype4                           1                                 5
          vv
clus       UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 3
  subtype2                                 0
  subtype3                                 0
  subtype4                                 1
D3V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        1
  CHEST - CHEST WALL                                             2        2
  CHEST - LUNG/PLEURA                                            0        1
  CHEST - OTHER (PLEASE SPECIFY                                  0        1
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         1        5
  HEAD AND NECK - HEAD                                           1        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                4        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        2
  LOWER EXTREMITY - GROIN                                        1        0
  LOWER EXTREMITY - LOWER LEG/CALF                               2        4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        3
  LOWER EXTREMITY - THIGH/KNEE                                  14       13
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               1        1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             25        5
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       2        0
  SUPERFICIAL TRUNK - BUTTOCK                                    1        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              0        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                              3        0
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             0        2
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          1        0
  GYNECOLOGICAL - UTERUS                                        14        2
  HEAD AND NECK - HEAD                                           1        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          1        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               1        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 1        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                3        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        1
  LOWER EXTREMITY - FOOT/ANKLE                                   0        2
  LOWER EXTREMITY - GROIN                                        0        1
  LOWER EXTREMITY - LOWER LEG/CALF                               2        7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        1
  LOWER EXTREMITY - THIGH/KNEE                                   3       10
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        3        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       5        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             18       17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             2        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        2
  SUPERFICIAL TRUNK - BACK                                       1        2
  SUPERFICIAL TRUNK - BUTTOCK                                    1        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        5
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        1
[1] 29  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
          cls
clus        0  1
  subtype1 27 32
  subtype2 23 22
  subtype3 40 21
  subtype4 27 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   32
  subtype2   23   22
  subtype3   40   21
  subtype4   27   30
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       27       23       40       27
  MALE         32       22       21       30
[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"
D3V5, binary
          cls
clus        0  1
  subtype1 42 17
  subtype2 25 19
  subtype3 52  6
  subtype4 39 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   17
  subtype2   25   19
  subtype3   52    6
  subtype4   39   17
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        42       25       52       39
  YES       17       19        6       17
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA
  subtype1                           30
  subtype2                            7
  subtype3                            1
  subtype4                           16
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        0
  subtype2                                                                        0
  subtype3                                                                        0
  subtype4                                                                        1
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                    3
  subtype2                   16
  subtype3                   57
  subtype4                    6
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                2               14
  subtype2                                                2                2
  subtype3                                                2                0
  subtype4                                                3                6
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       4
  subtype2                                                      10
  subtype3                                                       1
  subtype4                                                      14
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        1                           0
  subtype2                                        0                           1
  subtype3                                        0                           0
  subtype4                                        0                           0
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             0
  subtype2                             3
  subtype3                             0
  subtype4                             1
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          5
  subtype2                                          4
  subtype3                                          0
  subtype4                                         10
D3V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   30
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            3
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                2
  MYXOFIBROSARCOMA                                                               14
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        1
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      5
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                    7
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           16
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                2
  MYXOFIBROSARCOMA                                                                2
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     1
  SYNOVIAL SARCOMA - MONOPHASIC                                                   3
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      4
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           57
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                2
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      0
                                                                          clus
vv                                                                         subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                                   16
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                            6
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                3
  MYXOFIBROSARCOMA                                                                6
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                     10
[1] 10  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 35 21  1  2
  subtype2 20 14  3  8
  subtype3 41 10  1  9
  subtype4 32 19  2  3
D3V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       35       20       41       32
  R1       21       14       10       19
  R2        1        3        1        2
  RX        2        8        9        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    56
  subtype2     1                         4    39
  subtype3     2                         4    53
  subtype4     2                         3    47
D3V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        2        2
  BLACK OR AFRICAN AMERICAN        2        4        4        3
  WHITE                           56       39       53       47
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
          cls
clus        0  1
  subtype1  2 55
  subtype2  1 35
  subtype3  0 52
  subtype4  0 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   55
  subtype2    1   35
  subtype3    0   52
  subtype4    0   49
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        0        0
  NOT HISPANIC OR LATINO       55       35       52       49
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 20  7
  subtype2 25 12
  subtype3 27 22
  subtype4 48 20
  subtype5 11  8
  subtype6 10 12
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      27       37       49       68       19       22 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       7       12       22       20        8       12 
$subtype1
TCGA-3B-A9HI TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A3LW TCGA-DX-A3U5 
       50.01        32.71        59.24        74.66       124.73        31.86 
TCGA-DX-A48N TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 
       24.69        67.20        23.54        50.50        74.10        64.21 
TCGA-DX-A8BG TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       17.95        60.66        12.00         9.21        77.88       106.55 
TCGA-DX-AB35 TCGA-DX-AB3A TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-LI-A9QH TCGA-MB-A8JK 
       30.51        32.15         4.57        19.89        13.35        21.73 
TCGA-PT-A8TR TCGA-SI-AA8B TCGA-Z4-A9VC 
       20.52         8.61        13.38 

$subtype2
TCGA-3B-A9HJ TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
       36.30        14.04        38.24        18.54        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41         6.28        27.81        60.30 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M2 
        9.70        83.38        54.77        43.76        33.44        34.68 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A7EU TCGA-DX-A8BK 
       28.96        17.79        21.63        66.31        12.20        61.97 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-AB2H TCGA-DX-AB32 
       33.07        38.17        35.77       124.37        15.85       101.98 
TCGA-DX-AB37 TCGA-K1-A6RU TCGA-MB-A5Y9 TCGA-QQ-A5VA TCGA-RN-AAAQ TCGA-VT-A80J 
       84.66        23.38         8.28        18.08        16.77        26.17 
TCGA-X6-A8C3 
       15.95 

$subtype3
TCGA-3B-A9HL TCGA-3R-A8YX TCGA-DX-A3U8 TCGA-DX-A48K TCGA-DX-A6YQ TCGA-DX-A6YX 
       19.69         0.56         4.54        31.27         3.06        16.87 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BP 
       21.30        34.49        15.22        14.43         9.34        14.07 
TCGA-DX-A8BQ TCGA-DX-A8BS TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2O 
       51.91        27.95        19.43         6.58        17.79        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB36 TCGA-FX-A3TO 
       12.07        66.74        13.28        50.40        60.00        20.32 
TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-N1-A6IA 
        3.22       143.41         5.19        11.70        25.41         7.36 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VB 
        6.35        20.94        17.65        48.59        35.90       188.15 
TCGA-QQ-A8VF TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-UE-A6QU TCGA-VT-A80G 
      111.98        18.94        17.52        22.82        13.41        10.72 
TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 
       22.62        26.43        36.82        25.71        16.83        35.08 
TCGA-Z4-AAPG 
       15.98 

$subtype4
TCGA-3B-A9HV TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A23V TCGA-DX-A3U7 TCGA-DX-A3U9 
       14.37        18.64        26.56        66.87        51.02        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       61.91        55.07        50.43        34.88        81.90         9.73 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        40.80        46.03        26.47       102.41        47.57 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EL 
       25.15        24.59        66.05        23.44        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ES TCGA-DX-AB2W TCGA-FX-A3NJ TCGA-FX-A3RE 
       48.36        15.62        20.05       106.45        31.13        21.70 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
       34.88        15.91        12.62        33.30        52.11         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IS-A3K6 TCGA-IS-A3K8 
       80.48        26.93        19.53         1.38        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28        22.62        16.41       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-MB-A5YA TCGA-MO-A47P TCGA-PC-A5DK 
       62.17       123.78        17.36         0.49         7.46       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5VD TCGA-UE-A6QT 
       37.55        38.63        81.01        18.08        37.12        13.22 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 
       38.27         9.04        29.92        18.08        18.35        38.96 
TCGA-X9-A971 TCGA-Z4-AAPF 
       15.58        15.95 

$subtype5
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3M1 
       12.85        36.69         8.58         9.04        86.83        44.68 
TCGA-DX-A3U6 TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A8BM TCGA-DX-A8BT TCGA-DX-A8BU 
       35.77         9.11        16.18        44.68        35.54        36.69 
TCGA-DX-AATS TCGA-DX-AB2G TCGA-DX-AB3B TCGA-MB-A8JL TCGA-MO-A47R TCGA-QQ-A5V9 
        1.15        15.72        50.89        19.73        10.45        46.82 
TCGA-X9-A973 
       36.43 

