[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/22507207/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SARC-TP/22542442/SARC-TP.mergedcluster.txt"

nPatients in clinical file=261, in cluster file=261, common to both=261
[1]  10 261
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
95 60 39 63 
 1  2  3  4 
95 60 39 63 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
55 57 73 76 
 1  2  3  4 
55 57 73 76 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
60 45 61 57 
 1  2  3  4 
60 45 61 57 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6 
25 36 50 68 22 22 
 1  2  3  4  5  6 
25 36 50 68 22 22 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
116  78  65 
  1   2   3 
116  78  65 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
48 21 50 47 31 29 33 
 1  2  3  4  5  6  7 
48 21 50 47 31 29 33 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
107  51 101 
  1   2   3 
107  51 101 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 84  38 115  22 
  1   2   3   4 
 84  38 115  22 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4  5 
60 27 48 23 40 
 1  2  3  4  5 
60 27 48 23 40 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
59 50 21 43 25 
 1  2  3  4  5 
59 50 21 43 25 
[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 261 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=96,	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=159,	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 261 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 54 41
  subtype2 39 21
  subtype3 30  9
  subtype4 36 27
subtype1 subtype2 subtype3 subtype4 
      95       60       39       63 
subtype1 subtype2 subtype3 subtype4 
      41       21        9       27 
$subtype1
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A8BH TCGA-DX-A8BP 
       31.53        34.68        16.18        67.20        14.43        14.07 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB3A TCGA-IS-A3K6 
       12.07       106.45        13.28        30.51        32.15        28.21 
TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-SG-A849 TCGA-X6-A8C6 
       22.62         8.28         6.35        20.94        17.52        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       50.01        19.69        44.91        18.64        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04        32.71        68.61        12.85        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LS 
       54.21        85.02        74.66         6.28         9.70         9.04 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3UD 
      136.44        33.44        44.68        31.86        51.02        50.43 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       85.45        35.28        31.96         3.06        41.00        78.28 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A8BK 
       86.30        64.21        21.30        34.49        30.35        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX 
       45.14        47.87        40.77       150.35        40.44        19.43 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-FX-A2QS 
        1.15        17.79        12.00        66.74       106.55        49.15 
TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A3RQ 
       20.32        67.63         4.57        19.53         3.22        37.12 
TCGA-IW-A3M5 TCGA-K1-A42W TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MO-A47R TCGA-N1-A6IA 
        5.92        62.17        35.28        25.41        10.45         7.36 
TCGA-PC-A5DO TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH 
       81.01        46.82        18.08        35.90       111.98        10.52 
TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D 
        3.88        25.35        32.75        13.41        10.72        12.46 
TCGA-WK-A8XX TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-Z4-AAPG 
       38.27        45.34        19.17        20.65        15.98 

$subtype2
TCGA-3B-A9HJ TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       36.30        15.85        40.60        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-FX-A3NK TCGA-IS-A3K8 TCGA-WK-A8XT TCGA-3B-A9HT TCGA-DX-A1L3 
       84.66        16.60       159.29        41.49        54.74        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       66.94         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3U6 
        8.58        95.38        79.17        49.05        86.83        35.77 
TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
        4.54        73.87         9.73        28.96        36.85        26.99 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BZ TCGA-DX-AB2G 
      152.12        29.49        48.20        20.05         6.58        15.72 
TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A8OO TCGA-IS-A3K7 
       65.98         9.21        50.89        71.31         8.05       171.09 
TCGA-K1-A3PO TCGA-K1-A6RT TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DN 
       53.33        17.36        17.98        22.39        11.57        38.63 
TCGA-QQ-A5V2 TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-UE-A6QT TCGA-WK-A8XO 
        1.84       130.32        64.77         0.72        13.22        11.93 
TCGA-WK-A8XQ TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.80        29.46        36.43         4.37        13.38        15.95 

$subtype3
TCGA-DX-A7EL TCGA-HB-A43Z TCGA-IF-A4AK TCGA-QQ-A8VB TCGA-VT-A80J TCGA-3B-A9HP 
       75.32        37.02        52.27       188.15        26.17        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-DX-A3UA TCGA-DX-A3UC 
       68.55        25.25        10.32        38.47        10.68        68.55 
TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6YX 
       46.03        59.84        37.58        37.41        82.68        16.87 
TCGA-DX-A6Z2 TCGA-DX-A8BJ TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
      101.23         9.34        31.13        21.70        19.89        15.48 
TCGA-HS-A5N8 TCGA-IE-A4EK TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN TCGA-MB-A5YA 
        0.72         1.38        85.97         3.91       101.26         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-RN-AAAQ 
       19.73        14.99       122.96        37.55        13.08        16.77 
TCGA-SI-AA8C TCGA-WK-A8XY TCGA-X6-A8C5 
       19.63        65.46        50.86 

$subtype4
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       34.36        15.22        17.95        12.62        52.11        26.93 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DP TCGA-3B-A9HR TCGA-3B-A9HV TCGA-3B-A9HX 
       11.70        17.75        18.08        88.57        14.37        42.84 
TCGA-3B-A9I0 TCGA-DX-A3U9 TCGA-DX-A3UE TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O 
       36.03        14.99        34.88        45.99        24.26        52.77 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6YV TCGA-DX-A7EM 
       26.47       108.82        15.95        36.33        50.50        62.20 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2O TCGA-DX-AB2T 
       38.17        27.95        36.69        60.66        86.10        77.88 
TCGA-DX-AB2Z TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A6BZ 
       50.40        34.88        33.30         9.80        80.48        19.89 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A42X TCGA-K1-A6RU 
       25.22        13.58        16.41         1.05       123.78        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A8JK TCGA-QC-AA9N 
        5.19        63.81        16.41        30.31        21.73        17.65 
TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-WK-A8XS 
       48.59        37.12        18.94        22.82         8.61        84.79 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       22.62         8.58        63.35        26.43        35.90        18.08 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X9-A971 
       30.84        35.18        27.32 

subtype1 subtype2 subtype3 subtype4 
    0.56     0.72     0.49     1.05 
subtype1 subtype2 subtype3 subtype4 
  150.35   171.09   188.15   123.78 
subtype1 subtype2 subtype3 subtype4 
   31.53    34.65    37.02    27.95 
[1] "0.6 - 150.3 (31.5)" "0.7 - 171.1 (34.7)" "0.5 - 188.2 (37.0)"
[4] "1.1 - 123.8 (27.9)"
D1V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  2                   0
  subtype2              0                  2                   2
  subtype3              1                  1                   0
  subtype4              0                  2                   0
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             1
  subtype2                   0                             0
  subtype3                   1                             0
  subtype4                   0                             1
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                      6                    0
  subtype2                     0                      2                    1
  subtype3                     1                      7                    1
  subtype4                     0                     13                    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                                              1
  subtype4                                              1
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               1
  subtype2                               5
  subtype3                               1
  subtype4                               3
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       0                            0
  subtype2                                       2                            2
  subtype3                                       0                            1
  subtype4                                       0                            1
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       0                                8
  subtype2                       1                                1
  subtype3                       0                                1
  subtype4                       1                                7
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       4                           17
  subtype2                                       0                            7
  subtype3                                       0                            4
  subtype4                                       1                           16
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       0
  subtype3                                       3
  subtype4                                       1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         0
  subtype2                                         1
  subtype3                                         0
  subtype4                                         1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                2
  subtype2                                                3
  subtype3                                                0
  subtype4                                                0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        3
  subtype2                                        2
  subtype3                                        2
  subtype4                                        1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       1
  subtype2                                                       0
  subtype3                                                       1
  subtype4                                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          1
  subtype2                                          0
  subtype3                                          0
  subtype4                                          0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                38
  subtype2                                                18
  subtype3                                                 9
  subtype4                                                 8
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  1
  subtype3                                                  2
  subtype4                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  1                        2
  subtype2                                  0                        2
  subtype3                                  0                        0
  subtype4                                  1                        1
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  subtype1                           0                         0
  subtype2                           1                         1
  subtype3                           1                         0
  subtype4                           2                         0
          vv
clus       UPPER EXTREMITY - SHOULDER/AXILLA UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 4                                 3
  subtype2                                 0                                 2
  subtype3                                 1                                 0
  subtype4                                 2                                 0
D1V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             2        2
  CHEST - LUNG/PLEURA                                            0        2
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         6        2
  HEAD AND NECK - HEAD                                           0        1
  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                                1        5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        2
  LOWER EXTREMITY - FOOT/ANKLE                                   0        2
  LOWER EXTREMITY - GROIN                                        0        1
  LOWER EXTREMITY - LOWER LEG/CALF                               8        1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        4        0
  LOWER EXTREMITY - THIGH/KNEE                                  17        7
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               2        3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       3        2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             38       18
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        0
  SUPERFICIAL TRUNK - BACK                                       2        2
  SUPERFICIAL TRUNK - BUTTOCK                                    0        1
  SUPERFICIAL TRUNK - FLANK                                      0        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              4        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              3        2
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 1        0
  CHEST - CHEST WALL                                             1        2
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            1        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        1
  GYNECOLOGICAL - OVARY                                          1        0
  GYNECOLOGICAL - UTERUS                                         7       13
  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                 1        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                1        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   1        1
  LOWER EXTREMITY - GROIN                                        0        1
  LOWER EXTREMITY - LOWER LEG/CALF                               1        7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        1
  LOWER EXTREMITY - THIGH/KNEE                                   4       16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        3        1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       2        1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              9        8
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             2        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        1
  SUPERFICIAL TRUNK - BACK                                       0        1
  SUPERFICIAL TRUNK - BUTTOCK                                    1        2
  SUPERFICIAL TRUNK - FLANK                                      0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        2
  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"
D1V4, binary
          cls
clus        0  1
  subtype1 44 51
  subtype2 26 34
  subtype3 27 12
  subtype4 42 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   51
  subtype2   26   34
  subtype3   27   12
  subtype4   42   21
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       44       26       27       42
  MALE         51       34       12       21
[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 63 30
  subtype2 46 13
  subtype3 29  8
  subtype4 41 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63   30
  subtype2   46   13
  subtype3   29    8
  subtype4   41   21
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        63       46       29       41
  YES       30       13        8       21
[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                           32             0
  subtype2                           27             2
  subtype3                            0             0
  subtype4                            0             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                   21
  subtype2                   10
  subtype3                   32
  subtype4                   40
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                3               10
  subtype2                                                2                5
  subtype3                                                3                1
  subtype4                                                1                8
          vv
clus       PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       16
  subtype2                                                        1
  subtype3                                                        2
  subtype4                                                        9
          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                                         13
  subtype2                                          2
  subtype3                                          1
  subtype4                                          5
D1V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   32
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           21
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                3
  MYXOFIBROSARCOMA                                                               10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                       16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                     13
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   27
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                           10
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                2
  MYXOFIBROSARCOMA                                                                5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        2
  SYNOVIAL SARCOMA - BIPHASIC                                                     2
  SYNOVIAL SARCOMA - MONOPHASIC                                                   6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      2
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    0
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           32
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                3
  MYXOFIBROSARCOMA                                                                1
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      1
                                                                          clus
vv                                                                         subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                                    0
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           40
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                                8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      5
[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 49 35  4  7
  subtype2 40 14  1  5
  subtype3 26  5  2  5
  subtype4 37 15  2  9
D1V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       49       40       26       37
  R1       35       14        5       15
  R2        4        1        2        2
  RX        7        5        5        9
[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     4                         4    85
  subtype2     2                         3    54
  subtype3     0                         4    33
  subtype4     0                         7    52
D1V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        2        0        0
  BLACK OR AFRICAN AMERICAN        4        3        4        7
  WHITE                           85       54       33       52
[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  2 86
  subtype2  2 48
  subtype3  1 34
  subtype4  0 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   86
  subtype2    2   48
  subtype3    1   34
  subtype4    0   52
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        2        1        0
  NOT HISPANIC OR LATINO       86       48       34       52
[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 43 12
  subtype2 34 23
  subtype3 49 24
  subtype4 36 40
subtype1 subtype2 subtype3 subtype4 
      55       57       73       76 
subtype1 subtype2 subtype3 subtype4 
      12       23       24       40 
$subtype1
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A8BG TCGA-DX-A8BH 
       36.30        31.53        34.68        16.18        17.95        14.43 
TCGA-DX-A8BP TCGA-DX-AB32 TCGA-DX-AB37 TCGA-MB-A5Y9 TCGA-SG-A849 TCGA-VT-A80J 
       14.07       101.98        84.66         8.28        17.52        26.17 
TCGA-3B-A9HI TCGA-3B-A9HT TCGA-DX-A1KU TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L4 
       50.01        54.74        14.04        45.11        85.02        66.94 
TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
        5.26        66.87        95.38        79.17         9.04        86.83 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A7ES 
       31.86        35.77         4.54        28.96        36.85        20.05 
TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-AB2L 
       61.97        40.77        51.91       150.35        40.44        65.98 
TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-K1-A3PO TCGA-K1-A6RT 
        9.21        50.40        67.63         3.22        53.33        17.36 
TCGA-MB-A8JK TCGA-MJ-A68J TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VG TCGA-RN-A68Q 
       21.73        17.98         1.84        18.08        64.77         0.72 
TCGA-RN-AAAQ TCGA-SI-A71P TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO 
       16.77        25.35        13.22        13.41        12.46        11.93 
TCGA-X9-A973 
       36.43 