$subtype6
TCGA-DX-A3UA TCGA-DX-A6B8 TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-AB2J TCGA-DX-AB30 
       10.68        15.95        29.49        48.20        40.60        22.85 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-HS-A5N8 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-LI-A67I 
       71.31        31.63         0.72         5.92         1.05        22.03 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
       13.08         1.84        64.77        10.52         0.72         3.88 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-X6-A8C7 
       25.35        32.75        19.63        17.72 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.57     5.26     0.56     0.49     1.15     0.72 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  124.73   124.37   188.15   123.78    86.83    71.31 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  31.860   33.440   19.430   30.525   35.540   18.675 
[1] "4.6 - 124.7 (31.9)" "5.3 - 124.4 (33.4)" "0.6 - 188.2 (19.4)"
[4] "0.5 - 123.8 (30.5)" "1.1 - 86.8 (35.5)"  "0.7 - 71.3 (18.7)" 
D4V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  1                   0
  subtype2              0                  1                   0
  subtype3              0                  3                   0
  subtype4              0                  0                   0
  subtype5              1                  0                   0
  subtype6              0                  1                   1
          vv
clus       CHEST - OTHER (PLEASE SPECIFY GYNECOLOGICAL - OVARY
  subtype1                             0                     0
  subtype2                             0                     0
  subtype3                             0                     0
  subtype4                             1                     1
  subtype5                             0                     0
  subtype6                             1                     0
          vv
clus       GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                      1                    0
  subtype2                      0                    0
  subtype3                      3                    0
  subtype4                     16                    1
  subtype5                      0                    0
  subtype6                      2                    1
          vv
clus       HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                                     0
  subtype2                                     0
  subtype3                                     0
  subtype4                                     0
  subtype5                                     0
  subtype6                                     1
          vv
clus       LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                                0
  subtype2                                0
  subtype3                                0
  subtype4                                1
  subtype5                                0
  subtype6                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              0
  subtype3                                              0
  subtype4                                              1
  subtype5                                              0
  subtype6                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               0
  subtype2                               4
  subtype3                               0
  subtype4                               3
  subtype5                               1
  subtype6                               3
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       0                            0
  subtype2                                       1                            0
  subtype3                                       1                            0
  subtype4                                       0                            1
  subtype5                                       0                            1
  subtype6                                       0                            2
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       0                                1
  subtype2                       1                                4
  subtype3                       1                                8
  subtype4                       0                                2
  subtype5                       0                                0
  subtype6                       0                                0
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       0                            9
  subtype2                                       1                            5
  subtype3                                       4                           14
  subtype4                                       0                            5
  subtype5                                       0                            2
  subtype6                                       0                            5
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       0
  subtype3                                       0
  subtype4                                       3
  subtype5                                       0
  subtype6                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                0
  subtype2                                                1
  subtype3                                                0
  subtype4                                                0
  subtype5                                                1
  subtype6                                                0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        1
  subtype2                                        0
  subtype3                                        0
  subtype4                                        5
  subtype5                                        0
  subtype6                                        1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       0
  subtype2                                                       0
  subtype3                                                       0
  subtype4                                                       1
  subtype5                                                       0
  subtype6                                                       1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          0
  subtype4                                          1
  subtype5                                          0
  subtype6                                          0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                10
  subtype2                                                16
  subtype3                                                 6
  subtype4                                                21
  subtype5                                                12
  subtype6                                                 0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  0
  subtype4                                                  2
  subtype5                                                  0
  subtype6                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  0                        2
  subtype2                                  0                        0
  subtype3                                  2                        1
  subtype4                                  0                        1
  subtype5                                  0                        0
  subtype6                                  0                        1
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK UPPER EXTREMITY - SHOULDER/AXILLA
  subtype1                           1                                 0
  subtype2                           0                                 2
  subtype3                           3                                 2
  subtype4                           0                                 1
  subtype5                           0                                 1
  subtype6                           0                                 1
          vv
clus       UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 1
  subtype2                                 1
  subtype3                                 1
  subtype4                                 1
  subtype5                                 0
  subtype6                                 0
D4V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             1        1
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         1        0
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                0        4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        1
  LOWER EXTREMITY - FOOT/ANKLE                                   0        0
  LOWER EXTREMITY - GROIN                                        0        1
  LOWER EXTREMITY - LOWER LEG/CALF                               1        4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        1
  LOWER EXTREMITY - THIGH/KNEE                                   9        5
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       1        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             10       16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       2        0
  SUPERFICIAL TRUNK - BUTTOCK                                    1        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              0        2
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1        1
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             3        0
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        1
  GYNECOLOGICAL - OVARY                                          0        1
  GYNECOLOGICAL - UTERUS                                         3       16
  HEAD AND NECK - HEAD                                           0        1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                0        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        1
  LOWER EXTREMITY - GROIN                                        1        0
  LOWER EXTREMITY - LOWER LEG/CALF                               8        2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        4        0
  LOWER EXTREMITY - THIGH/KNEE                                  14        5
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        3
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              6       21
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             2        0
  SUPERFICIAL TRUNK - BACK                                       1        1
  SUPERFICIAL TRUNK - BUTTOCK                                    3        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              2        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1        1
                                                         clus
vv                                                        subtype5 subtype6
  CHEST - BREAST                                                 1        0
  CHEST - CHEST WALL                                             0        1
  CHEST - LUNG/PLEURA                                            0        1
  CHEST - OTHER (PLEASE SPECIFY                                  0        1
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         0        2
  HEAD AND NECK - HEAD                                           0        1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        1
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                1        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   1        2
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               0        0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        0
  LOWER EXTREMITY - THIGH/KNEE                                   2        5
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               1        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             12        0
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       0        1
  SUPERFICIAL TRUNK - BUTTOCK                                    0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        0
[1] 29  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
          cls
clus        0  1
  subtype1 12 15
  subtype2 14 23
  subtype3 23 26
  subtype4 46 22
  subtype5  8 11
  subtype6 14  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   15
  subtype2   14   23
  subtype3   23   26
  subtype4   46   22
  subtype5    8   11
  subtype6   14    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       12       14       23       46        8       14
  MALE         15       23       26       22       11        8
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
          cls
clus        0  1
  subtype1 17 10
  subtype2 28  9
  subtype3 28 20
  subtype4 58  7
  subtype5 15  4
  subtype6 12  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   10
  subtype2   28    9
  subtype3   28   20
  subtype4   58    7
  subtype5   15    4
  subtype6   12    9
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        17       28       28       58       15       12
  YES       10        9       20        7        4        9
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA
  subtype1                           11
  subtype2                           24
  subtype3                            4
  subtype4                            3
  subtype5                           10
  subtype6                            2
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        0
  subtype2                                                                        0
  subtype3                                                                        0
  subtype4                                                                        0
  subtype5                                                                        0
  subtype6                                                                        1
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                    1
  subtype2                    0
  subtype3                   12
  subtype4                   62
  subtype5                    2
  subtype6                    5
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                0               10
  subtype2                                                1                5
  subtype3                                                2                5
  subtype4                                                0                0
  subtype5                                                0                0
  subtype6                                                6                2
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       2
  subtype2                                                       5
  subtype3                                                      15
  subtype4                                                       1
  subtype5                                                       4
  subtype6                                                       2
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        0                           0
  subtype2                                        0                           0
  subtype3                                        0                           0
  subtype4                                        1                           0
  subtype5                                        0                           0
  subtype6                                        0                           1
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             0
  subtype2                             0
  subtype3                             0
  subtype4                             0
  subtype5                             1
  subtype6                             3
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          3
  subtype2                                          2
  subtype3                                         11
  subtype4                                          1
  subtype5                                          2
  subtype6                                          0
D4V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   11
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                               10
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      3
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   24
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            0
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                                5
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      2
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    4
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           12
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                2
  MYXOFIBROSARCOMA                                                                5
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                     11
                                                                          clus
vv                                                                         subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                                    3
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           62
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        1
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      1
                                                                          clus
vv                                                                         subtype5
  DEDIFFERENTIATED LIPOSARCOMA                                                   10
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            2
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      2
                                                                          clus
vv                                                                         subtype6
  DEDIFFERENTIATED LIPOSARCOMA                                                    2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                            5
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                6
  MYXOFIBROSARCOMA                                                                2
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     1
  SYNOVIAL SARCOMA - MONOPHASIC                                                   3
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      0
[1] 10  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 15 10  1  1
  subtype2 18 15  1  2
  subtype3 27 15  1  6
  subtype4 49 12  1  6
  subtype5  9  9  1  0
  subtype6 10  3  2  7
D4V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       15       18       27       49        9       10
  R1       10       15       15       12        9        3
  R2        1        1        1        1        1        2
  RX        1        2        6        6        0        7
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    26
  subtype2     1                         0    36
  subtype3     1                         5    39
  subtype4     3                         5    57
  subtype5     1                         0    18
  subtype6     0                         2    19
D4V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        1        1        3        1
  BLACK OR AFRICAN AMERICAN        1        0        5        5        0
  WHITE                           26       36       39       57       18
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        2
  WHITE                           19
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
          cls
clus        0  1
  subtype1  1 25
  subtype2  0 35
  subtype3  2 40
  subtype4  0 59
  subtype5  0 16
  subtype6  0 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   25
  subtype2    0   35
  subtype3    2   40
  subtype4    0   59
  subtype5    0   16
  subtype6    0   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        2        0        0        0
  NOT HISPANIC OR LATINO       25       35       40       59       16       16
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 77 39
  subtype2 53 25
  subtype3 34 30
subtype1 subtype2 subtype3 
     116       78       64 
subtype1 subtype2 subtype3 
      39       25       30 
$subtype1
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HS TCGA-3B-A9HT 
       50.01        36.30        19.69        31.53        44.91        54.74 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        0.56        14.04        38.24        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
        6.28        27.81         9.70        83.38        54.77        43.76 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       86.83        33.44        34.68        31.86        35.77         4.54 
TCGA-DX-A48K TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       31.27        28.96         9.11        17.79        21.63         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
       34.55        66.31        67.20        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU 
       74.10        64.21        21.30        20.05        15.22        12.20 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       17.95        14.43        61.97        33.07        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       35.77        14.07        51.91       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       36.69        60.66        19.43         6.58        17.79        12.00 
TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       15.72        86.10        12.07        66.74         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB35 
      106.55       106.45        13.28        50.40       101.98        30.51 
TCGA-DX-AB37 TCGA-FX-A3TO TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
       84.66        20.32        48.30         3.22        19.89        37.12 
TCGA-IS-A3K7 TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y8 
      143.41        17.36        23.38         5.19        13.35        25.41 
TCGA-MB-A5Y9 TCGA-MB-A8JK TCGA-MJ-A68J TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QC-A7B5 
        8.28        21.73        17.98         6.35        20.94        13.08 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SG-A849 
        1.84        46.82        48.59        35.90        18.94        17.52 
TCGA-SI-A71O TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-VT-AB3D TCGA-WK-A8XO 
       22.82        13.22        13.41        26.17        12.46        11.93 
TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       22.62        26.43        36.82        25.71        15.95        16.83 
TCGA-X6-A8C6 TCGA-Z4-AAPG 
       35.08        15.98 

$subtype2
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       53.49        68.55        88.57        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A3U7 
       10.32        38.47        36.03        18.64        26.56        51.02 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        61.91        55.07        50.43        34.88        81.90 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
        9.73        24.26        40.80        46.03        26.47       102.41 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EL 
       25.15        24.59        66.05        23.44        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 
       48.36        15.62        31.13        19.89        15.48        34.88 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       15.91        12.62        33.30        52.11         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       26.93        19.53         1.38        25.22        52.27        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
      116.88        13.58        73.28        22.62        16.41       101.26 
TCGA-K1-A42W TCGA-K1-A42X TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5YA 
       62.17       123.78        36.36        16.41        35.28         0.49 
TCGA-MJ-A68H TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP 
       14.99         7.46       120.20        37.55        81.01        18.08 
TCGA-QQ-A5VD TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB 
       37.12        72.72        38.27        65.46        56.61         9.04 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X9-A971 
       63.35        29.92        18.08        18.35        38.96        15.58 

$subtype3
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A3LS 
       32.71        12.85        74.66        60.30         8.58         9.04 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A7EI 
      124.73        44.68        10.68        24.69        15.95        34.49 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BJ TCGA-DX-AATS TCGA-DX-AB2H 
      135.48        29.49        48.20         9.34         1.15        15.85 
TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       40.60        22.85        60.00        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A8OO TCGA-HB-A3YV TCGA-HS-A5N8 
       31.63        16.60        21.70         8.05         4.57         0.72 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
        5.92         1.05         3.91        53.33        11.70        22.03 
TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PT-A8TR 
       19.73        22.39        10.45         7.36        38.63        20.52 
TCGA-QC-AA9N TCGA-QQ-A5VA TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       17.65        18.08       188.15       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q 
       10.52         0.72        16.77         3.88        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 
        8.61        19.63        10.72         4.80        41.49        17.72 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       36.43         4.37        13.38        15.95 

subtype1 subtype2 subtype3 
    0.56     0.49     0.72 
subtype1 subtype2 subtype3 
  143.41   123.78   188.15 
subtype1 subtype2 subtype3 
   27.12    34.88    19.68 
[1] "0.6 - 143.4 (27.1)" "0.5 - 123.8 (34.9)" "0.7 - 188.2 (19.7)"
D5V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  4                   0
  subtype2              0                  0                   0
  subtype3              1                  3                   2
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             0
  subtype2                   1                             1
  subtype3                   0                             1
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                      1                    2
  subtype2                     0                     22                    0
  subtype3                     1                      6                    0
          vv
clus       HEAD AND NECK - NECK HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                    0                                     1
  subtype2                    0                                     0
  subtype3                    1                                     1
          vv
clus       LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                                0
  subtype2                                0
  subtype3                                1
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              2
  subtype3                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               5
  subtype2                               3
  subtype3                               3
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       1                            0
  subtype2                                       0                            1
  subtype3                                       1                            3
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       2                               13
  subtype2                       0                                3
  subtype3                       0                                1
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       4                           31
  subtype2                                       0                            6
  subtype3                                       1                            7
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       4
  subtype3                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         0
  subtype2                                         1
  subtype3                                         1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                2
  subtype2                                                0
  subtype3                                                3
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        0
  subtype2                                        5
  subtype3                                        3
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       0
  subtype2                                                       1
  subtype3                                                       1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          0
  subtype2                                          1
  subtype3                                          0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                35
  subtype2                                                22
  subtype3                                                15
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  3
  subtype3                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  2                        3
  subtype2                                  0                        1
  subtype3                                  0                        1
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  subtype1                           2                         0
  subtype2                           0                         0
  subtype3                           2                         1
          vv
clus       UPPER EXTREMITY - SHOULDER/AXILLA UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 4                                 4
  subtype2                                 1                                 0
  subtype3                                 2                                 1
D5V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             4        0
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        1
  CHEST - OTHER (PLEASE SPECIFY                                  0        1
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         1       22
  HEAD AND NECK - HEAD                                           2        0
  HEAD AND NECK - NECK                                           0        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          1        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                5        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        1
  LOWER EXTREMITY - GROIN                                        2        0
  LOWER EXTREMITY - LOWER LEG/CALF                              13        3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        4        0
  LOWER EXTREMITY - THIGH/KNEE                                  31        6
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               2        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             35       22
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             2        0
  SUPERFICIAL TRUNK - BACK                                       3        1
  SUPERFICIAL TRUNK - BUTTOCK                                    2        0
  SUPERFICIAL TRUNK - FLANK                                      0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              4        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                              4        0
                                                         clus
vv                                                        subtype3
  CHEST - BREAST                                                 1
  CHEST - CHEST WALL                                             3
  CHEST - LUNG/PLEURA                                            2
  CHEST - MEDIASTINUM                                            0
  CHEST - OTHER (PLEASE SPECIFY                                  1
  GYNECOLOGICAL - OVARY                                          1
  GYNECOLOGICAL - UTERUS                                         6
  HEAD AND NECK - HEAD                                           0
  HEAD AND NECK - NECK                                           1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          1
  LOWER ABDOMINAL/PELVIC - BLADDER                               1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0
  LOWER ABDOMINAL/PELVIC - PELVIC                                3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1
  LOWER EXTREMITY - FOOT/ANKLE                                   3
  LOWER EXTREMITY - GROIN                                        0
  LOWER EXTREMITY - LOWER LEG/CALF                               1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1
  LOWER EXTREMITY - THIGH/KNEE                                   7
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             15
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0
  SUPERFICIAL TRUNK - BACK                                       1
  SUPERFICIAL TRUNK - BUTTOCK                                    2
  SUPERFICIAL TRUNK - FLANK                                      1
  UPPER EXTREMITY - SHOULDER/AXILLA                              2
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1
[1] 33  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
          cls
clus        0  1
  subtype1 50 66
  subtype2 55 23
  subtype3 36 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   66
  subtype2   55   23
  subtype3   36   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       50       55       36
  MALE         66       23       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"
D5V5, binary
          cls
clus        0  1
  subtype1 68 46
  subtype2 63 10
  subtype3 49 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68   46
  subtype2   63   10
  subtype3   49   15
     clus
vv    subtype1 subtype2 subtype3
  NO        68       63       49
  YES       46       10       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"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  subtype1                           38             0
  subtype2                            1             0
  subtype3                           19             2
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        1
  subtype2                                                                        0
  subtype3                                                                        0
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                   12
  subtype2                   77
  subtype3                   15
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                1               22
  subtype2                                                0                0
  subtype3                                                8                2
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                      26
  subtype2                                                       0
  subtype3                                                       3
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        0                           0
  subtype2                                        0                           0
  subtype3                                        2                           2
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             0
  subtype2                             0
  subtype3                             6
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                         16
  subtype2                                          0
  subtype3                                          5
D5V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   38
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                           12
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                               22
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        26
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                     16
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                    1
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           77
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      0
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                   19
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           15
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                8
  MYXOFIBROSARCOMA                                                                2
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        2
  SYNOVIAL SARCOMA - BIPHASIC                                                     2
  SYNOVIAL SARCOMA - MONOPHASIC                                                   6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      5
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 69 40  3  4
  subtype2 57 13  1  7
  subtype3 28 15  5 15
D5V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       69       57       28
  R1       40       13       15
  R2        3        1        5
  RX        4        7       15
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         6   103
  subtype2     2                         8    64
  subtype3     1                         4    58
D5V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        2        1
  BLACK OR AFRICAN AMERICAN        6        8        4
  WHITE                          103       64       58
[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"
D5V9, binary
          cls
clus         0   1
  subtype1   3 104
  subtype2   0  66
  subtype3   2  52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  104
  subtype2    0   66
  subtype3    2   52
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        0        2
  NOT HISPANIC OR LATINO      104       66       52
[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 30 17
  subtype2 20  3
  subtype3 34 16
  subtype4 26 21
  subtype5 18 11
  subtype6 20  9
  subtype7 16 17
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      47       23       50       47       29       29       33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      17        3       16       21       11        9       17 
$subtype1
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HO TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       50.01        19.69        31.53        32.71        38.24        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       54.21        59.24        33.53        66.87         6.28        27.81 
TCGA-DX-A2J0 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A6BF 
        9.70        86.83        33.44        34.68        31.86         9.11 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ 
       34.55        66.31        67.20        23.54        50.50        74.10 
TCGA-DX-A6Z0 TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT 
       64.21        12.20        17.95        38.17       124.37        35.54 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2T 
       60.66        19.43        12.00        15.72        86.10        77.88 
TCGA-DX-AB2V TCGA-DX-AB35 TCGA-FX-A3TO TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
      106.55        30.51        20.32         3.22        19.89        37.12 
TCGA-K1-A6RU TCGA-LI-A9QH TCGA-QQ-A5V9 TCGA-UE-A6QU TCGA-X6-A8C6 
       23.38        13.35        46.82        13.41        35.08 

$subtype2
TCGA-3B-A9HJ TCGA-DX-A1KZ TCGA-DX-A23T TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       36.30        36.69         5.26        83.38        54.77        43.76 
TCGA-DX-A3U6 TCGA-DX-A6BE TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BL 
       35.77        28.96        20.05        15.22        61.97        33.07 
TCGA-DX-A8BO TCGA-DX-AB2S TCGA-DX-AB32 TCGA-DX-AB37 TCGA-KD-A5QS TCGA-MB-A5Y9 
       35.77         9.21       101.98        84.66        36.36         8.28 
TCGA-MB-A8JK TCGA-MJ-A68J TCGA-QC-A6FX TCGA-UE-A6QT TCGA-VT-AB3D 
       21.73        17.98        20.94        13.22        12.46 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ 
       53.49        68.55        88.57        25.25        10.32        38.47 
TCGA-3B-A9I0 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       36.03        51.02        14.99        55.07        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       81.90         9.73        24.26        40.80        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EL 
      102.41        25.15        66.05        23.44        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-FX-A3NJ TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A3OV 
       48.36        15.62        31.13        12.62        33.30        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-K1-A3PN TCGA-K1-A42W 
       19.53         1.38        25.22        52.27       101.26        62.17 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP 
        0.49        14.99       120.20        37.55        81.01        18.08 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-X6-A7WA TCGA-X6-A7WD 
       72.72        38.27        65.46        56.61        29.92        18.35 
TCGA-X6-A8C5 TCGA-X9-A971 
       38.96        15.58 

$subtype4
TCGA-3B-A9HS TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3LW 
       44.91        14.04        12.85        74.66         8.58       124.73 
TCGA-DX-A3M1 TCGA-DX-A48N TCGA-DX-A6BH TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ 
       44.68        24.69        21.63        34.49       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A8BM TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB3A 
       48.20        44.68        15.85        40.60        22.85        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NK TCGA-FX-A8OO TCGA-HB-A3YV 
       50.89        71.31        31.63        16.60         8.05         4.57 
TCGA-HS-A5N8 TCGA-IW-A3M5 TCGA-JV-A75J TCGA-LI-A67I TCGA-MJ-A850 TCGA-MO-A47R 
        0.72         5.92         3.91        22.03        22.39        10.45 
TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-QQ-A8VH 
       38.63        20.52        17.65       188.15        64.77        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
        0.72        16.77         3.88        25.35        32.75        19.63 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A9VC 
        4.80        41.49        17.72        36.43        13.38 

$subtype5
TCGA-3B-A9HT TCGA-3R-A8YX TCGA-DX-A3U8 TCGA-DX-A48K TCGA-DX-A6YQ TCGA-DX-A6YX 
       54.74         0.56         4.54        31.27         3.06        16.87 
TCGA-DX-A7EF TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BU TCGA-DX-AB2E 
       21.30        14.43        14.07        51.91        36.69        17.79 
TCGA-DX-AB2Q TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB36 TCGA-K1-A6RT 
       66.74       106.45        13.28        50.40        60.00        17.36 
TCGA-KF-A41W TCGA-PC-A5DM TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A849 TCGA-VT-A80J 
       11.70         6.35        35.90       111.98        17.52        26.17 
TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-Z4-AAPF TCGA-Z4-AAPG 
       26.43        15.95        16.83        15.95        15.98 

$subtype6
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A3UB TCGA-DX-A6B9 
       14.37        42.84        18.64        26.56        61.91        24.59 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N9 
       21.70        19.89        15.48        34.88        15.91        52.11 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
        9.80        26.93        28.21       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PO TCGA-K1-A42X TCGA-KD-A5QT TCGA-KD-A5QU 
       22.62        16.41        53.33       123.78        16.41        35.28 
TCGA-MO-A47P TCGA-QQ-A5VD TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WB 
        7.46        37.12         9.04        63.35        18.08 