$subtype2
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A3NK 
       15.85        40.60        22.85        30.51        32.15        16.60 
TCGA-IS-A3K8 TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-3B-A9HL TCGA-DX-A1KX TCGA-DX-A1KY 
      159.29       188.15        41.49        19.69        68.61        12.85 
TCGA-DX-A23R TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A48N 
       74.66        27.81        60.30         8.58       136.44        35.28 
TCGA-DX-A6B9 TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ 
       37.41        26.99        78.28        34.49       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A8BM TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2T 
       48.20        47.87        60.66        12.00        15.72        77.88 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A8OO TCGA-HB-A3L4 
       50.89        71.31        21.70        19.89         8.05        34.88 
TCGA-HS-A5N8 TCGA-IF-A3RQ TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A6RU TCGA-MB-A8JL 
        0.72        37.12         5.92         3.91        23.38        19.73 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A8VD 
       22.39        11.57        38.63        26.73        17.65       130.32 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XQ TCGA-X6-A8C7 
       10.52         3.88        32.75        19.63         4.80        29.46 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

$subtype3
TCGA-DX-A7EL TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       75.32        37.02        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-PC-A5DP TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       28.21        22.62        18.08        53.49        68.55        88.57 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       18.64        26.56        51.02        14.99        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O 
       50.43        34.88        85.45         9.73        24.26        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA 
       46.03        26.47       108.82        59.84        37.58        82.68 
TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-FX-A3NJ TCGA-FX-A76Y 
       36.33       101.23        62.20        30.35        31.13        15.48 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
       33.30         9.80        80.48        19.53         1.38        25.22 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A42X 
       13.58        85.97        16.41       101.26        62.17       123.78 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL 
       16.41        35.28         0.49        14.99       122.96        37.55 
TCGA-PC-A5DO TCGA-QQ-A5VD TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
       81.01        37.12        84.79        38.27        65.46        56.61 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 
        8.58        63.35        35.90        18.08        30.84        50.86 
TCGA-X9-A971 
       27.32 

$subtype4
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-AB2P TCGA-DX-AB2W 
       67.20        34.36        15.22        23.70        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB36 TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QC-A6FX 
       13.28        60.00        11.70        17.75         6.35        20.94 
TCGA-X6-A8C6 TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L1 
       35.08        44.91         0.56        32.71        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A23U TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LY 
       33.53        76.41         6.28         9.70        49.05        33.44 
TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ 
       44.68        10.68        45.99        15.95        31.96         3.06 
TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
       41.00        50.50        16.87        86.30        64.21        21.30 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX 
        9.34        45.14        38.17        27.95        36.69        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V 
        6.58         1.15        17.79        86.10        66.74       106.55 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-JV-A5VF 
       49.15        20.32         4.57        19.89       171.09         1.05 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MO-A47R TCGA-N1-A6IA 
        5.19        63.81        30.31        25.41        10.45         7.36 
TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A6Z4 
       13.08        46.82        48.59        35.90       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        45.34 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-Z4-AAPG 
       35.18        19.17        20.65        15.98 

subtype1 subtype2 subtype3 subtype4 
    0.72     0.72     0.49     0.56 
subtype1 subtype2 subtype3 subtype4 
  150.35   188.15   123.78   171.09 
subtype1 subtype2 subtype3 subtype4 
  31.530   27.810   37.020   24.555 
[1] "0.7 - 150.3 (31.5)" "0.7 - 188.2 (27.8)" "0.5 - 123.8 (37.0)"
[4] "0.6 - 171.1 (24.6)"
D2V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  1                   0
  subtype2              1                  1                   2
  subtype3              0                  0                   0
  subtype4              0                  5                   0
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             0
  subtype2                   0                             1
  subtype3                   1                             1
  subtype4                   0                             0
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                      0                    1
  subtype2                     1                      7                    0
  subtype3                     0                     18                    0
  subtype4                     0                      4                    1
          vv
clus       HEAD AND NECK - NECK HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                    0                                     2
  subtype2                    1                                     0
  subtype3                    0                                     0
  subtype4                    0                                     0
          vv
clus       LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                                1
  subtype2                                0
  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                               2
  subtype2                               3
  subtype3                               3
  subtype4                               3
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       1                            0
  subtype2                                       1                            2
  subtype3                                       0                            1
  subtype4                                       0                            1
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       1                                4
  subtype2                       0                                0
  subtype3                       0                                3
  subtype4                       1                               10
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       0                           12
  subtype2                                       1                            8
  subtype3                                       0                            6
  subtype4                                       4                           19
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       1
  subtype3                                       3
  subtype4                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         0
  subtype2                                         1
  subtype3                                         1
  subtype4                                         0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                2
  subtype2                                                2
  subtype3                                                0
  subtype4                                                1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        0
  subtype2                                        3
  subtype3                                        4
  subtype4                                        1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       0
  subtype2                                                       0
  subtype3                                                       1
  subtype4                                                       1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          1
  subtype4                                          0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                18
  subtype2                                                17
  subtype3                                                23
  subtype4                                                16
          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                                  0                        0
  subtype3                                  0                        1
  subtype4                                  1                        2
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  subtype1                           0                         0
  subtype2                           2                         1
  subtype3                           0                         0
  subtype4                           2                         0
          vv
clus       UPPER EXTREMITY - SHOULDER/AXILLA UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 3                                 3
  subtype2                                 0                                 1
  subtype3                                 1                                 0
  subtype4                                 3                                 1
D2V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        1
  CHEST - CHEST WALL                                             1        1
  CHEST - LUNG/PLEURA                                            0        2
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        1
  GYNECOLOGICAL - OVARY                                          0        1
  GYNECOLOGICAL - UTERUS                                         0        7
  HEAD AND NECK - HEAD                                           1        0
  HEAD AND NECK - NECK                                           0        1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                          2        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               1        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                2        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        1
  LOWER EXTREMITY - FOOT/ANKLE                                   0        2
  LOWER EXTREMITY - GROIN                                        1        0
  LOWER EXTREMITY - LOWER LEG/CALF                               4        0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        1
  LOWER EXTREMITY - THIGH/KNEE                                  12        8
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               2        2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             18       17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        0
  SUPERFICIAL TRUNK - BACK                                       2        0
  SUPERFICIAL TRUNK - BUTTOCK                                    0        2
  SUPERFICIAL TRUNK - FLANK                                      0        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              3        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              3        1
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             0        5
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            1        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                        18        4
  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                 2        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                3        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   1        1
  LOWER EXTREMITY - GROIN                                        0        1
  LOWER EXTREMITY - LOWER LEG/CALF                               3       10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        4
  LOWER EXTREMITY - THIGH/KNEE                                   6       19
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        3        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       4        1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                     1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             23       16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             3        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        1
  SUPERFICIAL TRUNK - BACK                                       1        2
  SUPERFICIAL TRUNK - BUTTOCK                                    0        2
  SUPERFICIAL TRUNK - FLANK                                      0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        3
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        1
[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"
D2V4, binary
          cls
clus        0  1
  subtype1 23 32
  subtype2 35 22
  subtype3 49 24
  subtype4 35 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   32
  subtype2   35   22
  subtype3   49   24
  subtype4   35   41
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       23       35       49       35
  MALE         32       22       24       41
[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"
D2V5, binary
          cls
clus        0  1
  subtype1 35 18
  subtype2 44 13
  subtype3 59 10
  subtype4 43 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   18
  subtype2   44   13
  subtype3   59   10
  subtype4   43   33
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        35       44       59       43
  YES       18       13       10       33
[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                           23             0
  subtype2                           22             2
  subtype3                            0             0
  subtype4                           14             0
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        1
  subtype2                                                                        0
  subtype3                                                                        0
  subtype4                                                                        0
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                    4
  subtype2                   11
  subtype3                   73
  subtype4                   17
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                4                5
  subtype2                                                4                5
  subtype3                                                0                0
  subtype4                                                1               15
          vv
clus       PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                        9
  subtype2                                                        2
  subtype3                                                        0
  subtype4                                                       18
          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                                          9
  subtype2                                          1
  subtype3                                          0
  subtype4                                         11
D2V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   23
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                            4
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                4
  MYXOFIBROSARCOMA                                                                5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      9
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   22
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           11
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                4
  MYXOFIBROSARCOMA                                                                5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        2
  SYNOVIAL SARCOMA - BIPHASIC                                                     2
  SYNOVIAL SARCOMA - MONOPHASIC                                                   6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      1
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    0
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           73
  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                                                   14
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           17
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                               15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                       18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                     11
[1] 11  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 27 20  1  6
  subtype2 33 13  3  8
  subtype3 54 13  1  5
  subtype4 41 24  4  7
D2V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       27       33       54       41
  R1       20       13       13       24
  R2        1        3        1        4
  RX        6        8        5        7
[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                         2    50
  subtype2     1                         4    51
  subtype3     1                         7    61
  subtype4     2                         5    66
D2V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        1        2
  BLACK OR AFRICAN AMERICAN        2        4        7        5
  WHITE                           50       51       61       66
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus        0  1
  subtype1  1 50
  subtype2  2 44
  subtype3  0 62
  subtype4  2 67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   50
  subtype2    2   44
  subtype3    0   62
  subtype4    2   67
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        0        2
  NOT HISPANIC OR LATINO       50       44       62       67
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 43 17
  subtype2 18 27
  subtype3 44 17
  subtype4 34 23
subtype1 subtype2 subtype3 subtype4 
      60       45       61       57 
subtype1 subtype2 subtype3 subtype4 
      17       27       17       23 
$subtype1
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EU TCGA-DX-A8BG 
       36.30        34.68        67.20        34.36        23.70        17.95 
TCGA-DX-AB2H TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB3A TCGA-3B-A9HI 
       15.85       106.45        22.85        30.51        32.15        50.01 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        32.71        68.61        18.54        85.02        33.53 
TCGA-DX-A23R TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       74.66        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A48N 
       79.17        49.05       136.44        33.44        31.86        35.28 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ 
       28.96        36.85        26.99        78.28        50.50        86.30 
TCGA-DX-A6Z0 TCGA-DX-A7ES TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F TCGA-DX-AB2L 
       64.21        20.05        60.66        19.43        12.00        65.98 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A3TO TCGA-IE-A6BZ 
       86.10         9.21        77.88       106.55        20.32        19.89 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-MB-A8JK TCGA-PC-A5DN TCGA-PT-A8TR TCGA-SI-A71Q 
       17.36        23.38        21.73        38.63        26.73        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-X6-A8C4 TCGA-Z4-A9VC TCGA-Z4-AAPF 
        8.61        19.63        13.22        20.65        13.38        15.95 