$subtype7
TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LS TCGA-DX-A3UA TCGA-DX-A6B8 
       42.54        76.41        60.30         9.04        10.68        15.95 
TCGA-DX-A6BG TCGA-DX-A8BJ TCGA-DX-A8BS TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2P 
       17.79         9.34        27.95         6.58         1.15        12.07 
TCGA-HB-A2OT TCGA-IS-A3K7 TCGA-JV-A5VF TCGA-K1-A6RV TCGA-MB-A5Y8 TCGA-MB-A8JL 
       48.30       143.41         1.05         5.19        25.41        19.73 
TCGA-N1-A6IA TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VD 
        7.36        13.08         1.84        18.08        48.59       130.32 
TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8Y0 
       18.94        22.82         8.61        10.72        11.93        22.62 
TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-Z4-A8JB 
       36.82        25.71         4.37 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    3.22     5.26     0.49     0.72     0.56     7.46     1.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  124.37   101.98   120.20   188.15   111.98   123.78   143.41 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   33.53    33.07    38.37    22.39    17.52    24.59    17.79 
[1] "3.2 - 124.4 (33.5)" "5.3 - 102.0 (33.1)" "0.5 - 120.2 (38.4)"
[4] "0.7 - 188.2 (22.4)" "0.6 - 112.0 (17.5)" "7.5 - 123.8 (24.6)"
[7] "1.1 - 143.4 (17.8)"
D6V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  2                   0
  subtype2              0                  1                   0
  subtype3              0                  0                   0
  subtype4              0                  1                   2
  subtype5              0                  1                   0
  subtype6              0                  0                   0
  subtype7              1                  2                   0
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             0
  subtype2                   0                             0
  subtype3                   1                             1
  subtype4                   0                             1
  subtype5                   0                             0
  subtype6                   0                             0
  subtype7                   0                             0
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                      0                    0
  subtype2                     0                      1                    1
  subtype3                     0                      1                    0
  subtype4                     0                      4                    0
  subtype5                     0                      1                    0
  subtype6                     1                     20                    0
  subtype7                     0                      2                    1
          vv
clus       HEAD AND NECK - NECK HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                    0                                     0
  subtype2                    0                                     0
  subtype3                    0                                     0
  subtype4                    1                                     1
  subtype5                    0                                     1
  subtype6                    0                                     0
  subtype7                    0                                     0
          vv
clus       LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                                0
  subtype2                                0
  subtype3                                0
  subtype4                                0
  subtype5                                0
  subtype6                                1
  subtype7                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              0
  subtype3                                              2
  subtype4                                              0
  subtype5                                              0
  subtype6                                              0
  subtype7                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               2
  subtype2                               0
  subtype3                               2
  subtype4                               3
  subtype5                               0
  subtype6                               1
  subtype7                               3
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       0                            0
  subtype2                                       0                            0
  subtype3                                       0                            0
  subtype4                                       0                            2
  subtype5                                       1                            0
  subtype6                                       0                            1
  subtype7                                       1                            1
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       0                                2
  subtype2                       1                                3
  subtype3                       0                                3
  subtype4                       0                                0
  subtype5                       0                                7
  subtype6                       0                                0
  subtype7                       1                                2
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       1                           11
  subtype2                                       0                            3
  subtype3                                       0                            6
  subtype4                                       0                            7
  subtype5                                       2                           10
  subtype6                                       0                            0
  subtype7                                       2                            7
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       0
  subtype3                                       2
  subtype4                                       0
  subtype5                                       0
  subtype6                                       2
  subtype7                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         0
  subtype2                                         0
  subtype3                                         1
  subtype4                                         1
  subtype5                                         0
  subtype6                                         0
  subtype7                                         0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                1
  subtype2                                                1
  subtype3                                                0
  subtype4                                                2
  subtype5                                                0
  subtype6                                                0
  subtype7                                                1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        0
  subtype2                                        0
  subtype3                                        4
  subtype4                                        3
  subtype5                                        0
  subtype6                                        1
  subtype7                                        0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       0
  subtype2                                                       0
  subtype3                                                       1
  subtype4                                                       1
  subtype5                                                       0
  subtype6                                                       0
  subtype7                                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          1
  subtype4                                          0
  subtype5                                          0
  subtype6                                          0
  subtype7                                          0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                23
  subtype2                                                 6
  subtype3                                                21
  subtype4                                                12
  subtype5                                                 2
  subtype6                                                 1
  subtype7                                                 7
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  2
  subtype4                                                  0
  subtype5                                                  0
  subtype6                                                  1
  subtype7                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  0                        1
  subtype2                                  1                        2
  subtype3                                  0                        1
  subtype4                                  0                        1
  subtype5                                  1                        0
  subtype6                                  0                        0
  subtype7                                  0                        0
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  subtype1                           1                         0
  subtype2                           0                         0
  subtype3                           0                         0
  subtype4                           2                         1
  subtype5                           0                         0
  subtype6                           0                         0
  subtype7                           1                         0
          vv
clus       UPPER EXTREMITY - SHOULDER/AXILLA UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 2                                 1
  subtype2                                 1                                 2
  subtype3                                 1                                 0
  subtype4                                 1                                 0
  subtype5                                 1                                 2
  subtype6                                 0                                 0
  subtype7                                 1                                 0
D6V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             2        1
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         0        1
  HEAD AND NECK - HEAD                                           0        1
  HEAD AND NECK - NECK                                           0        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                2        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        0
  LOWER EXTREMITY - GROIN                                        0        1
  LOWER EXTREMITY - LOWER LEG/CALF                               2        3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        0
  LOWER EXTREMITY - THIGH/KNEE                                  11        3
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               1        1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             23        6
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        1
  SUPERFICIAL TRUNK - BACK                                       1        2
  SUPERFICIAL TRUNK - BUTTOCK                                    1        0
  SUPERFICIAL TRUNK - FLANK                                      0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              2        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1        2
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             0        1
  CHEST - LUNG/PLEURA                                            0        2
  CHEST - MEDIASTINUM                                            1        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        1
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         1        4
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           0        1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        1
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 2        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                2        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        2
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               3        0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        0
  LOWER EXTREMITY - THIGH/KNEE                                   6        7
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        2        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       4        3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             21       12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             2        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       1        1
  SUPERFICIAL TRUNK - BUTTOCK                                    0        2
  SUPERFICIAL TRUNK - FLANK                                      0        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        0
                                                         clus
vv                                                        subtype5 subtype6
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             1        0
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        0
  GYNECOLOGICAL - OVARY                                          0        1
  GYNECOLOGICAL - UTERUS                                         1       20
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           0        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          1        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                0        1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        1
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               7        0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        2        0
  LOWER EXTREMITY - THIGH/KNEE                                  10        0
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              2        1
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        0
  SUPERFICIAL TRUNK - BACK                                       0        0
  SUPERFICIAL TRUNK - BUTTOCK                                    0        0
  SUPERFICIAL TRUNK - FLANK                                      0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              2        0
                                                         clus
vv                                                        subtype7
  CHEST - BREAST                                                 1
  CHEST - CHEST WALL                                             2
  CHEST - LUNG/PLEURA                                            0
  CHEST - MEDIASTINUM                                            0
  CHEST - OTHER (PLEASE SPECIFY                                  0
  GYNECOLOGICAL - OVARY                                          0
  GYNECOLOGICAL - UTERUS                                         2
  HEAD AND NECK - HEAD                                           1
  HEAD AND NECK - NECK                                           0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0
  LOWER ABDOMINAL/PELVIC - PELVIC                                3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1
  LOWER EXTREMITY - FOOT/ANKLE                                   1
  LOWER EXTREMITY - GROIN                                        1
  LOWER EXTREMITY - LOWER LEG/CALF                               2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        2
  LOWER EXTREMITY - THIGH/KNEE                                   7
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              7
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0
  SUPERFICIAL TRUNK - BACK                                       0
  SUPERFICIAL TRUNK - BUTTOCK                                    1
  SUPERFICIAL TRUNK - FLANK                                      0
  UPPER EXTREMITY - SHOULDER/AXILLA                              1
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0
[1] 33  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
          cls
clus        0  1
  subtype1 21 26
  subtype2 10 13
  subtype3 30 20
  subtype4 25 22
  subtype5 14 15
  subtype6 25  4
  subtype7 16 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   26
  subtype2   10   13
  subtype3   30   20
  subtype4   25   22
  subtype5   14   15
  subtype6   25    4
  subtype7   16   17
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       21       10       30       25       14       25       16
  MALE         26       13       20       22       15        4       17
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 32 14
  subtype2 13  9
  subtype3 40  8
  subtype4 33 14
  subtype5 18 11
  subtype6 25  2
  subtype7 19 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   14
  subtype2   13    9
  subtype3   40    8
  subtype4   33   14
  subtype5   18   11
  subtype6   25    2
  subtype7   19   13
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        32       13       40       33       18       25       19
  YES       14        9        8       14       11        2       13
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  subtype1                           22             0
  subtype2                           10             0
  subtype3                            0             0
  subtype4                           16             0
  subtype5                            2             0
  subtype6                            1             0
  subtype7                            7             2
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        0
  subtype2                                                                        0
  subtype3                                                                        0
  subtype4                                                                        0
  subtype5                                                                        0
  subtype6                                                                        0
  subtype7                                                                        1
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                    0
  subtype2                    1
  subtype3                   50
  subtype4                    7
  subtype5                    8
  subtype6                   28
  subtype7                   10
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                0               14
  subtype2                                                0                3
  subtype3                                                0                0
  subtype4                                                8                2
  subtype5                                                0                5
  subtype6                                                0                0
  subtype7                                                1                0
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       6
  subtype2                                                       6
  subtype3                                                       0
  subtype4                                                       2
  subtype5                                                       9
  subtype6                                                       0
  subtype7                                                       6
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        0                           0
  subtype2                                        0                           0
  subtype3                                        0                           0
  subtype4                                        1                           2
  subtype5                                        1                           0
  subtype6                                        0                           0
  subtype7                                        0                           0
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             0
  subtype2                             0
  subtype3                             0
  subtype4                             6
  subtype5                             0
  subtype6                             0
  subtype7                             0
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          5
  subtype2                                          3
  subtype3                                          0
  subtype4                                          3
  subtype5                                          4
  subtype6                                          0
  subtype7                                          6
D6V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   22
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            0
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                               14
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      5
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   10
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                3
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      3
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    0
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           50
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      0
                                                                          clus
vv                                                                         subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                                   16
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            7
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                8
  MYXOFIBROSARCOMA                                                                2
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        1
  SYNOVIAL SARCOMA - BIPHASIC                                                     2
  SYNOVIAL SARCOMA - MONOPHASIC                                                   6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      3
                                                                          clus
vv                                                                         subtype5
  DEDIFFERENTIATED LIPOSARCOMA                                                    2
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            8
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                5
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        1
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      4
                                                                          clus
vv                                                                         subtype6
  DEDIFFERENTIATED LIPOSARCOMA                                                    1
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           28
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      0
                                                                          clus
vv                                                                         subtype7
  DEDIFFERENTIATED LIPOSARCOMA                                                    7
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                           10
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      6
[1] 11  7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 25 21  1  0
  subtype2 14  6  0  3
  subtype3 38 11  0  1
  subtype4 21 11  5  9
  subtype5 18  8  1  2
  subtype6 20  2  1  6
  subtype7 18  9  1  5
D6V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       25       14       38       21       18       20       18
  R1       21        6       11       11        8        2        9
  R2        1        0        0        5        1        1        1
  RX        0        3        1        9        2        6        5
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    45
  subtype2     1                         2    20
  subtype3     0                         5    44
  subtype4     1                         2    43
  subtype5     1                         0    24
  subtype6     2                         3    21
  subtype7     0                         5    28
D6V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        1        0        1        1
  BLACK OR AFRICAN AMERICAN        1        2        5        2        0
  WHITE                           45       20       44       43       24
                           clus
vv                          subtype6 subtype7
  ASIAN                            2        0
  BLACK OR AFRICAN AMERICAN        3        5
  WHITE                           21       28
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus        0  1
  subtype1  1 44
  subtype2  1 21
  subtype3  0 46
  subtype4  2 37
  subtype5  1 24
  subtype6  0 21
  subtype7  0 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   44
  subtype2    1   21
  subtype3    0   46
  subtype4    2   37
  subtype5    1   24
  subtype6    0   21
  subtype7    0   29
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        1        0        2        1        0
  NOT HISPANIC OR LATINO       44       21       46       37       24       21
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO       29
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 65 44
  subtype2 35 16
  subtype3 63 35
subtype1 subtype2 subtype3 
     109       51       98 
subtype1 subtype2 subtype3 
      44       16       35 
$subtype1
TCGA-3B-A9HI TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       50.01        44.91         0.56        32.71        38.24        18.54 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 
       54.77         9.04        43.76       124.73        44.68        34.68 
TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR 
       35.77        31.27        24.69        17.79        21.63        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EO 
       66.31        67.20        50.50        21.30        34.49       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BL TCGA-DX-A8BN 
       29.49        48.20        15.22        12.20        33.07        38.17 
TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       35.54        19.43         1.15        12.00        15.72        15.85 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB35 
       40.60        86.10        12.07       106.55        13.28        30.51 
TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NK 
       60.00        32.15        50.89        71.31        31.63        16.60 
TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 
       20.32         8.05         4.57        19.89        37.12       143.41 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RV TCGA-KF-A41W 
        5.92        16.41         1.05         3.91         5.19        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R 
       13.35        25.41         8.28        19.73        22.39        10.45 
TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-AA9N 
        7.36         6.35        38.63        20.52        20.94        17.65 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VH TCGA-RN-A68Q 
       46.82        48.59       188.15       130.32        10.52         0.72 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        17.52        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A7W8 TCGA-X6-A7WC 
       19.63        11.93         4.80        41.49        26.43        36.82 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       35.08        17.72        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

$subtype2
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A23Y 
       36.30        19.69        31.53        36.69        54.21         6.28 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3UA TCGA-DX-A6BE TCGA-DX-A6BF 
       86.83        33.44        31.86        10.68        28.96         9.11 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7ES 
       16.18         3.06        23.54        16.87        74.10        20.05 
TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ 
       14.43        61.97        44.68        35.77        14.07        51.91 
TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
      124.37        60.66         6.58        66.74         9.21        77.88 
TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB37 TCGA-HB-A2OT TCGA-K1-A6RT TCGA-K1-A6RU 
      106.45        50.40        84.66        48.30        17.36        23.38 
TCGA-KD-A5QS TCGA-MB-A8JK TCGA-MJ-A68J TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VD 
       36.36        21.73        17.98        13.08        18.08        37.12 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SI-A71O TCGA-UE-A6QU TCGA-VT-A80J 
      111.98        64.77        16.77        22.82        13.41        26.17 
TCGA-VT-AB3D TCGA-WK-A8Y0 TCGA-X6-A8C2 
       12.46        22.62        25.71 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       53.49        68.55        88.57        54.74        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        38.47        36.03        18.64        26.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       14.04        12.85        51.02         4.54        14.99        61.91 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       55.07        50.43        34.88        81.90         9.73        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       40.80        46.03        26.47       102.41        47.57        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       15.95        24.59        66.05        23.44        64.21        88.31 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BS 
       75.32        48.36        15.62        17.95         9.34        27.95 
TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB30 TCGA-DX-AB32 TCGA-FX-A3NJ TCGA-FX-A3RE 
       36.69        17.79        22.85       101.98        31.13        21.70 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       19.89        15.48        34.88        15.91        12.62        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.72         9.80        80.48        26.93        19.53         3.22 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        1.38        25.22        52.27        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       73.28        22.62       101.26        53.33        62.17       123.78 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MO-A47P 
       16.41        35.28        22.03         0.49        14.99         7.46 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VC 
      120.20        37.55        81.01        18.08         1.84        35.90 
TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
       13.22        10.72        72.72        38.27        65.46        56.61 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 
        9.04        63.35        29.92        18.08        18.35        15.95 
TCGA-X6-A8C5 TCGA-X9-A971 
       38.96        15.58 

subtype1 subtype2 subtype3 
    0.56     3.06     0.49 
subtype1 subtype2 subtype3 
  188.15   124.37   123.78 
subtype1 subtype2 subtype3 
   25.35    26.17    27.44 
[1] "0.6 - 188.2 (25.4)" "3.1 - 124.4 (26.2)" "0.5 - 123.8 (27.4)"
D7V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              1                  3                   2
  subtype2              0                  2                   0
  subtype3              0                  2                   0
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             1
  subtype2                   0                             0
  subtype3                   1                             1
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                      6                    0
  subtype2                     0                      1                    1
  subtype3                     1                     21                    1
          vv
clus       HEAD AND NECK - NECK HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                    1                                     1
  subtype2                    0                                     0
  subtype3                    0                                     1
          vv
clus       LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                                0
  subtype2                                0
  subtype3                                1
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              0
  subtype3                                              2
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               8
  subtype2                               0
  subtype3                               3
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       1                            2
  subtype2                                       0                            2
  subtype3                                       1                            0
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       1                                6
  subtype2                       1                                6
  subtype3                       0                                4
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       2                           15
  subtype2                                       2                           15
  subtype3                                       1                           14
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       0
  subtype3                                       4
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         1
  subtype2                                         0
  subtype3                                         1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                4
  subtype2                                                1
  subtype3                                                0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        3
  subtype2                                        0
  subtype3                                        5
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       1
  subtype2                                                       0
  subtype3                                                       1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                36
  subtype2                                                13
  subtype3                                                25
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  3
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  1                        2
  subtype2                                  1                        2
  subtype3                                  0                        1
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  subtype1                           3                         1
  subtype2                           1                         0
  subtype3                           0                         0
          vv
clus       UPPER EXTREMITY - SHOULDER/AXILLA UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 2                                 4
  subtype2                                 2                                 1
  subtype3                                 3                                 0
D7V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 1        0
  CHEST - CHEST WALL                                             3        2
  CHEST - LUNG/PLEURA                                            2        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         6        1
  HEAD AND NECK - HEAD                                           0        1
  HEAD AND NECK - NECK                                           1        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          1        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                8        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   2        2
  LOWER EXTREMITY - GROIN                                        1        1
  LOWER EXTREMITY - LOWER LEG/CALF                               6        6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        2        2
  LOWER EXTREMITY - THIGH/KNEE                                  15       15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               4        1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       3        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             36       13
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        1
  SUPERFICIAL TRUNK - BACK                                       2        2
  SUPERFICIAL TRUNK - BUTTOCK                                    3        1
  SUPERFICIAL TRUNK - FLANK                                      1        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              2        2
  UPPER EXTREMITY - UPPER ARM/ELBOW                              4        1
                                                         clus
vv                                                        subtype3
  CHEST - BREAST                                                 0
  CHEST - CHEST WALL                                             2
  CHEST - LUNG/PLEURA                                            0
  CHEST - MEDIASTINUM                                            1
  CHEST - OTHER (PLEASE SPECIFY                                  1
  GYNECOLOGICAL - OVARY                                          1
  GYNECOLOGICAL - UTERUS                                        21
  HEAD AND NECK - HEAD                                           1
  HEAD AND NECK - NECK                                           0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          1
  LOWER ABDOMINAL/PELVIC - BLADDER                               1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 2
  LOWER ABDOMINAL/PELVIC - PELVIC                                3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1
  LOWER EXTREMITY - FOOT/ANKLE                                   0
  LOWER EXTREMITY - GROIN                                        0
  LOWER EXTREMITY - LOWER LEG/CALF                               4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1
  LOWER EXTREMITY - THIGH/KNEE                                  14
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             25
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0
  SUPERFICIAL TRUNK - BACK                                       1
  SUPERFICIAL TRUNK - BUTTOCK                                    0
  SUPERFICIAL TRUNK - FLANK                                      0
  UPPER EXTREMITY - SHOULDER/AXILLA                              3
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0
[1] 33  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
          cls
clus        0  1
  subtype1 52 57
  subtype2 25 26
  subtype3 63 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52   57
  subtype2   25   26
  subtype3   63   35
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       52       25       63
  MALE         57       26       35
[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"
D7V5, binary
          cls
clus        0  1
  subtype1 81 28
  subtype2 29 21
  subtype3 71 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   81   28
  subtype2   29   21
  subtype3   71   21
     clus
vv    subtype1 subtype2 subtype3
  NO        81       29       71
  YES       28       21       21
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  subtype1                           41             2
  subtype2                           15             0
  subtype3                            3             0
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        0
  subtype2                                                                        0
  subtype3                                                                        1
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                   17
  subtype2                    6
  subtype3                   81
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                6                8
  subtype2                                                3                9
  subtype3                                                0                7
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                      14
  subtype2                                                      12
  subtype3                                                       3
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        2                           2
  subtype2                                        0                           0
  subtype3                                        0                           0
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             6
  subtype2                             0
  subtype3                             0
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                         11
  subtype2                                          6
  subtype3                                          3
D7V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   41
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           17
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                6
  MYXOFIBROSARCOMA                                                                8
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        2
  SYNOVIAL SARCOMA - BIPHASIC                                                     2
  SYNOVIAL SARCOMA - MONOPHASIC                                                   6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                     11
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   15
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            6
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                3
  MYXOFIBROSARCOMA                                                                9
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      6
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    3
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                           81
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                7
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      3
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 57 36  6 10
  subtype2 29 13  0  8
  subtype3 68 19  3  8
D7V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       57       29       68
  R1       36       13       19
  R2        6        0        3
  RX       10        8        8
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         6   101
  subtype2     1                         4    44
  subtype3     4                         8    81
D7V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        4
  BLACK OR AFRICAN AMERICAN        6        4        8
  WHITE                          101       44       81
[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"
D7V9, binary
          cls
clus        0  1
  subtype1  3 94
  subtype2  2 47
  subtype3  0 81
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   94
  subtype2    2   47
  subtype3    0   81
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        2        0
  NOT HISPANIC OR LATINO       94       47       81
[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 49 32
  subtype2 36 17
  subtype3 66 35
  subtype4 12 11
subtype1 subtype2 subtype3 subtype4 
      81       53      101       23 
subtype1 subtype2 subtype3 subtype4 
      32       17       35       11 
$subtype1
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW 
       50.01        19.69        31.53        44.91         0.56        32.71 
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23T 
       38.24        18.54        59.24        33.53        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 
       76.41        66.87        27.81        60.30         9.70        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 
       54.77         9.04        43.76       124.73        44.68        34.68 
TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR 
       10.68        24.69         9.11        17.79        21.63        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BK 
       66.31        67.20        16.87        15.22        12.20        61.97 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F 
       33.07        38.17        35.54        19.43         1.15        12.00 
TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z 
       15.72        86.10        12.07       106.55        13.28        50.40 
TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3NK TCGA-FX-A3TO TCGA-HB-A3YV 
       30.51        32.15        31.63        16.60        20.32         4.57 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W 
       19.89        37.12       143.41        23.38         5.19        11.70 
TCGA-LI-A9QH TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PT-A8TR 
       13.35        10.45         7.36         6.35        38.63        20.52 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-SG-A6Z4 
       20.94        13.08        46.82        48.59       130.32        18.94 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C6 
       17.52         8.61        11.93        26.43        36.82        35.08 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
        4.37        13.38        15.98 

$subtype2
TCGA-3B-A9HJ TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23Y TCGA-DX-A3LU 
       36.30        36.69        54.21        42.54         6.28        86.83 
TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A6BE TCGA-DX-A6BK TCGA-DX-A6YQ 
       33.44        35.77        31.27        28.96        16.18         3.06 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ES TCGA-DX-A8BH 
       50.50        74.10        21.30        34.49        20.05        14.43 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ 
       44.68        35.77        51.91       124.37        60.66         6.58 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB36 TCGA-DX-AB37 
       66.74         9.21        77.88       106.45        60.00        84.66 
TCGA-FX-A3RE TCGA-HB-A2OT TCGA-K1-A6RT TCGA-KD-A5QS TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       21.70        48.30        17.36        36.36        25.41         8.28 
TCGA-MB-A8JK TCGA-MJ-A68J TCGA-QC-AA9N TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF 
       21.73        17.98        17.65        18.08        35.90       111.98 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71O TCGA-SI-A71P TCGA-UE-A6QU 
       64.77         0.72        16.77        22.82        25.35        13.41 
TCGA-VT-A80J TCGA-VT-AB3D TCGA-WK-A8Y0 TCGA-X6-A8C2 TCGA-Z4-AAPF 
       26.17        12.46        22.62        25.71        15.95 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       53.49        68.55        88.57        54.74        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        38.47        36.03        18.64        26.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       14.04        12.85        31.86        51.02         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       61.91        55.07        50.43        34.88        81.90         9.73 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        40.80        46.03        26.47       102.41        47.57 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YU 
       25.15        15.95        24.59        66.05        23.44        23.54 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BG 
       64.21        88.31        75.32        48.36        15.62        17.95 
TCGA-DX-A8BJ TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB30 
        9.34        14.07        27.95        36.69        17.79        22.85 
TCGA-DX-AB32 TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HB-A43Z 
      101.98        31.13        19.89        15.48        34.88        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        33.30         0.72         9.80        80.48        26.93 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       19.53         3.22         1.38        25.22        52.27        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
      116.88        13.58        73.28        22.62        16.41       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
       53.33        62.17       123.78        16.41        35.28        22.03 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO 
        0.49        14.99         7.46       120.20        37.55        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XS 
       18.08         1.84        37.12        13.22        10.72        72.72 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       38.27        65.46        56.61         9.04        63.35        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X9-A971 
       18.08        18.35        15.95        38.96        15.58 