$subtype2
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB36 TCGA-HS-A5N9 TCGA-LI-A9QH TCGA-PC-A5DM 
       40.60        12.07        60.00        52.11        17.75         6.35 
TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9I1 TCGA-DX-A1KY TCGA-DX-A3M1 TCGA-DX-A3UA 
       35.08        19.69        18.64        12.85        44.68        10.68 
TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EQ TCGA-DX-A7ER 
       45.99        15.95        21.30        34.49        29.49        48.20 
TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2Q TCGA-DX-AB3C 
        9.34        38.17        36.69         1.15        66.74        71.31 
TCGA-FX-A2QS TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-IE-A4EJ TCGA-IW-A3M5 TCGA-JV-A5VF 
       49.15        34.88         4.57         3.22         5.92         1.05 
TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-QC-AA9N 
        5.19        30.31        19.73        10.45         7.36        17.65 
TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       35.90       111.98        10.52        18.94         3.88        22.82 
TCGA-VT-A80G TCGA-X6-A7WC TCGA-X6-A8C7 
       10.72        45.34        29.46 

$subtype3
TCGA-DX-A7EL TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 
       75.32        37.02        12.62        26.93        28.21       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-3B-A9HV TCGA-3B-A9I3 
       22.62        11.70        18.08       188.15        14.37        26.56 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       51.02        14.99        73.87        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       85.45         9.73        24.26        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
      108.82        59.84        37.58        37.41        82.68        36.33 
TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HS-A5N7 
      101.23        62.20        30.35        31.13        21.70        33.30 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IS-A3KA TCGA-IW-A3M4 
        9.80        80.48        19.53         1.38        13.58        85.97 
TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-MB-A5YA 
       16.41       101.26        53.33        62.17       123.78         0.49 
TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-RN-A68Q 
       11.57       122.96        37.55        81.01        13.08         0.72 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 
       38.27         8.58        35.90        18.08        30.84        50.86 
TCGA-X9-A971 
       27.32 

$subtype4
TCGA-DX-A6BK TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2X TCGA-DX-AB32 
       16.18        15.22        14.43        14.07        13.28       101.98 
TCGA-DX-AB37 TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-3R-A8YX 
       84.66         8.28        20.94        17.52        26.17         0.56 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23Y TCGA-DX-A2J0 
       45.11        54.21        66.94         5.26         6.28         9.70 
TCGA-DX-A2J1 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A6BF 
       95.38         9.04        86.83        35.77         4.54        31.96 
TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
        3.06        16.87        61.97        45.14        47.87        40.77 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E 
       51.91       150.35        27.95        40.44         6.58        17.79 
TCGA-DX-AB2G TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-HS-A5N8 TCGA-IS-A3K7 TCGA-MB-A5Y8 
       15.72        50.40        50.89         0.72       171.09        25.41 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VG 
        1.84        46.82        18.08        48.59        37.12        64.77 
TCGA-RN-AAAQ TCGA-SI-A71P TCGA-UE-A6QU TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C2 
       16.77        25.35        13.41        22.62        26.43        35.18 
TCGA-X6-A8C3 TCGA-X9-A973 TCGA-Z4-AAPG 
       19.17        36.43        15.98 

subtype1 subtype2 subtype3 subtype4 
    8.58     1.05     0.49     0.56 
subtype1 subtype2 subtype3 subtype4 
  136.44   111.98   188.15   171.09 
subtype1 subtype2 subtype3 subtype4 
   32.73    19.73    35.90    25.41 
[1] "8.6 - 136.4 (32.7)" "1.1 - 112.0 (19.7)" "0.5 - 188.2 (35.9)"
[4] "0.6 - 171.1 (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                           15
  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                                  15       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 33
  subtype2 23 22
  subtype3 40 21
  subtype4 27 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   33
  subtype2   23   22
  subtype3   40   21
  subtype4   27   30
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       27       23       40       27
  MALE         33       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 43 17
  subtype2 23 21
  subtype3 52  6
  subtype4 38 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   17
  subtype2   23   21
  subtype3   52    6
  subtype4   38   18
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        43       23       52       38
  YES       17       21        6       18
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       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               15
  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                                                               15
  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 22  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       22       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    57
  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                           57       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 18  7
  subtype2 25 11
  subtype3 27 23
  subtype4 47 21
  subtype5 12 10
  subtype6 10 12
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      25       36       50       68       22       22 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       7       11       23       21       10       12 
$subtype1
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB35 TCGA-DX-AB3A TCGA-3B-A9HI 
       67.20        34.36        17.95        30.51        32.15        50.01 
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A6YV 
       32.71        85.02       136.44        31.86        35.28        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2S TCGA-DX-AB2T 
       86.30        64.21        60.66        12.00         9.21        77.88 
TCGA-DX-AB2V TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-MB-A8JK TCGA-PT-A8TR TCGA-SI-AA8B 
      106.55         4.57        19.89        21.73        26.73         8.61 
TCGA-Z4-A9VC 
       13.38 

$subtype2
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A7EU TCGA-DX-AB2H TCGA-DX-AB32 TCGA-DX-AB37 
       36.30        34.68        23.70        15.85       101.98        84.66 
TCGA-MB-A5Y9 TCGA-VT-A80J TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 
        8.28        26.17        14.04        68.61        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
       33.53        66.94        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-A6BE 
        9.70        95.38        79.17        49.05        33.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN 
       36.85        26.99        78.28        61.97        45.14        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-AB2L TCGA-K1-A6RU TCGA-QQ-A5VA TCGA-RN-AAAQ 
       40.77       150.35        65.98        23.38        18.08        16.77 

$subtype3
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB36 
       15.22        14.43        14.07        12.07        13.28        60.00 
TCGA-KF-A41W TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-X6-A8C6 
       11.70         6.35        20.94       188.15        17.52        35.08 
TCGA-3B-A9HL TCGA-3R-A8YX TCGA-DX-A3U8 TCGA-DX-A48K TCGA-DX-A6YQ TCGA-DX-A6YX 
       19.69         0.56         4.54        45.99         3.06        16.87 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BQ TCGA-DX-A8BS TCGA-DX-A8BX 
       21.30        34.49         9.34        51.91        27.95        19.43 
TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2Z TCGA-FX-A3TO 
        6.58        17.79        86.10        66.74        50.40        20.32 
TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-K1-A6RV TCGA-MB-A5Y8 TCGA-N1-A6IA TCGA-QC-AA9N 
        3.22       171.09         5.19        25.41         7.36        17.65 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-UE-A6QU 
       48.59        35.90       111.98        18.94        22.82        13.41 
TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 
       10.72        22.62        26.43        45.34        35.18        19.17 
TCGA-X6-A8C4 TCGA-Z4-AAPG 
       20.65        15.98 

$subtype4
TCGA-DX-A7EL TCGA-DX-AB2W TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       75.32       106.45        37.02        12.62        52.11        26.93 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-PC-A5DP TCGA-3B-A9HV TCGA-3B-A9I1 
       28.21       159.29        22.62        18.08        14.37        18.64 
TCGA-3B-A9I3 TCGA-DX-A23V TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       26.56        66.87        51.02        14.99        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O 
       50.43        34.88        85.45         9.73        24.26        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       46.03        26.47       108.82        59.84        37.58        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ES 
       82.68        36.33       101.23        62.20        30.35        20.05 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV 
       31.13        21.70        34.88        33.30         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-K1-A3PN 
       19.53         1.38        13.58        85.97        16.41       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-MB-A5YA TCGA-MO-A47P 
       53.33        62.17       123.78        17.36         0.49        11.57 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5VD TCGA-UE-A6QT 
      122.96        37.55        38.63        81.01        37.12        13.22 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 
       38.27         8.58        35.90        18.08        30.84        50.86 
TCGA-X9-A971 TCGA-Z4-AAPF 
       27.32        15.95 

$subtype5
TCGA-DX-A6BK TCGA-LI-A9QH TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A23T 
       16.18        17.75        12.85        45.11        74.66         5.26 
TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A6BF 
        8.58         9.04        86.83        44.68        35.77        31.96 
TCGA-DX-A8BM TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2G TCGA-DX-AB3B 
       47.87        40.44        36.69         1.15        15.72        50.89 
TCGA-MB-A8JL TCGA-MO-A47R TCGA-QQ-A5V9 TCGA-X9-A973 
       19.73        10.45        46.82        36.43 

$subtype6
TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-A3UA TCGA-DX-A6B8 TCGA-DX-A7EQ TCGA-DX-A7ER 
       40.60        22.85        10.68        15.95        29.49        48.20 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-HS-A5N8 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-LI-A67I 
       71.31        49.15         0.72         5.92         1.05        30.31 
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        29.46 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.57     6.28     0.56     0.49     1.15     0.72 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  136.44   150.35   188.15   159.29    86.83    71.31 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  32.710   36.575   19.560   36.115   33.865   21.240 
[1] "4.6 - 136.4 (32.7)" "6.3 - 150.3 (36.6)" "0.6 - 188.2 (19.6)"
[4] "0.5 - 159.3 (36.1)" "1.1 - 86.8 (33.9)"  "0.7 - 71.3 (21.2)" 
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                                0
  subtype2                       1                                3
  subtype3                       1                                9
  subtype4                       0                                2
  subtype5                       0                                1
  subtype6                       0                                0
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       0                            9
  subtype2                                       1                            6
  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                                                 9
  subtype2                                                15
  subtype3                                                 6
  subtype4                                                21
  subtype5                                                14
  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                               0        3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        1
  LOWER EXTREMITY - THIGH/KNEE                                   9        6
  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              9       15
  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                               9        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                               1        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             14        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 10 15
  subtype2 12 24
  subtype3 24 26
  subtype4 46 22
  subtype5 11 11
  subtype6 14  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   15
  subtype2   12   24
  subtype3   24   26
  subtype4   46   22
  subtype5   11   11
  subtype6   14    8
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       10       12       24       46       11       14
  MALE         15       24       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 16  9
  subtype2 27  9
  subtype3 27 22
  subtype4 58  7
  subtype5 17  5
  subtype6 11 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    9
  subtype2   27    9
  subtype3   27   22
  subtype4   58    7
  subtype5   17    5
  subtype6   11   10
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        16       27       27       58       17       11
  YES        9        9       22        7        5       10
[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                           10
  subtype2                           23
  subtype3                            4
  subtype4                            3
  subtype5                           12
  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                6
  subtype4                                                0                0
  subtype5                                                0                0
  subtype6                                                6                2
          vv
clus       PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                        1
  subtype2                                                        5
  subtype3                                                       15
  subtype4                                                        1
  subtype5                                                        5
  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                                                   10
  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                        1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      3
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   23
  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                                                                6
  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                                                   12
  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                        5
  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  9  0  1
  subtype2 18 14  1  2
  subtype3 27 16  1  6
  subtype4 49 12  1  6
  subtype5  9 11  2  0
  subtype6 10  3  2  7
D4V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       15       18       27       49        9       10
  R1        9       14       16       12       11        3
  R2        0        1        1        1        2        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    24
  subtype2     0                         0    36
  subtype3     2                         5    39
  subtype4     3                         5    57
  subtype5     1                         0    21
  subtype6     0                         2    19
D4V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        2        3        1
  BLACK OR AFRICAN AMERICAN        1        0        5        5        0
  WHITE                           24       36       39       57       21
                           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 23
  subtype2  0 33
  subtype3  2 41
  subtype4  0 59
  subtype5  0 19
  subtype6  0 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   23
  subtype2    0   33
  subtype3    2   41
  subtype4    0   59
  subtype5    0   19
  subtype6    0   16
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        2        0        0        0
  NOT HISPANIC OR LATINO       23       33       41       59       19       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 76 40
  subtype2 51 27
  subtype3 34 31
subtype1 subtype2 subtype3 
     116       78       65 
subtype1 subtype2 subtype3 
      40       27       31 
$subtype1
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET 
       36.30        31.53        34.68        67.20        34.36        15.22 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2W 
       23.70        17.95        14.43        14.07        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-LI-A9QH TCGA-MB-A5Y9 
       13.28       101.98        30.51        84.66        17.75         8.28 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HI 
        6.35        20.94        17.52        26.17        35.08        50.01 
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX 
       19.69        44.91        54.74         0.56        14.04        68.61 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       45.11        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2J0 
        5.26        76.41        66.87         6.28        27.81         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
       95.38        79.17        49.05        86.83        33.44        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A48K TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       35.77         4.54        45.99        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX 
       26.99         3.06        41.00        78.28        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL 
       86.30        64.21        21.30        20.05        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       47.87        38.17        40.77        51.91       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       40.44        60.66        19.43         6.58        17.79        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       15.72        65.98        86.10        66.74         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A3TO TCGA-HB-A2OT TCGA-IE-A4EJ TCGA-IE-A6BZ 
      106.55        50.40        20.32        67.63         3.22        19.89 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-MB-A5Y8 
       37.12       171.09        17.36        23.38         5.19        25.41 
TCGA-MB-A8JK TCGA-MJ-A68J TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       21.73        17.98        13.08         1.84        46.82        48.59 
TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D 
       35.90        18.94        22.82        13.22        13.41        12.46 
TCGA-WK-A8XO TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 
       11.93        22.62        26.43        45.34        35.18        19.17 
TCGA-X6-A8C4 TCGA-Z4-AAPG 
       20.65        15.98 