$subtype4
TCGA-DX-A2IZ TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-AB2H TCGA-DX-AB2J 
        8.58       135.48        29.49        48.20        15.85        40.60 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A8OO TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
       50.89        71.31         8.05         5.92         1.05         3.91 
TCGA-MB-A8JL TCGA-MJ-A850 TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71Q 
       19.73        22.39       188.15        10.52         3.88        32.75 
TCGA-SI-AA8C TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 TCGA-X9-A973 
       19.63         4.80        41.49        17.72        36.43 

subtype1 subtype2 subtype3 subtype4 
    0.56     0.72     0.49     1.05 
subtype1 subtype2 subtype3 subtype4 
  143.41   124.37   123.78   188.15 
subtype1 subtype2 subtype3 subtype4 
   24.69    28.96    26.93    19.73 
[1] "0.6 - 143.4 (24.7)" "0.7 - 124.4 (29.0)" "0.5 - 123.8 (26.9)"
[4] "1.1 - 188.2 (19.7)"
D8V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  1                   0
  subtype2              0                  2                   0
  subtype3              0                  3                   0
  subtype4              1                  1                   2
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             0
  subtype2                   0                             0
  subtype3                   1                             1
  subtype4                   0                             1
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                      4                    1
  subtype2                     1                      1                    0
  subtype3                     0                     21                    1
  subtype4                     0                      2                    0
          vv
clus       HEAD AND NECK - NECK HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                    0                                     0
  subtype2                    0                                     1
  subtype3                    0                                     1
  subtype4                    1                                     0
          vv
clus       LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                                0
  subtype2                                0
  subtype3                                1
  subtype4                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              0
  subtype3                                              2
  subtype4                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               4
  subtype2                               0
  subtype3                               4
  subtype4                               3
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       1                            1
  subtype2                                       0                            0
  subtype3                                       1                            1
  subtype4                                       0                            2
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       1                                3
  subtype2                       1                                9
  subtype3                       0                                4
  subtype4                       0                                0
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       2                           14
  subtype2                                       2                           13
  subtype3                                       1                           14
  subtype4                                       0                            3
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       0
  subtype3                                       4
  subtype4                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         1
  subtype2                                         0
  subtype3                                         1
  subtype4                                         0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                4
  subtype2                                                0
  subtype3                                                0
  subtype4                                                1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        1
  subtype2                                        0
  subtype3                                        5
  subtype4                                        2
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       1
  subtype2                                                       0
  subtype3                                                       1
  subtype4                                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          1
  subtype4                                          0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                33
  subtype2                                                13
  subtype3                                                26
  subtype4                                                 2
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  3
  subtype4                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  1                        2
  subtype2                                  1                        2
  subtype3                                  0                        1
  subtype4                                  0                        0
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  subtype1                           1                         0
  subtype2                           2                         0
  subtype3                           0                         0
  subtype4                           1                         1
          vv
clus       UPPER EXTREMITY - SHOULDER/AXILLA UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 2                                 3
  subtype2                                 2                                 2
  subtype3                                 3                                 0
  subtype4                                 0                                 0
D8V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             1        2
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        0
  GYNECOLOGICAL - OVARY                                          0        1
  GYNECOLOGICAL - UTERUS                                         4        1
  HEAD AND NECK - HEAD                                           1        0
  HEAD AND NECK - NECK                                           0        0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          0        1
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                4        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   1        0
  LOWER EXTREMITY - GROIN                                        1        1
  LOWER EXTREMITY - LOWER LEG/CALF                               3        9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        2        2
  LOWER EXTREMITY - THIGH/KNEE                                  14       13
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               4        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       1        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             33       13
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        1
  SUPERFICIAL TRUNK - BACK                                       2        2
  SUPERFICIAL TRUNK - BUTTOCK                                    1        2
  SUPERFICIAL TRUNK - FLANK                                      0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              2        2
  UPPER EXTREMITY - UPPER ARM/ELBOW                              3        2
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 0        1
  CHEST - CHEST WALL                                             3        1
  CHEST - LUNG/PLEURA                                            0        2
  CHEST - MEDIASTINUM                                            1        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        1
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                        21        2
  HEAD AND NECK - HEAD                                           1        0
  HEAD AND NECK - NECK                                           0        1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          1        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               1        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 2        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                4        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   1        2
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               4        0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        0
  LOWER EXTREMITY - THIGH/KNEE                                  14        3
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        4        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       5        2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             26        2
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             3        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       1        0
  SUPERFICIAL TRUNK - BUTTOCK                                    0        1
  SUPERFICIAL TRUNK - FLANK                                      0        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              3        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        0
[1] 33  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
          cls
clus        0  1
  subtype1 34 47
  subtype2 27 26
  subtype3 63 38
  subtype4 16  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   47
  subtype2   27   26
  subtype3   63   38
  subtype4   16    7
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       34       27       63       16
  MALE         47       26       38        7
[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"
D8V5, binary
          cls
clus        0  1
  subtype1 60 21
  subtype2 31 21
  subtype3 74 21
  subtype4 16  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60   21
  subtype2   31   21
  subtype3   74   21
  subtype4   16    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        60       31       74       16
  YES       21       21       21        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  subtype1                           36             2
  subtype2                           15             0
  subtype3                            4             0
  subtype4                            4             0
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        0
  subtype2                                                                        0
  subtype3                                                                        1
  subtype4                                                                        0
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                   12
  subtype2                    7
  subtype3                   81
  subtype4                    4
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                0                9
  subtype2                                                5                7
  subtype3                                                0                8
  subtype4                                                4                0
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                      15
  subtype2                                                       9
  subtype3                                                       4
  subtype4                                                       1
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        0                           0
  subtype2                                        1                           0
  subtype3                                        0                           0
  subtype4                                        1                           2
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             0
  subtype2                             0
  subtype3                             0
  subtype4                             6
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          7
  subtype2                                          9
  subtype3                                          3
  subtype4                                          1
D8V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   36
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           12
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                9
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      7
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   15
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            7
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                5
  MYXOFIBROSARCOMA                                                                7
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        1
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      9
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    4
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                           81
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                8
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      3
                                                                          clus
vv                                                                         subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                                    4
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            4
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                4
  MYXOFIBROSARCOMA                                                                0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                         1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        1
  SYNOVIAL SARCOMA - BIPHASIC                                                     2
  SYNOVIAL SARCOMA - MONOPHASIC                                                   6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      1
[1] 11  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 39 35  3  4
  subtype2 31 10  0 11
  subtype3 70 21  3  7
  subtype4 14  2  3  4
D8V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       39       31       70       14
  R1       35       10       21        2
  R2        3        0        3        3
  RX        4       11        7        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    76
  subtype2     1                         5    46
  subtype3     4                         9    83
  subtype4     0                         2    21
D8V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        4        0
  BLACK OR AFRICAN AMERICAN        2        5        9        2
  WHITE                           76       46       83       21
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus        0  1
  subtype1  1 75
  subtype2  2 49
  subtype3  0 84
  subtype4  2 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   75
  subtype2    2   49
  subtype3    0   84
  subtype4    2   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        0        2
  NOT HISPANIC OR LATINO       75       49       84       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"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 51 34
  subtype2 39 26
  subtype3 33 14
subtype1 subtype2 subtype3 
      85       65       47 
subtype1 subtype2 subtype3 
      34       26       14 
$subtype1
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX 
       50.01        19.69        44.91         0.56        32.71        38.24 
TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       18.54        74.66         5.26        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 
        8.58         9.70        83.38         9.04       124.73        44.68 
TCGA-DX-A3M2 TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6YR 
       34.68        31.27        24.69        28.96         9.11        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A7EI TCGA-DX-A7EQ TCGA-DX-A7EU TCGA-DX-A8BN 
       66.31        67.20        34.49        29.49        12.20        38.17 
TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       35.54        19.43         1.15        12.00        15.72        15.85 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB35 TCGA-DX-AB36 
       40.60        86.10        12.07       106.55        30.51        60.00 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NK TCGA-FX-A3RE 
       32.15        50.89        71.31        31.63        16.60        21.70 
TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 
       20.32         8.05         4.57        37.12       143.41         5.92 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JL 
        1.05         3.91         5.19        11.70        13.35        19.73 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-AA9N 
       22.39        10.45         6.35        38.63        20.52        17.65 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71Q 
      188.15       130.32        10.52        18.94         3.88        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A7WC 
        8.61        19.63        11.93         4.80        41.49        36.82 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       35.08        17.72        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

$subtype2
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       53.49        68.55        88.57        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 
       38.47        18.64        26.56        14.04        12.85        31.86 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A6BA TCGA-DX-A6BB 
       51.02        14.99        24.26        40.80        66.05        23.44 
TCGA-DX-A6YU TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BU TCGA-DX-A8BV 
       23.54        20.05        17.95         9.34        36.69        60.66 
TCGA-DX-AB30 TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       22.85        31.13        15.48        15.91        12.62        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IF-A4AJ 
        0.72         9.80        80.48        26.93        19.53        25.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
       52.27        13.58        73.28        22.62        16.41       101.26 
TCGA-K1-A3PO TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA 
       53.33        36.36        16.41        35.28        22.03         0.49 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5VD 
       21.73        14.99       120.20        81.01        18.08        37.12 
TCGA-SI-A71O TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB 
       22.82        72.72        38.27        65.46        56.61         9.04 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C5 TCGA-X9-A971 
       63.35        29.92        18.08        38.96        15.58 