$subtype2
TCGA-DX-A7EL TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       75.32        37.02        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-PC-A5DP TCGA-3B-A9HP TCGA-3B-A9HQ 
       28.21       159.29        22.62        18.08        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       88.57        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB 
       36.03        18.64        26.56        51.02        14.99        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       68.55        50.43        34.88        85.45         9.73        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
       52.77        46.03        26.47       108.82        37.58        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-FX-A3NJ 
       82.68        36.33       101.23        62.20        30.35        31.13 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV 
       19.89        15.48        34.88        33.30         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE 
       19.53         1.38        25.22        13.58        85.97        16.41 
TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A42X TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
      101.26        62.17       123.78        63.81        16.41        35.28 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO 
        0.49        14.99        11.57       122.96        37.55        81.01 
TCGA-QQ-A5VD TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB 
       37.12        84.79        38.27        65.46        56.61         8.58 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X9-A971 
       63.35        35.90        18.08        30.84        50.86        27.32 

$subtype3
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK 
       15.85        40.60        22.85        60.00        32.15        16.60 
TCGA-KF-A41W TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A23R 
       11.70       188.15        41.49        32.71        12.85        74.66 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3UA 
       60.30         8.58         9.04       136.44        44.68        10.68 
TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       35.28        15.95        34.49       152.12        29.49        48.20 
TCGA-DX-A8BJ TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.34        36.69         1.15        50.89        71.31        49.15 
TCGA-FX-A3RE TCGA-FX-A8OO TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IW-A3M5 TCGA-JV-A5VF 
       21.70         8.05         4.57         0.72         5.92         1.05 
TCGA-JV-A75J TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R 
        3.91        53.33        30.31        19.73        22.39        10.45 
TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A5VA TCGA-QQ-A8VD 
        7.36        38.63        26.73        17.65        18.08       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 
      111.98        64.77        10.52         0.72        16.77         3.88 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XQ 
       25.35        32.75         8.61        19.63        10.72         4.80 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        36.43         4.37        13.38        15.95 

subtype1 subtype2 subtype3 
    0.56     0.49     0.72 
subtype1 subtype2 subtype3 
  171.09   159.29   188.15 
subtype1 subtype2 subtype3 
  31.020   36.675   21.700 
[1] "0.6 - 171.1 (31.0)" "0.5 - 159.3 (36.7)" "0.7 - 188.2 (21.7)"
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                            8
          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                                   8
  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 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   66
  subtype2   55   23
  subtype3   36   29
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       50       55       36
  MALE         66       23       29
[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 67 47
  subtype2 64 10
  subtype3 48 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   67   47
  subtype2   64   10
  subtype3   48   17
     clus
vv    subtype1 subtype2 subtype3
  NO        67       64       48
  YES       47       10       17
[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               23
  subtype2                                                0                0
  subtype3                                                8                2
          vv
clus       PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       25
  subtype2                                                        0
  subtype3                                                        4
          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                                                               23
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                       25
  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                        4
  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 16  5 15
D5V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       69       57       28
  R1       40       13       16
  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    59
D5V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        2        1
  BLACK OR AFRICAN AMERICAN        6        8        4
  WHITE                          103       64       59
[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 18
  subtype2 17  4
  subtype3 33 17
  subtype4 26 21
  subtype5 17 14
  subtype6 20  9
  subtype7 18 15
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      48       21       50       47       31       29       33 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      18        4       17       21       14        9       15 
$subtype1
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EU TCGA-DX-A8BG 
       31.53        34.68        67.20        34.36        23.70        17.95 
TCGA-DX-AB35 TCGA-LI-A9QH TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-DX-A1KW 
       30.51        17.75        35.08        50.01        19.69        32.71 
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23V 
       68.61        18.54        54.21        85.02        33.53        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2J0 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
        6.28        27.81         9.70        86.83        33.44        31.86 
TCGA-DX-A6BF TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 
       31.96        41.00        78.28        50.50        86.30        64.21 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX 
       45.14        38.17       150.35        40.44        60.66        19.43 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A3TO 
       12.00        15.72        86.10        77.88       106.55        20.32 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-K1-A6RU TCGA-QQ-A5V9 TCGA-UE-A6QU 
        3.22        19.89        37.12        23.38        46.82        13.41 

$subtype2
TCGA-3B-A9HJ TCGA-DX-A7ET TCGA-DX-AB32 TCGA-DX-AB37 TCGA-MB-A5Y9 TCGA-QC-A6FX 
       36.30        15.22       101.98        84.66         8.28        20.94 
TCGA-DX-A1KZ TCGA-DX-A23T TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3U6 TCGA-DX-A6BE 
       45.11         5.26        95.38        79.17        35.77        28.96 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-AB2S TCGA-KD-A5QS TCGA-MB-A8JK 
       20.05        61.97        40.77         9.21        63.81        21.73 
TCGA-MJ-A68J TCGA-UE-A6QT TCGA-VT-AB3D 
       17.98        13.22        12.46 

$subtype3
TCGA-DX-A7EL TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-PC-A5DP TCGA-3B-A9HP TCGA-3B-A9HQ 
       75.32        12.62        52.27        18.08        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A3U7 
       88.57        25.25        10.32        38.47        36.03        51.02 
TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       14.99        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 
       24.26        52.77        46.03        26.47       108.82        37.58 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-FX-A3NJ 
       82.68        36.33       101.23        62.20        30.35        31.13 
TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-K1-A3PN 
       33.30        80.48        19.53         1.38        25.22       101.26 
TCGA-K1-A42W TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO 
       62.17         0.49        14.99       122.96        37.55        81.01 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-X6-A7WA TCGA-X6-A7WD 
       84.79        38.27        65.46        56.61        35.90        30.84 
TCGA-X6-A8C5 TCGA-X9-A971 
       50.86        27.32 

$subtype4
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-QQ-A8VB 
       15.85        40.60        22.85        32.15        16.60       188.15 
TCGA-WK-A8XT TCGA-3B-A9HS TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2IZ 
       41.49        44.91        14.04        12.85        74.66         8.58 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A48N TCGA-DX-A6BH TCGA-DX-A7EI TCGA-DX-A7EO 
      136.44        44.68        35.28        26.99        34.49       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BM TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       29.49        48.20        47.87        50.89        71.31        49.15 
TCGA-FX-A8OO TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IW-A3M5 TCGA-JV-A75J TCGA-LI-A67I 
        8.05         4.57         0.72         5.92         3.91        30.31 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A8VG 
       22.39        10.45        38.63        26.73        17.65        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-AA8C TCGA-WK-A8XQ TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A9VC 
       19.63         4.80        29.46        36.43        13.38 

$subtype5
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB36 TCGA-KF-A41W 
       14.43        14.07       106.45        13.28        60.00        11.70 
TCGA-PC-A5DM TCGA-SG-A849 TCGA-VT-A80J TCGA-3B-A9HT TCGA-3R-A8YX TCGA-DX-A3U8 
        6.35        17.52        26.17        54.74         0.56         4.54 
TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BQ 
       45.99        15.95         3.06        16.87        21.30        51.91 
TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB2Q TCGA-DX-AB2Z TCGA-K1-A6RT TCGA-QQ-A5VA 
       36.69        17.79        66.74        50.40        17.36        18.08 
TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-Z4-AAPF 
       35.90       111.98        26.43        19.17        20.65        15.95 
TCGA-Z4-AAPG 
       15.98 

$subtype6
TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       37.02        52.11        26.93        28.21       159.29        22.62 
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        73.87        37.41 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HS-A5NA TCGA-IS-A3KA 
       21.70        19.89        15.48        34.88         9.80        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-K1-A3PO TCGA-K1-A42X TCGA-KD-A5QT TCGA-KD-A5QU 
       85.97        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 
       11.57        37.12         8.58        63.35        18.08 