$subtype3
TCGA-DX-A1KZ TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A6YQ 
       36.69        33.44        35.77         4.54        10.68         3.06 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL 
       16.87        74.10        15.22        14.43        61.97        33.07 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       44.68        35.77        14.07        51.91       124.37        27.95 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
       66.74         9.21        77.88       106.45        13.28        50.40 
TCGA-DX-AB32 TCGA-DX-AB37 TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-K1-A6RT TCGA-K1-A6RU 
      101.98        84.66        48.30         3.22        17.36        23.38 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-QQ-A5VC 
       25.41         8.28        20.94        13.08        48.59        35.90 
TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80J 
       64.77        16.77        17.52        25.35        13.41        26.17 
TCGA-VT-AB3D TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 
       12.46        22.62        26.43        25.71        15.95 

subtype1 subtype2 subtype3 
    0.56     0.49     3.06 
subtype1 subtype2 subtype3 
  188.15   120.20   124.37 
subtype1 subtype2 subtype3 
   21.70    25.25    25.71 
[1] "0.6 - 188.2 (21.7)" "0.5 - 120.2 (25.2)" "3.1 - 124.4 (25.7)"
D9V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              1                  3                   1
  subtype2              0                  2                   0
  subtype3              0                  2                   0
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             1
  subtype2                   1                             1
  subtype3                   0                             0
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     1                      5                    0
  subtype2                     0                     16                    0
  subtype3                     0                      0                    1
          vv
clus       HEAD AND NECK - NECK LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                    1                                0
  subtype2                    0                                1
  subtype3                    0                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              2
  subtype3                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               5
  subtype2                               3
  subtype3                               0
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       1                            2
  subtype2                                       0                            1
  subtype3                                       1                            1
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       0                                3
  subtype2                       0                                2
  subtype3                       1                                8
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       2                           12
  subtype2                                       1                           11
  subtype3                                       1                           18
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       2
  subtype3                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         1
  subtype2                                         1
  subtype3                                         0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                3
  subtype2                                                0
  subtype3                                                0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        3
  subtype2                                        2
  subtype3                                        0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       1
  subtype2                                                       0
  subtype3                                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                33
  subtype2                                                16
  subtype3                                                 3
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  2
  subtype3                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  0                        1
  subtype2                                  0                        0
  subtype3                                  2                        3
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK UPPER EXTREMITY - SHOULDER/AXILLA
  subtype1                           2                                 1
  subtype2                           0                                 1
  subtype3                           0                                 3
          vv
clus       UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 2
  subtype2                                 0
  subtype3                                 2
D9V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 1        0
  CHEST - CHEST WALL                                             3        2
  CHEST - LUNG/PLEURA                                            1        0
  CHEST - MEDIASTINUM                                            0        1
  CHEST - OTHER (PLEASE SPECIFY                                  1        1
  GYNECOLOGICAL - OVARY                                          1        0
  GYNECOLOGICAL - UTERUS                                         5       16
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           1        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                5        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   2        1
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               3        2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        2        1
  LOWER EXTREMITY - THIGH/KNEE                                  12       11
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               3        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       3        2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             33       16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       1        0
  SUPERFICIAL TRUNK - BUTTOCK                                    2        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                              2        0
                                                         clus
vv                                                        subtype3
  CHEST - BREAST                                                 0
  CHEST - CHEST WALL                                             2
  CHEST - LUNG/PLEURA                                            0
  CHEST - MEDIASTINUM                                            0
  CHEST - OTHER (PLEASE SPECIFY                                  0
  GYNECOLOGICAL - OVARY                                          0
  GYNECOLOGICAL - UTERUS                                         0
  HEAD AND NECK - HEAD                                           1
  HEAD AND NECK - NECK                                           0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0
  LOWER ABDOMINAL/PELVIC - PELVIC                                0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1
  LOWER EXTREMITY - FOOT/ANKLE                                   1
  LOWER EXTREMITY - GROIN                                        1
  LOWER EXTREMITY - LOWER LEG/CALF                               8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1
  LOWER EXTREMITY - THIGH/KNEE                                  18
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              3
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             2
  SUPERFICIAL TRUNK - BACK                                       3
  SUPERFICIAL TRUNK - BUTTOCK                                    0
  UPPER EXTREMITY - SHOULDER/AXILLA                              3
  UPPER EXTREMITY - UPPER ARM/ELBOW                              2
[1] 30  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
          cls
clus        0  1
  subtype1 43 42
  subtype2 43 22
  subtype3 25 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   42
  subtype2   43   22
  subtype3   25   22
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       43       43       25
  MALE         42       22       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"
D9V5, binary
          cls
clus        0  1
  subtype1 65 20
  subtype2 45 17
  subtype3 24 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65   20
  subtype2   45   17
  subtype3   24   22
     clus
vv    subtype1 subtype2 subtype3
  NO        65       45       24
  YES       20       17       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"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR LEIOMYOSARCOMA (LMS)
  subtype1                           35             2                   15
  subtype2                            4             0                   52
  subtype3                            4             0                    5
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                4                6
  subtype2                                                1                5
  subtype3                                                3                9
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       9
  subtype2                                                       3
  subtype3                                                      16
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        2                           1
  subtype2                                        0                           0
  subtype3                                        0                           0
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             5
  subtype2                             0
  subtype3                             0
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          6
  subtype2                                          0
  subtype3                                         10
D9V6, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                  35        4
  DESMOID TUMOR                                                  2        0
  LEIOMYOSARCOMA (LMS)                                          15       52
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)               4        1
  MYXOFIBROSARCOMA                                               6        5
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA        9        3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                       2        0
  SYNOVIAL SARCOMA - BIPHASIC                                    1        0
  SYNOVIAL SARCOMA - MONOPHASIC                                  5        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                     6        0
                                                         clus
vv                                                        subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                   4
  DESMOID TUMOR                                                  0
  LEIOMYOSARCOMA (LMS)                                           5
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)               3
  MYXOFIBROSARCOMA                                               9
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA       16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                       0
  SYNOVIAL SARCOMA - BIPHASIC                                    0
  SYNOVIAL SARCOMA - MONOPHASIC                                  0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                    10
[1] 10  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 40 31  6  8
  subtype2 43 13  2  7
  subtype3 32 11  0  3
D9V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       40       43       32
  R1       31       13       11
  R2        6        2        0
  RX        8        7        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         3    80
  subtype2     1                         6    54
  subtype3     2                         4    38
D9V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        2
  BLACK OR AFRICAN AMERICAN        3        6        4
  WHITE                           80       54       38
[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"
D9V9, binary
          cls
clus        0  1
  subtype1  2 73
  subtype2  0 58
  subtype3  2 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   73
  subtype2    0   58
  subtype3    2   41
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        0        2
  NOT HISPANIC OR LATINO       73       58       41
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 18  6
  subtype2 21 12
  subtype3 22 16
  subtype4 13 11
  subtype5 10  1
  subtype6 11 11
  subtype7 16  6
  subtype8 12 11
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      24       33       38       24       11       22       22       23 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       6       12       16       11        1       11        6       11 
$subtype1
TCGA-3B-A9HI TCGA-DX-A1KZ TCGA-DX-A3LY TCGA-DX-A3UA TCGA-DX-A6BE TCGA-DX-A6YZ 
       50.01        36.69        33.44        10.68        28.96        74.10 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BV 
       61.97        33.07        44.68        38.17       124.37        60.66 
TCGA-DX-AB2T TCGA-DX-AB37 TCGA-FX-A3RE TCGA-K1-A6RU TCGA-KD-A5QS TCGA-LI-A9QH 
       77.88        84.66        21.70        23.38        36.36        13.35 
TCGA-MB-A8JK TCGA-QC-AA9N TCGA-SI-A71O TCGA-WK-A8XQ TCGA-X9-A973 TCGA-Z4-A9VC 
       21.73        17.65        22.82         4.80        36.43        13.38 

$subtype2
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R 
       19.69        44.91        32.71        38.24        18.54        74.66 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LW 
       66.87        27.81        60.30         9.70        83.38       124.73 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6YR TCGA-DX-A6YS 
       44.68        34.68        24.69         9.11        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A7EU TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F 
       67.20        12.20        35.54        19.43         1.15        12.00 
TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A2QS 
       15.72        86.10       106.55        30.51        32.15        31.63 
TCGA-FX-A3NK TCGA-HB-A3YV TCGA-IF-A3RQ 
       16.60         4.57        37.12 

$subtype3
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ 
       53.49        68.55        88.57        25.25        10.32        38.47 
TCGA-3B-A9I1 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A6BA 
       18.64        51.02        14.99        24.26        40.80        66.05 
TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA 
       31.13        15.48        15.91        12.62        33.30         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IW-A3M4 TCGA-K1-A3PN 
       80.48        19.53        25.22        52.27        73.28       101.26 
TCGA-KD-A5QU TCGA-MB-A5YA TCGA-PC-A5DK TCGA-PC-A5DO TCGA-PC-A5DP TCGA-WK-A8XS 
       35.28         0.49       120.20        81.01        18.08        72.72 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46        56.61        63.35        29.92        18.08 
TCGA-X6-A8C5 TCGA-X9-A971 
       38.96        15.58 

$subtype4
TCGA-3B-A9HX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-DX-A6YU 
       42.84        14.04        12.85        31.86         4.54        23.54 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS 
       17.95        14.43         9.34        35.77        14.07        27.95 
TCGA-DX-A8BU TCGA-DX-AB30 TCGA-DX-AB32 TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EJ 
       36.69        22.85       101.98        48.30         0.72         3.22 
TCGA-IS-A3KA TCGA-LI-A67I TCGA-QQ-A5VC TCGA-WK-A8Y0 TCGA-X6-A8C2 TCGA-X6-A8C3 
       13.58        22.03        35.90        22.62        25.71        15.95 

$subtype5
TCGA-3B-A9I3 TCGA-DX-A6BB TCGA-DX-A7ES TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-JV-A5VE 
       26.56        23.44        20.05        26.93        22.62        16.41 
TCGA-K1-A3PO TCGA-KD-A5QT TCGA-MJ-A68H TCGA-QQ-A5VD TCGA-WP-A9GB 
       53.33        16.41        14.99        37.12         9.04 

$subtype6
TCGA-3R-A8YX TCGA-DX-A3LS TCGA-DX-A48K TCGA-DX-AB2P TCGA-DX-AB36 TCGA-FX-A3TO 
        0.56         9.04        31.27        12.07        60.00        20.32 
TCGA-IS-A3K7 TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-PC-A5DM TCGA-PC-A5DN 
      143.41        17.36         5.19        11.70         6.35        38.63 
TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-X6-A7W8 
       48.59       130.32        18.94         8.61        11.93        26.43 
TCGA-X6-A7WC TCGA-X6-A8C6 TCGA-Z4-A8JB TCGA-Z4-AAPG 
       36.82        35.08         4.37        15.98 

$subtype7
TCGA-DX-A23T TCGA-DX-A3U6 TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7ET TCGA-DX-A8BQ 
        5.26        35.77         3.06        16.87        15.22        51.91 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-MB-A5Y8 
       66.74         9.21       106.45        13.28        50.40        25.41 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SG-A849 
        8.28        20.94        13.08        64.77        16.77        17.52 
TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80J TCGA-VT-AB3D 
       25.35        13.41        26.17        12.46 

$subtype8
TCGA-DX-A2IZ TCGA-DX-A7EI TCGA-DX-A7EQ TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB3B 
        8.58        34.49        29.49        15.85        40.60        50.89 
TCGA-DX-AB3C TCGA-FX-A8OO TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-MB-A8JL 
       71.31         8.05         5.92         1.05         3.91        19.73 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-PT-A8TR TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 
       22.39        10.45        20.52       188.15        10.52         3.88 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XT TCGA-X6-A8C7 TCGA-Z4-AAPF 
       32.75        19.63        41.49        17.72        15.95 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    4.80     1.15     0.49     0.72     9.04     0.56     3.06     1.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  124.37   124.73   120.20   101.98    53.33   143.41   106.45   188.15 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
  34.900   32.710   36.775   22.325   22.620   18.150   17.195   19.630 
[1] "4.8 - 124.4 (34.9)" "1.1 - 124.7 (32.7)" "0.5 - 120.2 (36.8)"
[4] "0.7 - 102.0 (22.3)" "9.0 - 53.3 (22.6)"  "0.6 - 143.4 (18.1)"
[7] "3.1 - 106.5 (17.2)" "1.1 - 188.2 (19.6)"
D10V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  0                   0
  subtype2              0                  1                   0
  subtype3              0                  0                   0
  subtype4              0                  4                   0
  subtype5              0                  0                   0
  subtype6              0                  1                   0
  subtype7              0                  0                   0
  subtype8              1                  1                   1
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             0
  subtype2                   0                             0
  subtype3                   1                             1
  subtype4                   0                             0
  subtype5                   0                             0
  subtype6                   0                             0
  subtype7                   0                             0
  subtype8                   0                             1
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     1                      1                    0
  subtype2                     0                      0                    0
  subtype3                     0                      9                    0
  subtype4                     0                      2                    0
  subtype5                     0                      4                    0
  subtype6                     0                      2                    0
  subtype7                     0                      0                    1
  subtype8                     0                      3                    0
          vv
clus       HEAD AND NECK - NECK LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                    0                                0
  subtype2                    0                                0
  subtype3                    0                                0
  subtype4                    0                                0
  subtype5                    0                                1
  subtype6                    0                                0
  subtype7                    0                                0
  subtype8                    1                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              0
  subtype3                                              1
  subtype4                                              0
  subtype5                                              1
  subtype6                                              0
  subtype7                                              0
  subtype8                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               1
  subtype2                               2
  subtype3                               1
  subtype4                               0
  subtype5                               2
  subtype6                               0
  subtype7                               0
  subtype8                               2
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       0                            1
  subtype2                                       1                            0
  subtype3                                       0                            0
  subtype4                                       1                            0
  subtype5                                       0                            1
  subtype6                                       0                            0
  subtype7                                       0                            0
  subtype8                                       0                            2
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       0                                1
  subtype2                       0                                1
  subtype3                       0                                2
  subtype4                       0                                3
  subtype5                       0                                0
  subtype6                       1                                1
  subtype7                       0                                5
  subtype8                       0                                0
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       1                           10
  subtype2                                       1                            1
  subtype3                                       0                            6
  subtype4                                       0                            9
  subtype5                                       0                            0
  subtype6                                       1                            8
  subtype7                                       1                            4
  subtype8                                       0                            3
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
  subtype4                                       1
  subtype5                                       0
  subtype6                                       0
  subtype7                                       0
  subtype8                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         0
  subtype2                                         1
  subtype3                                         1
  subtype4                                         0
  subtype5                                         0
  subtype6                                         0
  subtype7                                         0
  subtype8                                         0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                1
  subtype2                                                0
  subtype3                                                0
  subtype4                                                0
  subtype5                                                0
  subtype6                                                1
  subtype7                                                0
  subtype8                                                1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        0
  subtype2                                        1
  subtype3                                        2
  subtype4                                        0
  subtype5                                        0
  subtype6                                        0
  subtype7                                        0
  subtype8                                        2
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       0
  subtype2                                                       1
  subtype3                                                       0
  subtype4                                                       0
  subtype5                                                       0
  subtype6                                                       0
  subtype7                                                       0
  subtype8                                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                 4
  subtype2                                                21
  subtype3                                                10
  subtype4                                                 3
  subtype5                                                 2
  subtype6                                                 7
  subtype7                                                 2
  subtype8                                                 3
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  2
  subtype4                                                  0
  subtype5                                                  0
  subtype6                                                  0
  subtype7                                                  0
  subtype8                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  0                        0
  subtype2                                  0                        1
  subtype3                                  0                        0
  subtype4                                  1                        0
  subtype5                                  0                        0
  subtype6                                  0                        0
  subtype7                                  1                        3
  subtype8                                  0                        0
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK UPPER EXTREMITY - SHOULDER/AXILLA
  subtype1                           1                                 1
  subtype2                           0                                 1
  subtype3                           0                                 1
  subtype4                           0                                 0
  subtype5                           0                                 0
  subtype6                           0                                 0
  subtype7                           0                                 2
  subtype8                           1                                 0
          vv
clus       UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 1
  subtype2                                 0
  subtype3                                 0
  subtype4                                 0
  subtype5                                 0
  subtype6                                 0
  subtype7                                 2
  subtype8                                 1
D10V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             0        1
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        0
  GYNECOLOGICAL - OVARY                                          1        0
  GYNECOLOGICAL - UTERUS                                         1        0
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                1        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        1
  LOWER EXTREMITY - FOOT/ANKLE                                   1        0
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               1        1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        1
  LOWER EXTREMITY - THIGH/KNEE                                  10        1
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               1        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              4       21
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       0        1
  SUPERFICIAL TRUNK - BUTTOCK                                    1        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1        0
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             0        4
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            1        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         9        2
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 1        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                1        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        1
  LOWER EXTREMITY - FOOT/ANKLE                                   0        0
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               2        3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        0
  LOWER EXTREMITY - THIGH/KNEE                                   6        9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        1        1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       2        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             10        3
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             2        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        1
  SUPERFICIAL TRUNK - BACK                                       0        0
  SUPERFICIAL TRUNK - BUTTOCK                                    0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        0
                                                         clus
vv                                                        subtype5 subtype6
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             0        1
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         4        2
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               1        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 1        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                2        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   1        0
  LOWER EXTREMITY - GROIN                                        0        1
  LOWER EXTREMITY - LOWER LEG/CALF                               0        1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        1
  LOWER EXTREMITY - THIGH/KNEE                                   0        8
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              2        7
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       0        0
  SUPERFICIAL TRUNK - BUTTOCK                                    0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              0        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        0
                                                         clus
vv                                                        subtype7 subtype8
  CHEST - BREAST                                                 0        1
  CHEST - CHEST WALL                                             0        1
  CHEST - LUNG/PLEURA                                            0        1
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        1
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         0        3
  HEAD AND NECK - HEAD                                           1        0
  HEAD AND NECK - NECK                                           0        1
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                0        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        2
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               5        0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        0
  LOWER EXTREMITY - THIGH/KNEE                                   4        3
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              2        3
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        0
  SUPERFICIAL TRUNK - BACK                                       3        0
  SUPERFICIAL TRUNK - BUTTOCK                                    0        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              2        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              2        1
[1] 30  8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
          cls
clus        0  1
  subtype1 11 13
  subtype2 11 22
  subtype3 28 10
  subtype4 14 10
  subtype5  7  4
  subtype6  9 13
  subtype7 12 10
  subtype8 19  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   13
  subtype2   11   22
  subtype3   28   10
  subtype4   14   10
  subtype5    7    4
  subtype6    9   13
  subtype7   12   10
  subtype8   19    4
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       11       11       28       14        7        9       12
  MALE         13       22       10       10        4       13       10
        clus
vv       subtype8
  FEMALE       19
  MALE          4
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1 12 11
  subtype2 27  6
  subtype3 28  9
  subtype4 13 10
  subtype5 10  0
  subtype6 16  6
  subtype7 11 11
  subtype8 17  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   11
  subtype2   27    6
  subtype3   28    9
  subtype4   13   10
  subtype5   10    0
  subtype6   16    6
  subtype7   11   11
  subtype8   17    6
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO        12       27       28       13       10       16       11       17
  YES       11        6        9       10        0        6       11        6
[1] 2 8
[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       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR LEIOMYOSARCOMA (LMS)
  subtype1                            7             0                    3
  subtype2                           22             0                    1
  subtype3                            0             0                   38
  subtype4                            3             0                    5
  subtype5                            1             0                   10
  subtype6                            4             2                    9
  subtype7                            2             0                    0
  subtype8                            4             0                    6
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                1                4
  subtype2                                                0                5
  subtype3                                                0                0
  subtype4                                                0                6
  subtype5                                                0                0
  subtype6                                                0                2
  subtype7                                                3                3
  subtype8                                                4                0
          vv
clus       PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       7
  subtype2                                                       4
  subtype3                                                       0
  subtype4                                                       6
  subtype5                                                       0
  subtype6                                                       2
  subtype7                                                       8
  subtype8                                                       1
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        0                           0
  subtype2                                        0                           0
  subtype3                                        0                           0
  subtype4                                        0                           0
  subtype5                                        0                           0
  subtype6                                        0                           0
  subtype7                                        0                           0
  subtype8                                        2                           1
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             0
  subtype2                             0
  subtype3                             0
  subtype4                             0
  subtype5                             0
  subtype6                             0
  subtype7                             0
  subtype8                             5
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          2
  subtype2                                          1
  subtype3                                          0
  subtype4                                          4
  subtype5                                          0
  subtype6                                          3
  subtype7                                          6
  subtype8                                          0
D10V6, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                   7       22
  DESMOID TUMOR                                                  0        0
  LEIOMYOSARCOMA (LMS)                                           3        1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)               1        0
  MYXOFIBROSARCOMA                                               4        5
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA        7        4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                       0        0
  SYNOVIAL SARCOMA - BIPHASIC                                    0        0
  SYNOVIAL SARCOMA - MONOPHASIC                                  0        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                     2        1
                                                         clus
vv                                                        subtype3 subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                   0        3
  DESMOID TUMOR                                                  0        0
  LEIOMYOSARCOMA (LMS)                                          38        5
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)               0        0
  MYXOFIBROSARCOMA                                               0        6
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA        0        6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                       0        0
  SYNOVIAL SARCOMA - BIPHASIC                                    0        0
  SYNOVIAL SARCOMA - MONOPHASIC                                  0        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                     0        4
                                                         clus
vv                                                        subtype5 subtype6
  DEDIFFERENTIATED LIPOSARCOMA                                   1        4
  DESMOID TUMOR                                                  0        2
  LEIOMYOSARCOMA (LMS)                                          10        9
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)               0        0
  MYXOFIBROSARCOMA                                               0        2
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA        0        2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                       0        0
  SYNOVIAL SARCOMA - BIPHASIC                                    0        0
  SYNOVIAL SARCOMA - MONOPHASIC                                  0        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                     0        3
                                                         clus
vv                                                        subtype7 subtype8
  DEDIFFERENTIATED LIPOSARCOMA                                   2        4
  DESMOID TUMOR                                                  0        0
  LEIOMYOSARCOMA (LMS)                                           0        6
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)               3        4
  MYXOFIBROSARCOMA                                               3        0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA        8        1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                       0        2
  SYNOVIAL SARCOMA - BIPHASIC                                    0        1
  SYNOVIAL SARCOMA - MONOPHASIC                                  0        5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                     6        0
[1] 10  8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 13  4  2  5
  subtype2 17 15  1  0
  subtype3 28  8  0  2
  subtype4 13  8  2  1
  subtype5  8  2  0  1
  subtype6  8 11  1  2
  subtype7 15  3  0  3
  subtype8 13  4  2  4
D10V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0       13       17       28       13        8        8       15       13
  R1        4       15        8        8        2       11        3        4
  R2        2        1        0        2        0        1        0        2
  RX        5        0        2        1        1        2        3        4
[1] 4 8
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         2    22
  subtype2     0                         0    33
  subtype3     0                         4    32
  subtype4     1                         2    19
  subtype5     1                         2     7
  subtype6     0                         0    21
  subtype7     1                         1    18
  subtype8     1                         2    20
D10V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        0        1        1
  BLACK OR AFRICAN AMERICAN        2        0        4        2        2
  WHITE                           22       33       32       19        7
                           clus
vv                          subtype6 subtype7 subtype8
  ASIAN                            0        1        1
  BLACK OR AFRICAN AMERICAN        0        1        2
  WHITE                           21       18       20
[1] 3 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus        0  1
  subtype1  0 23
  subtype2  1 31
  subtype3  0 34
  subtype4  0 20
  subtype5  0 10
  subtype6  0 19
  subtype7  2 19
  subtype8  1 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   23
  subtype2    1   31
  subtype3    0   34
  subtype4    0   20
  subtype5    0   10
  subtype6    0   19
  subtype7    2   19
  subtype8    1   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        0        0        0
  NOT HISPANIC OR LATINO       23       31       34       20       10       19
                        clus
vv                       subtype7 subtype8
  HISPANIC OR LATINO            2        1
  NOT HISPANIC OR LATINO       19       16
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