$subtype7
TCGA-DX-AB2P TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A3LS TCGA-DX-A3LT 
       12.07        66.94        76.41        60.30         9.04        49.05 
TCGA-DX-A3UA TCGA-DX-A6BG TCGA-DX-A8BJ TCGA-DX-A8BS TCGA-DX-A8BZ TCGA-DX-AATS 
       10.68        36.85         9.34        27.95         6.58         1.15 
TCGA-DX-AB2L TCGA-HB-A2OT TCGA-IS-A3K7 TCGA-JV-A5VF TCGA-K1-A6RV TCGA-MB-A5Y8 
       65.98        67.63       171.09         1.05         5.19        25.41 
TCGA-MB-A8JL TCGA-N1-A6IA TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A8VD 
       19.73         7.36        13.08         1.84        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 
       45.34        35.18         4.37 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    3.22     5.26     0.49     0.72     0.56     8.58     1.05 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  150.35   101.98   122.96   188.15   111.98   159.29   171.09 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   34.52    28.96    38.37    26.99    18.08    26.93    19.73 
[1] "3.2 - 150.3 (34.5)" "5.3 - 102.0 (29.0)" "0.5 - 123.0 (38.4)"
[4] "0.7 - 188.2 (27.0)" "0.6 - 112.0 (18.1)" "8.6 - 159.3 (26.9)"
[7] "1.1 - 171.1 (19.7)"
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                            8
          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                                                 3
  subtype6                                                 1
  subtype7                                                 6
          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                                 3                                 1
  subtype2                                 0                                 1
  subtype3                                 1                                 0
  subtype4                                 1                                 0
  subtype5                                 2                                 2
  subtype6                                 0                                 0
  subtype7                                 0                                 1
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                              3        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1        1
                                                         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              3        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                              2        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                                   8
  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              6
  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                              1
[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 27
  subtype2 10 11
  subtype3 30 20
  subtype4 25 22
  subtype5 15 16
  subtype6 25  4
  subtype7 15 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   27
  subtype2   10   11
  subtype3   30   20
  subtype4   25   22
  subtype5   15   16
  subtype6   25    4
  subtype7   15   18
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       21       10       30       25       15       25       15
  MALE         27       11       20       22       16        4       18
[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 15
  subtype2 13  8
  subtype3 40  8
  subtype4 32 15
  subtype5 18 13
  subtype6 25  2
  subtype7 19 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   15
  subtype2   13    8
  subtype3   40    8
  subtype4   32   15
  subtype5   18   13
  subtype6   25    2
  subtype7   19   13
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        32       13       40       32       18       25       19
  YES       15        8        8       15       13        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                            9             0
  subtype3                            0             0
  subtype4                           16             0
  subtype5                            3             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                    9
  subtype6                   28
  subtype7                    9
          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                1
          vv
clus       PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                        7
  subtype2                                                        5
  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                        7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      5
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                    9
  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                        5
  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                                                    3
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            9
  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)                                                            9
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                                1
  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 26 21  1  0
  subtype2 12  6  0  3
  subtype3 38 11  0  1
  subtype4 21 11  5  9
  subtype5 19  8  1  3
  subtype6 20  2  1  6
  subtype7 18 10  1  4
D6V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  R0       26       12       38       21       19       20       18
  R1       21        6       11       11        8        2       10
  R2        1        0        0        5        1        1        1
  RX        0        3        1        9        3        6        4
[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    46
  subtype2     1                         2    18
  subtype3     0                         5    44
  subtype4     1                         2    43
  subtype5     1                         0    26
  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                           46       18       44       43       26
                           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 45
  subtype2  1 19
  subtype3  0 46
  subtype4  2 37
  subtype5  1 25
  subtype6  0 21
  subtype7  0 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   45
  subtype2    1   19
  subtype3    0   46
  subtype4    2   37
  subtype5    1   25
  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       45       19       46       37       25       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 64 43
  subtype2 33 18
  subtype3 64 37
subtype1 subtype2 subtype3 
     107       51      101 
subtype1 subtype2 subtype3 
      43       18       37 
$subtype1
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-AB2H TCGA-DX-AB2J 
       34.68        67.20        15.22        23.70        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK 
       12.07        13.28        30.51        60.00        32.15        16.60 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB 
       11.70        17.75         8.28         6.35        20.94       188.15 
TCGA-SG-A849 TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HS TCGA-3R-A8YX 
       17.52        41.49        35.08        50.01        44.91         0.56 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       32.71        68.61        18.54        85.02        33.53        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BE 
      136.44        44.68        35.77        45.99        35.28        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A7EO 
       36.85        26.99        41.00        78.28        50.50       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BT TCGA-DX-A8BX 
       29.49        48.20        45.14        38.17        40.44        19.43 
TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2V 
        1.15        12.00        15.72        65.98        86.10       106.55 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A3YV 
       50.89        71.31        49.15        20.32         8.05         4.57 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
       19.89        37.12       171.09         5.92         1.05         3.91 
TCGA-K1-A6RV TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DN 
        5.19        19.73        22.39        10.45         7.36        38.63 
TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A8VD 
       26.73        13.08        17.65        46.82        48.59       130.32 
TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       10.52        18.94         3.88        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C7 
       19.63        11.93         4.80        26.43        45.34        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

$subtype2
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A8BH TCGA-DX-A8BP 
       36.30        31.53        16.18        34.36        14.43        14.07 
TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB37 TCGA-VT-A80J TCGA-3B-A9HL TCGA-DX-A1KZ 
      106.45       101.98        84.66        26.17        19.69        45.11 
TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3UA 
       54.21         6.28        86.83        33.44        31.86        10.68 
TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A8BK 
       31.96         3.06        16.87        86.30        64.21        61.97 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ 
       47.87        40.77        51.91       150.35        60.66         6.58 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-HB-A2OT TCGA-IE-A4EJ 
       66.74         9.21        77.88        50.40        67.63         3.22 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MJ-A68J 
       17.36        23.38        63.81        25.41        21.73        17.98 
TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SI-A71O TCGA-UE-A6QU 
       18.08       111.98        64.77        16.77        22.82        13.41 
TCGA-VT-AB3D TCGA-WK-A8Y0 TCGA-X6-A8C2 
       12.46        22.62        35.18 

$subtype3
TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-AB30 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       75.32        17.95        22.85        37.02        12.62        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-PC-A5DP TCGA-3B-A9HP 
       52.27        28.21       159.29        22.62        18.08        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       68.55        88.57        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       10.32        38.47        36.03        18.64        26.56        14.04 
TCGA-DX-A1KY TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       12.85        51.02         4.54        14.99        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O 
       50.43        34.88        85.45         9.73        24.26        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       108.82        59.84        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       37.41        82.68        36.33       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BS TCGA-DX-A8BU 
       62.20        30.35        20.05         9.34        27.95        36.69 
TCGA-DX-AB2E TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 
       17.79        31.13        21.70        19.89        15.48        34.88 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK 
       33.30         0.72         9.80        80.48        19.53         1.38 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO 
       25.22        13.58        85.97        16.41       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA 
       62.17       123.78        16.41        35.28        30.31         0.49 
TCGA-MJ-A68H TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QQ-A5V2 
       14.99        11.57       122.96        37.55        81.01         1.84 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-RN-A68Q TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XS 
       35.90        37.12         0.72        13.22        10.72        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       38.27        65.46        56.61         8.58        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X9-A971 
       18.08        30.84        19.17        50.86        27.32 

subtype1 subtype2 subtype3 
    0.56     3.06     0.49 
subtype1 subtype2 subtype3 
  188.15   150.35   159.29 
subtype1 subtype2 subtype3 
   29.46    31.96    31.13 
[1] "0.6 - 188.2 (29.5)" "3.1 - 150.3 (32.0)" "0.5 - 159.3 (31.1)"
D7V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              1                  3                   2
  subtype2              0                  3                   0
  subtype3              0                  1                   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                    1
  subtype2                     0                      1                    0
  subtype3                     1                     21                    1
          vv
clus       HEAD AND NECK - NECK HEAD AND NECK - OTHER (PLEASE SPECIFY
  subtype1                    1                                     0
  subtype2                    0                                     0
  subtype3                    0                                     2
          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                               7
  subtype2                               0
  subtype3                               4
          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                       1                                5
  subtype2                       1                                7
  subtype3                       0                                4
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       2                           15
  subtype2                                       2                           17
  subtype3                                       1                           13
          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                                                11
  subtype3                                                27
          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        3
  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                                           1        0
  HEAD AND NECK - NECK                                           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                                7        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   2        1
  LOWER EXTREMITY - GROIN                                        1        1
  LOWER EXTREMITY - LOWER LEG/CALF                               5        7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        2        2
  LOWER EXTREMITY - THIGH/KNEE                                  15       17
  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       11
  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                                             1
  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                          2
  LOWER ABDOMINAL/PELVIC - BLADDER                               1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 2
  LOWER ABDOMINAL/PELVIC - PELVIC                                4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1
  LOWER EXTREMITY - FOOT/ANKLE                                   1
  LOWER EXTREMITY - GROIN                                        0
  LOWER EXTREMITY - LOWER LEG/CALF                               4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1
  LOWER EXTREMITY - THIGH/KNEE                                  13
  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             27
  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 47 60
  subtype2 27 24
  subtype3 66 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47   60
  subtype2   27   24
  subtype3   66   35
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       47       27       66
  MALE         60       24       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 79 28
  subtype2 26 24
  subtype3 75 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   79   28
  subtype2   26   24
  subtype3   75   21
     clus
vv    subtype1 subtype2 subtype3
  NO        79       26       75
  YES       28       24       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                           13             0
  subtype3                            5             0
          vv
clus       GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  subtype1                                                                        0
  subtype2                                                                        0
  subtype3                                                                        1
          vv
clus       LEIOMYOSARCOMA (LMS)
  subtype1                   16
  subtype2                    5
  subtype3                   83
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                5                9
  subtype2                                                3               11
  subtype3                                                1                5
          vv
clus       PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       14
  subtype2                                                       11
  subtype3                                                        4
          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                                         10
  subtype2                                          8
  subtype3                                          2
D7V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   41
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           16
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                5
  MYXOFIBROSARCOMA                                                                9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                       14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        2
  SYNOVIAL SARCOMA - BIPHASIC                                                     2
  SYNOVIAL SARCOMA - MONOPHASIC                                                   6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                     10
                                                                          clus
vv                                                                         subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                                   13
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            5
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                3
  MYXOFIBROSARCOMA                                                               11
  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                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    5
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                           83
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                                5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      2
[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 55 36  6 10
  subtype2 28 15  0  7
  subtype3 71 18  3  9
D7V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       55       28       71
  R1       36       15       18
  R2        6        0        3
  RX       10        7        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         5   100
  subtype2     1                         4    44
  subtype3     4                         9    83
D7V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        4
  BLACK OR AFRICAN AMERICAN        5        4        9
  WHITE                          100       44       83
[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 92
  subtype2  2 45
  subtype3  0 85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   92
  subtype2    2   45
  subtype3    0   85
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        2        0
  NOT HISPANIC OR LATINO       92       45       85
[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 50 34
  subtype2 26 12
  subtype3 73 42
  subtype4 12 10
subtype1 subtype2 subtype3 subtype4 
      84       38      115       22 
subtype1 subtype2 subtype3 subtype4 
      34       12       42       10 
$subtype1
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-AB2P 
       31.53        34.68        67.20        15.22        23.70        12.07 
TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-KF-A41W TCGA-LI-A9QH 
       13.28        30.51        32.15        16.60        11.70        17.75 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-SG-A849 TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
        6.35        20.94        17.52        35.08        50.01        19.69 
TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 
       44.91         0.56        32.71        68.61        18.54        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6BF 
       49.05       136.44        44.68        10.68        35.28        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A8BK 
       36.85        26.99        41.00        78.28        16.87        61.97 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F 
       45.14        38.17        40.44        19.43         1.15        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A2QS 
       15.72        65.98        66.74       106.55        50.40        49.15 
TCGA-FX-A3TO TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 
       20.32         4.57        19.89        37.12       171.09         5.92 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-MO-A47R TCGA-N1-A6IA TCGA-PT-A8TR TCGA-QC-A7B5 
       23.38         5.19        10.45         7.36        26.73        13.08 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SI-AA8B 
       46.82        48.59       130.32        10.52        18.94         8.61 
TCGA-WK-A8XO TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       11.93        26.43        45.34         4.37        13.38        15.98 

$subtype2
TCGA-3B-A9HJ TCGA-DX-A6BK TCGA-DX-AB2W TCGA-DX-AB36 TCGA-DX-AB37 TCGA-MB-A5Y9 
       36.30        16.18       106.45        60.00        84.66         8.28 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A48K TCGA-DX-A6BE 
       45.11        54.21        86.83        35.77        45.99        28.96 
TCGA-DX-A6YQ TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7ES TCGA-DX-A8BM 
        3.06        50.50        86.30        21.30        20.05        47.87 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T 
       51.91       150.35        60.66        86.10         9.21        77.88 
TCGA-FX-A3RE TCGA-K1-A6RT TCGA-MB-A5Y8 TCGA-MJ-A68J TCGA-QQ-A5VA TCGA-QQ-A8VF 
       21.70        17.36        25.41        17.98        18.08       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-AB3D TCGA-Z4-AAPF 
       12.46        15.95 

$subtype3
TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB30 
       34.36        75.32        17.95        14.43        14.07        22.85 
TCGA-DX-AB32 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
      101.98        37.02        12.62        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-PC-A5DP TCGA-VT-A80J TCGA-3B-A9HP TCGA-3B-A9HQ 
      159.29        22.62        18.08        26.17        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       88.57        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY 
       38.47        36.03        18.64        26.56        14.04        12.85 
TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
        6.28        33.44        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 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        52.77        46.03        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z0 
       37.58        15.95        37.41        82.68        36.33        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BJ TCGA-DX-A8BO 
      101.23        34.49        62.20        30.35         9.34        40.77 
TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-FX-A3NJ TCGA-FX-A48G 
       27.95        36.69         6.58        17.79        31.13        19.89 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       15.48        67.63        34.88        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3KA 
       80.48        19.53         3.22         1.38        25.22        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       85.97        16.41       101.26        53.33        62.17       123.78 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK 
       63.81        16.41        35.28        30.31         0.49        21.73 
TCGA-MJ-A68H TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-AA9N 
       14.99        11.57       122.96        37.55        81.01        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XS 
        1.84        35.90        37.12        13.22        10.72        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       38.27        65.46        56.61        22.62         8.58        63.35 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 
       35.90        18.08        30.84        35.18        19.17        50.86 
TCGA-X9-A971 
       27.32 

$subtype4
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-DX-A2IZ TCGA-DX-A7EO 
       15.85        40.60       188.15        41.49         8.58       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A8OO TCGA-JV-A5VF 
       29.49        48.20        50.89        71.31         8.05         1.05 
TCGA-JV-A75J TCGA-MB-A8JL TCGA-MJ-A850 TCGA-PC-A5DN TCGA-SG-A6Z7 TCGA-SI-A71Q 
        3.91        19.73        22.39        38.63         3.88        32.75 
TCGA-SI-AA8C TCGA-WK-A8XQ TCGA-X6-A8C7 TCGA-X9-A973 
       19.63         4.80        29.46        36.43 

subtype1 subtype2 subtype3 subtype4 
    0.56     0.72     0.49     1.05 
subtype1 subtype2 subtype3 subtype4 
  171.09   150.35   159.29   188.15 
subtype1 subtype2 subtype3 subtype4 
  29.160   32.365   33.300   29.475 
[1] "0.6 - 171.1 (29.2)" "0.7 - 150.3 (32.4)" "0.5 - 159.3 (33.3)"
[4] "1.1 - 188.2 (29.5)"
D8V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  1                   0
  subtype2              0                  1                   0
  subtype3              0                  4                   0
  subtype4              1                  1                   2
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             1
  subtype2                   0                             0
  subtype3                   1                             1
  subtype4                   0                             0
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                      5                    1
  subtype2                     1                      0                    0
  subtype3                     0                     22                    1
  subtype4                     0                      1                    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                                6
  subtype3                       0                                7
  subtype4                       0                                0
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       2                           15
  subtype2                                       2                           10
  subtype3                                       1                           17
  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                                                 9
  subtype3                                                29
  subtype4                                                 3
          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                                  0                        2
  subtype3                                  1                        1
  subtype4                                  0                        0
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  subtype1                           1                         0
  subtype2                           0                         0
  subtype3                           2                         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        1
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          0        1
  GYNECOLOGICAL - UTERUS                                         5        0
  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        6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        2        2
  LOWER EXTREMITY - THIGH/KNEE                                  15       10
  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        9
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        0
  SUPERFICIAL TRUNK - BACK                                       2        2
  SUPERFICIAL TRUNK - BUTTOCK                                    1        0
  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                                             4        1
  CHEST - LUNG/PLEURA                                            0        2
  CHEST - MEDIASTINUM                                            1        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                        22        1
  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                               7        0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        0
  LOWER EXTREMITY - THIGH/KNEE                                  17        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             29        3
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             3        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             1        0
  SUPERFICIAL TRUNK - BACK                                       1        0
  SUPERFICIAL TRUNK - BUTTOCK                                    2        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 35 49
  subtype2 18 20
  subtype3 72 43
  subtype4 15  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   49
  subtype2   18   20
  subtype3   72   43
  subtype4   15    7
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       35       18       72       15
  MALE         49       20       43        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 24
  subtype2 22 16
  subtype3 83 26
  subtype4 15  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60   24
  subtype2   22   16
  subtype3   83   26
  subtype4   15    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        60       22       83       15
  YES       24       16       26        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                           37             2
  subtype2                           11             0
  subtype3                            7             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                    4
  subtype3                   84
  subtype4                    4
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                1               10
  subtype2                                                5                7
  subtype3                                                0                8
  subtype4                                                3                0
          vv
clus       PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                       15
  subtype2                                                        6
  subtype3                                                        7
  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                                          4
  subtype3                                          8
  subtype4                                          1
D8V6, multiclass
                                                                          clus
vv                                                                         subtype1
  DEDIFFERENTIATED LIPOSARCOMA                                                   37
  DESMOID TUMOR                                                                   2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                           12
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                1
  MYXOFIBROSARCOMA                                                               10
  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                                                   11
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        0
  LEIOMYOSARCOMA (LMS)                                                            4
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                5
  MYXOFIBROSARCOMA                                                                7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        1
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      4
                                                                          clus
vv                                                                         subtype3
  DEDIFFERENTIATED LIPOSARCOMA                                                    7
  DESMOID TUMOR                                                                   0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS        1
  LEIOMYOSARCOMA (LMS)                                                           84
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                0
  MYXOFIBROSARCOMA                                                                8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                        7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                        0
  SYNOVIAL SARCOMA - BIPHASIC                                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                      8
                                                                          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)                                3
  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 41 35  3  5
  subtype2 23  6  0  8
  subtype3 77 25  3 10
  subtype4 13  3  3  3
D8V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       41       23       77       13
  R1       35        6       25        3
  R2        3        0        3        3
  RX        5        8       10        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    79
  subtype2     1                         2    34
  subtype3     4                        12    94
  subtype4     0                         2    20
D8V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        4        0
  BLACK OR AFRICAN AMERICAN        2        2       12        2
  WHITE                           79       34       94       20
[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  2 75
  subtype2  1 36
  subtype3  0 97
  subtype4  2 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   75
  subtype2    1   36
  subtype3    0   97
  subtype4    2   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        0        2
  NOT HISPANIC OR LATINO       75       36       97       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 37 23
  subtype2 20  7
  subtype3 31 17
  subtype4  8 15
  subtype5 26 14
subtype1 subtype2 subtype3 subtype4 subtype5 
      60       27       48       23       40 
subtype1 subtype2 subtype3 subtype4 subtype5 
      23        7       17       15       14 
$subtype1
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A7EU TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       34.68        67.20        23.70        15.85        40.60        12.07 
TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-KF-A41W TCGA-QQ-A8VB TCGA-X6-A8C6 
       60.00        32.15        16.60        11.70       188.15        35.08 
TCGA-3B-A9HI TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23Z 
       50.01        44.91         0.56        74.66         5.26        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LS TCGA-DX-A48K 
       60.30         8.58         9.70        95.38         9.04        45.99 
TCGA-DX-A48N TCGA-DX-A6YS TCGA-DX-A7EQ TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS 
       35.28        78.28        29.49        40.44        19.43         1.15 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB3B 
       12.00        15.72        65.98        86.10       106.55        50.89 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A3YV TCGA-MB-A8JL TCGA-MJ-A850 
       49.15        20.32         8.05         4.57        19.73        22.39 
TCGA-MO-A47R TCGA-PC-A5DN TCGA-PT-A8TR TCGA-QQ-A8VD TCGA-QQ-A8VH TCGA-SG-A6Z4 
       10.45        38.63        26.73       130.32        10.52        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-WK-A8XO TCGA-WK-A8XQ 
        3.88        32.75         8.61        19.63        11.93         4.80 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       29.46        36.43         4.37        13.38        15.95        15.98 

$subtype2
TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB35 TCGA-LI-A9QH TCGA-3B-A9HL TCGA-DX-A1KU 
       34.36        17.95        30.51        17.75        19.69        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A23V TCGA-DX-A3LW 
       32.71        68.61        45.11        18.54        66.87       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6YR 
       33.44        44.68        31.86        28.96        31.96        41.00 
TCGA-DX-A6YZ TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-AB2T TCGA-IE-A4EJ 
       86.30        47.87        38.17       150.35        77.88         3.22 
TCGA-IF-A3RQ TCGA-MB-A8JK TCGA-QC-AA9N 
       37.12        21.73        17.65 

$subtype3
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-PC-A5DP TCGA-3B-A9HP 
       37.02        12.62        52.27        22.62        18.08        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 
       68.55        88.57        25.25        10.32        38.47        18.64 
TCGA-3B-A9I3 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A6BA 
       26.56        51.02        14.99        24.26        52.77        82.68 
TCGA-DX-A6BB TCGA-DX-A7ES TCGA-DX-A8BV TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y 
       36.33        20.05        60.66        31.13        21.70        15.48 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IW-A3M4 
       33.30         9.80        80.48        19.53        25.22        85.97 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KD-A5QT TCGA-MB-A5YA TCGA-MJ-A68H TCGA-PC-A5DK 
      101.26        53.33        16.41         0.49        14.99       122.96 
TCGA-PC-A5DO TCGA-QQ-A5VD TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
       81.01        37.12        84.79        38.27        65.46        56.61 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C5 TCGA-X9-A971 
        8.58        63.35        35.90        18.08        50.86        27.32 

$subtype4
TCGA-DX-AB30 TCGA-IE-A4EH TCGA-WK-A8XT TCGA-3B-A9HX TCGA-DX-A1KY TCGA-DX-A3UA 
       22.85        26.93        41.49        42.84        12.85        10.68 
TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BU TCGA-DX-AB3C TCGA-HS-A5N8 TCGA-IS-A3KA 
       34.49         9.34        36.69        71.31         0.72        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RV TCGA-KD-A5QS 
        5.92        16.41         1.05         3.91         5.19        63.81 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-QQ-A5VC TCGA-SI-A71O TCGA-X6-A8C2 
       35.28        30.31        35.90        22.82        35.18 

$subtype5
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB32 
       15.22        14.43        14.07       106.45        13.28       101.98 
TCGA-DX-AB37 TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
       84.66         8.28         6.35        20.94        17.52        26.17 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A8BK TCGA-DX-A8BL 
       35.77         4.54         3.06        16.87        61.97        45.14 
TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BS TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2Z 
       40.77        51.91        27.95        66.74         9.21        50.40 
TCGA-HB-A2OT TCGA-IS-A3K7 TCGA-K1-A6RT TCGA-K1-A6RU TCGA-MB-A5Y8 TCGA-QC-A7B5 
       67.63       171.09        17.36        23.38        25.41        13.08 
TCGA-QQ-A5VB TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-AB3D 
       48.59        64.77        16.77        25.35        13.41        12.46 
TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C3 
       22.62        26.43        45.34        19.17 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.56     3.22     0.49     0.72     3.06 
subtype1 subtype2 subtype3 subtype4 subtype5 
  188.15   150.35   122.96    71.31   171.09 
subtype1 subtype2 subtype3 subtype4 subtype5 
  23.045   33.440   36.115   22.850   24.365 
[1] "0.6 - 188.2 (23.0)" "3.2 - 150.3 (33.4)" "0.5 - 123.0 (36.1)"
[4] "0.7 - 71.3 (22.9)"  "3.1 - 171.1 (24.4)"
D9V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              1                  2                   1
  subtype2              0                  2                   0
  subtype3              0                  0                   0
  subtype4              0                  1                   0
  subtype5              0                  2                   0
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             1
  subtype2                   0                             0
  subtype3                   1                             1
  subtype4                   0                             0
  subtype5                   0                             0
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     0                      2                    0
  subtype2                     0                      0                    0
  subtype3                     1                     11                    0
  subtype4                     0                      7                    0
  subtype5                     0                      1                    1
          vv
clus       HEAD AND NECK - NECK LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                    1                                0
  subtype2                    0                                0
  subtype3                    0                                1
  subtype4                    0                                0
  subtype5                    0                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              0
  subtype3                                              2
  subtype4                                              0
  subtype5                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               3
  subtype2                               1
  subtype3                               2
  subtype4                               2
  subtype5                               0
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       1                            2
  subtype2                                       0                            0
  subtype3                                       0                            1
  subtype4                                       0                            1
  subtype5                                       1                            0
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       0                                2
  subtype2                       0                                1
  subtype3                       0                                2
  subtype4                       0                                1
  subtype5                       1                                7
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       1                            9
  subtype2                                       0                            8
  subtype3                                       0                            6
  subtype4                                       1                            6
  subtype5                                       2                           13
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
  subtype4                                       1
  subtype5                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         1
  subtype2                                         0
  subtype3                                         1
  subtype4                                         0
  subtype5                                         0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                3
  subtype2                                                0
  subtype3                                                0
  subtype4                                                0
  subtype5                                                0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        2
  subtype2                                        0
  subtype3                                        2
  subtype4                                        1
  subtype5                                        0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       1
  subtype2                                                       0
  subtype3                                                       0
  subtype4                                                       0
  subtype5                                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                22
  subtype2                                                14
  subtype3                                                13
  subtype4                                                 2
  subtype5                                                 1
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  2
  subtype4                                                  0
  subtype5                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  0                        1
  subtype2                                  0                        0
  subtype3                                  0                        0
  subtype4                                  0                        0
  subtype5                                  2                        3
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK UPPER EXTREMITY - SHOULDER/AXILLA
  subtype1                           1                                 1
  subtype2                           1                                 0
  subtype3                           0                                 1
  subtype4                           0                                 0
  subtype5                           0                                 3
          vv
clus       UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 2
  subtype2                                 0
  subtype3                                 0
  subtype4                                 0
  subtype5                                 2
D9V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 1        0
  CHEST - CHEST WALL                                             2        2
  CHEST - LUNG/PLEURA                                            1        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         2        0
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           1        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                3        1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   2        0
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               2        1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        0
  LOWER EXTREMITY - THIGH/KNEE                                   9        8
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               3        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       2        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             22       14
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       1        0
  SUPERFICIAL TRUNK - BUTTOCK                                    1        1
  UPPER EXTREMITY - SHOULDER/AXILLA                              1        0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              2        0
                                                         clus
vv                                                        subtype3 subtype4
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             0        1
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            1        0
  CHEST - OTHER (PLEASE SPECIFY                                  1        0
  GYNECOLOGICAL - OVARY                                          1        0
  GYNECOLOGICAL - UTERUS                                        11        7
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               1        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 2        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                2        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0        0
  LOWER EXTREMITY - FOOT/ANKLE                                   1        1
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               2        1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        1
  LOWER EXTREMITY - THIGH/KNEE                                   6        6
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        1        1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       2        1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             13        2
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             2        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  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
  CHEST - BREAST                                                 0
  CHEST - CHEST WALL                                             2
  CHEST - LUNG/PLEURA                                            0
  CHEST - MEDIASTINUM                                            0
  CHEST - OTHER (PLEASE SPECIFY                                  0
  GYNECOLOGICAL - OVARY                                          0
  GYNECOLOGICAL - UTERUS                                         1
  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                                   0
  LOWER EXTREMITY - GROIN                                        1
  LOWER EXTREMITY - LOWER LEG/CALF                               7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        2
  LOWER EXTREMITY - THIGH/KNEE                                  13
  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              1
  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  5
[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 29 31
  subtype2 12 15
  subtype3 33 15
  subtype4 16  7
  subtype5 21 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   31
  subtype2   12   15
  subtype3   33   15
  subtype4   16    7
  subtype5   21   19
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       29       12       33       16       21
  MALE         31       15       15        7       19
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus        0  1
  subtype1 45 15
  subtype2 18  8
  subtype3 36 10
  subtype4 15  8
  subtype5 19 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45   15
  subtype2   18    8
  subtype3   36   10
  subtype4   15    8
  subtype5   19   21
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        45       18       36       15       19
  YES       15        8       10        8       21
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR LEIOMYOSARCOMA (LMS)
  subtype1                           23             2                    7
  subtype2                           15             0                    0
  subtype3                            1             0                   46
  subtype4                            2             0                   13
  subtype5                            2             0                    6
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                4                6
  subtype2                                                0                5
  subtype3                                                0                1
  subtype4                                                1                2
  subtype5                                                3                7
          vv
clus       PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                        7
  subtype2                                                        5
  subtype3                                                        0
  subtype4                                                        2
  subtype5                                                       14
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        2                           1
  subtype2                                        0                           0
  subtype3                                        0                           0
  subtype4                                        0                           0
  subtype5                                        0                           0
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             3
  subtype2                             0
  subtype3                             0
  subtype4                             2
  subtype5                             0
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          5
  subtype2                                          2
  subtype3                                          0
  subtype4                                          1
  subtype5                                          8
D9V6, multiclass
                                                          clus
vv                                                         subtype1 subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                   23       15
  DESMOID TUMOR                                                   2        0
  LEIOMYOSARCOMA (LMS)                                            7        0
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                4        0
  MYXOFIBROSARCOMA                                                6        5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA        7        5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                        2        0
  SYNOVIAL SARCOMA - BIPHASIC                                     1        0
  SYNOVIAL SARCOMA - MONOPHASIC                                   3        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                      5        2
                                                          clus
vv                                                         subtype3 subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                    1        2
  DESMOID TUMOR                                                   0        0
  LEIOMYOSARCOMA (LMS)                                           46       13
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                0        1
  MYXOFIBROSARCOMA                                                1        2
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA        0        2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                        0        0
  SYNOVIAL SARCOMA - BIPHASIC                                     0        0
  SYNOVIAL SARCOMA - MONOPHASIC                                   0        2
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                      0        1
                                                          clus
vv                                                         subtype5
  DEDIFFERENTIATED LIPOSARCOMA                                    2
  DESMOID TUMOR                                                   0
  LEIOMYOSARCOMA (LMS)                                            6
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                3
  MYXOFIBROSARCOMA                                                7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA       14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                        0
  SYNOVIAL SARCOMA - BIPHASIC                                     0
  SYNOVIAL SARCOMA - MONOPHASIC                                   0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                      8
[1] 10  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 30 22  2  6
  subtype2 12 10  3  2
  subtype3 34 10  0  4
  subtype4 12  5  3  3
  subtype5 27  9  0  3
D9V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       30       12       34       12       27
  R1       22       10       10        5        9
  R2        2        3        0        3        0
  RX        6        2        4        3        3
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    57
  subtype2     0                         2    25
  subtype3     1                         5    39
  subtype4     0                         2    20
  subtype5     2                         3    32
D9V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        1        0        2
  BLACK OR AFRICAN AMERICAN        1        2        5        2        3
  WHITE                           57       25       39       20       32
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
          cls
clus        0  1
  subtype1  1 51
  subtype2  0 27
  subtype3  0 43
  subtype4  1 18
  subtype5  2 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   51
  subtype2    0   27
  subtype3    0   43
  subtype4    1   18
  subtype5    2   33
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        0        0        1        2
  NOT HISPANIC OR LATINO       51       27       43       18       33
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 38 21
  subtype2 32 18
  subtype3 12  9
  subtype4 27 16
  subtype5 13 12
subtype1 subtype2 subtype3 subtype4 subtype5 
      59       50       21       43       25 
subtype1 subtype2 subtype3 subtype4 subtype5 
      21       18        9       16       12 
$subtype1
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A7EU TCGA-DX-AB2P TCGA-DX-AB35 TCGA-DX-AB36 
       34.68        67.20        23.70        12.07        30.51        60.00 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-KF-A41W TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       32.15        16.60        11.70        35.08        50.01        19.69 
TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R 
       44.91         0.56        32.71        68.61        18.54        74.66 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LS 
       66.87        27.81        60.30         9.70        95.38         9.04 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BF TCGA-DX-A6YR 
      136.44        44.68        45.99        35.28        31.96        41.00 
TCGA-DX-A6YS TCGA-DX-A8BN TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F 
       78.28        38.17        40.44        19.43         1.15        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2V TCGA-FX-A2QS TCGA-FX-A3RE 
       15.72        65.98        86.10       106.55        49.15        21.70 
TCGA-FX-A3TO TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-K1-A6RT TCGA-K1-A6RV 
       20.32         4.57        37.12       171.09        17.36         5.19 
TCGA-PC-A5DN TCGA-QC-AA9N TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-SG-A6Z4 TCGA-SI-AA8B 
       38.63        17.65        48.59       130.32        18.94         8.61 
TCGA-WK-A8XO TCGA-X6-A7WC TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-AAPG 
       11.93        45.34        36.43         4.37        15.98 

$subtype2
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-PC-A5DP 
       37.02        12.62        26.93        52.27        22.62        18.08 
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-3B-A9I3 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48O 
       18.64        26.56        51.02        14.99        24.26        52.77 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A7ES TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HS-A5N7 
       82.68        36.33        20.05        31.13        15.48        33.30 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 
        9.80        80.48        19.53        25.22        13.58        85.97 
TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5YA 
       16.41       101.26        53.33        16.41        35.28         0.49 
TCGA-MJ-A68H TCGA-PC-A5DK TCGA-PC-A5DO TCGA-QQ-A5VD TCGA-WK-A8XS TCGA-WK-A8XX 
       14.99       122.96        81.01        37.12        84.79        38.27 
TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46        56.61         8.58        63.35        35.90        18.08 
TCGA-X6-A8C5 TCGA-X9-A971 
       50.86        27.32 

$subtype3
TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB30 TCGA-DX-AB32 TCGA-3B-A9HX 
       34.36        17.95        14.07        22.85       101.98        42.84 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-DX-A8BJ TCGA-DX-A8BO 
       14.04        12.85        31.86         4.54         9.34        40.77 
TCGA-DX-A8BS TCGA-DX-A8BU TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-LI-A67I 
       27.95        36.69        67.63         0.72         3.22        30.31 
TCGA-WK-A8Y0 TCGA-X6-A8C2 TCGA-X6-A8C3 
       22.62        35.18        19.17 

$subtype4
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB37 TCGA-LI-A9QH 
       15.22        14.43       106.45        13.28        84.66        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-DX-A1KZ 
        8.28         6.35        20.94        17.52        26.17        45.11 
TCGA-DX-A23T TCGA-DX-A3LY TCGA-DX-A3U6 TCGA-DX-A3UA TCGA-DX-A6BE TCGA-DX-A6YQ 
        5.26        33.44        35.77        10.68        28.96         3.06 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BQ 
       16.87        86.30        61.97        45.14        47.87        51.91 
TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z 
      150.35        60.66        66.74         9.21        77.88        50.40 
TCGA-K1-A6RU TCGA-KD-A5QS TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-QC-A7B5 TCGA-QQ-A5VC 
       23.38        63.81        25.41        21.73        13.08        35.90 
TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SI-A71O TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-AB3D 
       64.77        16.77        22.82        25.35        13.41        12.46 
TCGA-X6-A7W8 
       26.43 

$subtype5
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-DX-A2IZ TCGA-DX-A7EI 
       15.85        40.60       188.15        41.49         8.58        34.49 
TCGA-DX-A7EQ TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A8OO TCGA-IW-A3M5 TCGA-JV-A5VF 
       29.49        50.89        71.31         8.05         5.92         1.05 
TCGA-JV-A75J TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47R TCGA-PT-A8TR TCGA-QQ-A8VH 
        3.91        19.73        22.39        10.45        26.73        10.52 
TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XQ TCGA-X6-A8C7 TCGA-Z4-A9VC 
        3.88        32.75        19.63         4.80        29.46        13.38 
TCGA-Z4-AAPF 
       15.95 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.56     0.49     0.72     3.06     1.05 
subtype1 subtype2 subtype3 subtype4 subtype5 
  171.09   122.96   101.98   150.35   188.15 
subtype1 subtype2 subtype3 subtype4 subtype5 
   34.68    34.29    22.85    25.41    19.63 
[1] "0.6 - 171.1 (34.7)" "0.5 - 123.0 (34.3)" "0.7 - 102.0 (22.9)"
[4] "3.1 - 150.3 (25.4)" "1.1 - 188.2 (19.6)"
D10V2, continuous
          vv
clus       CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  subtype1              0                  2                   0
  subtype2              0                  0                   0
  subtype3              0                  4                   0
  subtype4              0                  0                   0
  subtype5              1                  1                   1
          vv
clus       CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  subtype1                   0                             0
  subtype2                   1                             1
  subtype3                   0                             0
  subtype4                   0                             0
  subtype5                   0                             1
          vv
clus       GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS HEAD AND NECK - HEAD
  subtype1                     1                      2                    0
  subtype2                     0                     14                    0
  subtype3                     0                      1                    0
  subtype4                     0                      1                    1
  subtype5                     0                      3                    0
          vv
clus       HEAD AND NECK - NECK LOWER ABDOMINAL/PELVIC - BLADDER
  subtype1                    0                                0
  subtype2                    0                                1
  subtype3                    0                                0
  subtype4                    0                                0
  subtype5                    1                                0
          vv
clus       LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  subtype1                                              0
  subtype2                                              2
  subtype3                                              0
  subtype4                                              0
  subtype5                                              0
          vv
clus       LOWER ABDOMINAL/PELVIC - PELVIC
  subtype1                               3
  subtype2                               3
  subtype3                               0
  subtype4                               0
  subtype5                               2
          vv
clus       LOWER ABDOMINAL/PELVIC - SPERMATIC CORD LOWER EXTREMITY - FOOT/ANKLE
  subtype1                                       1                            0
  subtype2                                       0                            1
  subtype3                                       1                            0
  subtype4                                       0                            1
  subtype5                                       0                            2
          vv
clus       LOWER EXTREMITY - GROIN LOWER EXTREMITY - LOWER LEG/CALF
  subtype1                       1                                2
  subtype2                       0                                2
  subtype3                       0                                3
  subtype4                       0                                6
  subtype5                       0                                0
          vv
clus       LOWER EXTREMITY - OTHER (PLEASE SPECIFY LOWER EXTREMITY - THIGH/KNEE
  subtype1                                       1                           10
  subtype2                                       0                            6
  subtype3                                       0                            8
  subtype4                                       3                           14
  subtype5                                       0                            4
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - COLON
  subtype1                                       0
  subtype2                                       1
  subtype3                                       1
  subtype4                                       0
  subtype5                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  subtype1                                         1
  subtype2                                         1
  subtype3                                         0
  subtype4                                         0
  subtype5                                         0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  subtype1                                                1
  subtype2                                                0
  subtype3                                                0
  subtype4                                                0
  subtype5                                                2
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  subtype1                                        1
  subtype2                                        2
  subtype3                                        0
  subtype4                                        0
  subtype5                                        2
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  subtype1                                                       1
  subtype2                                                       0
  subtype3                                                       0
  subtype4                                                       0
  subtype5                                                       0
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  subtype1                                                28
  subtype2                                                12
  subtype3                                                 3
  subtype4                                                 6
  subtype5                                                 3
          vv
clus       RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  subtype1                                                  0
  subtype2                                                  2
  subtype3                                                  0
  subtype4                                                  0
  subtype5                                                  0
          vv
clus       SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  subtype1                                  0                        1
  subtype2                                  0                        0
  subtype3                                  0                        0
  subtype4                                  2                        3
  subtype5                                  0                        0
          vv
clus       SUPERFICIAL TRUNK - BUTTOCK UPPER EXTREMITY - SHOULDER/AXILLA
  subtype1                           1                                 1
  subtype2                           0                                 1
  subtype3                           0                                 0
  subtype4                           0                                 3
  subtype5                           1                                 0
          vv
clus       UPPER EXTREMITY - UPPER ARM/ELBOW
  subtype1                                 1
  subtype2                                 0
  subtype3                                 0
  subtype4                                 2
  subtype5                                 1
D10V3, multiclass
                                                         clus
vv                                                        subtype1 subtype2
  CHEST - BREAST                                                 0        0
  CHEST - CHEST WALL                                             2        0
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        1
  CHEST - OTHER (PLEASE SPECIFY                                  0        1
  GYNECOLOGICAL - OVARY                                          1        0
  GYNECOLOGICAL - UTERUS                                         2       14
  HEAD AND NECK - HEAD                                           0        0
  HEAD AND NECK - NECK                                           0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                3        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        1
  LOWER EXTREMITY - GROIN                                        1        0
  LOWER EXTREMITY - LOWER LEG/CALF                               2        2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        1        0
  LOWER EXTREMITY - THIGH/KNEE                                  10        6
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0        1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      1        1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               1        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       1        2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM             28       12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        0
  SUPERFICIAL TRUNK - BACK                                       1        0
  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                                             4        0
  CHEST - LUNG/PLEURA                                            0        0
  CHEST - MEDIASTINUM                                            0        0
  CHEST - OTHER (PLEASE SPECIFY                                  0        0
  GYNECOLOGICAL - OVARY                                          0        0
  GYNECOLOGICAL - UTERUS                                         1        1
  HEAD AND NECK - HEAD                                           0        1
  HEAD AND NECK - NECK                                           0        0
  LOWER ABDOMINAL/PELVIC - BLADDER                               0        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                0        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        1        0
  LOWER EXTREMITY - FOOT/ANKLE                                   0        1
  LOWER EXTREMITY - GROIN                                        0        0
  LOWER EXTREMITY - LOWER LEG/CALF                               3        6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0        3
  LOWER EXTREMITY - THIGH/KNEE                                   8       14
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        1        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0        0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               0        0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       0        0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              3        6
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0        0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0        2
  SUPERFICIAL TRUNK - BACK                                       0        3
  SUPERFICIAL TRUNK - BUTTOCK                                    0        0
  UPPER EXTREMITY - SHOULDER/AXILLA                              0        3
  UPPER EXTREMITY - UPPER ARM/ELBOW                              0        2
                                                         clus
vv                                                        subtype5
  CHEST - BREAST                                                 1
  CHEST - CHEST WALL                                             1
  CHEST - LUNG/PLEURA                                            1
  CHEST - MEDIASTINUM                                            0
  CHEST - OTHER (PLEASE SPECIFY                                  1
  GYNECOLOGICAL - OVARY                                          0
  GYNECOLOGICAL - UTERUS                                         3
  HEAD AND NECK - HEAD                                           0
  HEAD AND NECK - NECK                                           1
  LOWER ABDOMINAL/PELVIC - BLADDER                               0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                 0
  LOWER ABDOMINAL/PELVIC - PELVIC                                2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                        0
  LOWER EXTREMITY - FOOT/ANKLE                                   2
  LOWER EXTREMITY - GROIN                                        0
  LOWER EXTREMITY - LOWER LEG/CALF                               0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                        0
  LOWER EXTREMITY - THIGH/KNEE                                   4
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                        0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                      0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL               2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                       2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM              3
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES             0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                             0
  SUPERFICIAL TRUNK - BACK                                       0
  SUPERFICIAL TRUNK - BUTTOCK                                    1
  UPPER EXTREMITY - SHOULDER/AXILLA                              0
  UPPER EXTREMITY - UPPER ARM/ELBOW                              1
[1] 30  5
[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 23 36
  subtype2 36 14
  subtype3 12  9
  subtype4 21 22
  subtype5 19  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   36
  subtype2   36   14
  subtype3   12    9
  subtype4   21   22
  subtype5   19    6
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       23       36       12       21       19
  MALE         36       14        9       22        6
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1 46 13
  subtype2 39  9
  subtype3  9 11
  subtype4 21 22
  subtype5 18  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   13
  subtype2   39    9
  subtype3    9   11
  subtype4   21   22
  subtype5   18    7
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        46       39        9       21       18
  YES       13        9       11       22        7
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR LEIOMYOSARCOMA (LMS)
  subtype1                           27             2                   10
  subtype2                            1             0                   49
  subtype3                            3             0                    3
  subtype4                            6             0                    4
  subtype5                            6             0                    6
          vv
clus       MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST) MYXOFIBROSARCOMA
  subtype1                                                0                7
  subtype2                                                0                0
  subtype3                                                0                6
  subtype4                                                4                8
  subtype5                                                4                0
          vv
clus       PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  subtype1                                                        7
  subtype2                                                        0
  subtype3                                                        5
  subtype4                                                       15
  subtype5                                                        1
          vv
clus       SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED SYNOVIAL SARCOMA - BIPHASIC
  subtype1                                        0                           0
  subtype2                                        0                           0
  subtype3                                        0                           0
  subtype4                                        0                           0
  subtype5                                        2                           1
          vv
clus       SYNOVIAL SARCOMA - MONOPHASIC
  subtype1                             0
  subtype2                             0
  subtype3                             0
  subtype4                             0
  subtype5                             5
          vv
clus       UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  subtype1                                          6
  subtype2                                          0
  subtype3                                          4
  subtype4                                          6
  subtype5                                          0
D10V6, multiclass
                                                          clus
vv                                                         subtype1 subtype2
  DEDIFFERENTIATED LIPOSARCOMA                                   27        1
  DESMOID TUMOR                                                   2        0
  LEIOMYOSARCOMA (LMS)                                           10       49
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                0        0
  MYXOFIBROSARCOMA                                                7        0
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA        7        0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                        0        0
  SYNOVIAL SARCOMA - BIPHASIC                                     0        0
  SYNOVIAL SARCOMA - MONOPHASIC                                   0        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                      6        0
                                                          clus
vv                                                         subtype3 subtype4
  DEDIFFERENTIATED LIPOSARCOMA                                    3        6
  DESMOID TUMOR                                                   0        0
  LEIOMYOSARCOMA (LMS)                                            3        4
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                0        4
  MYXOFIBROSARCOMA                                                6        8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA        5       15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                        0        0
  SYNOVIAL SARCOMA - BIPHASIC                                     0        0
  SYNOVIAL SARCOMA - MONOPHASIC                                   0        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                      4        6
                                                          clus
vv                                                         subtype5
  DEDIFFERENTIATED LIPOSARCOMA                                    6
  DESMOID TUMOR                                                   0
  LEIOMYOSARCOMA (LMS)                                            6
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                4
  MYXOFIBROSARCOMA                                                0
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA        1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                        2
  SYNOVIAL SARCOMA - BIPHASIC                                     1
  SYNOVIAL SARCOMA - MONOPHASIC                                   5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                      0
[1] 10  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 26 27  2  4
  subtype2 37 10  0  3
  subtype3 10  8  2  1
  subtype4 28  7  1  6
  subtype5 14  4  3  4
D10V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       26       37       10       28       14
  R1       27       10        8        7        4
  R2        2        0        2        1        3
  RX        4        3        1        6        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         1    57
  subtype2     1                         6    40
  subtype3     1                         2    16
  subtype4     1                         2    38
  subtype5     1                         2    22
D10V8, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        1        1        1        1
  BLACK OR AFRICAN AMERICAN        1        6        2        2        2
  WHITE                           57       40       16       38       22
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus        0  1
  subtype1  1 53
  subtype2  0 45
  subtype3  0 17
  subtype4  2 40
  subtype5  1 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   53
  subtype2    0   45
  subtype3    0   17
  subtype4    2   40
  subtype5    1   17
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        0        0        2        1
  NOT HISPANIC OR LATINO       53       45       17       40       17
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
