[1] "ofn"        "-oTSARC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[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_Correlate_Genomic_Events_Preprocess/SARC-TP/22573934/transformed.cor.cli.txt"

nPatients in clinical file=261, in cluster file=247, common to both=247
[1]  17 247
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            85            162 
  TP53 MUTATED TP53 WILD-TYPE 
            85            162 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           24           223 
  RB1 MUTATED RB1 WILD-TYPE 
           24           223 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            36            211 
  ATRX MUTATED ATRX WILD-TYPE 
            36            211 
[1] "NUMBL MUTATION ANALYSIS"
[1] 3
  NUMBL MUTATED NUMBL WILD-TYPE 
              8             239 
  NUMBL MUTATED NUMBL WILD-TYPE 
              8             239 
[1] "MSH3 MUTATION ANALYSIS"
[1] 3
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            240 
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            240 
[1] "LTBP3 MUTATION ANALYSIS"
[1] 3
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             242 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             242 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
              5             242 
  EOMES MUTATED EOMES WILD-TYPE 
              5             242 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            240 
  PTEN MUTATED PTEN WILD-TYPE 
             7            240 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                240 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                240 
[1] "CABLES1 MUTATION ANALYSIS"
[1] 3
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               244 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               244 
[1] "TRAF7 MUTATION ANALYSIS"
[1] 3
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             243 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             243 
[1] "LOR MUTATION ANALYSIS"
[1] 3
  LOR MUTATED LOR WILD-TYPE 
            6           241 
  LOR MUTATED LOR WILD-TYPE 
            6           241 
[1] "R3HDM1 MUTATION ANALYSIS"
[1] 3
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               4              243 
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               4              243 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
            9           238 
  NF1 MUTATED NF1 WILD-TYPE 
            9           238 
[1] "COL4A3 MUTATION ANALYSIS"
[1] 3
  COL4A3 MUTATED COL4A3 WILD-TYPE 
               4              243 
  COL4A3 MUTATED COL4A3 WILD-TYPE 
               4              243 
[1] "MEGF9 MUTATION ANALYSIS"
[1] 3
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             244 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             244 
[1] "SCAP MUTATION ANALYSIS"
[1] 3
  SCAP MUTATED SCAP WILD-TYPE 
             3            244 
  SCAP MUTATED SCAP WILD-TYPE 
             3            244 
[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 247 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=92,	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=152,	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=17,	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 247 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 = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    54  31
  TP53 WILD-TYPE 100  62
  TP53 MUTATED TP53 WILD-TYPE 
            85            162 
  TP53 MUTATED TP53 WILD-TYPE 
            31             62 
$`TP53 MUTATED`
TCGA-DX-A3M2 TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2X 
       34.68        15.22        23.70        14.43        14.07        13.28 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-KF-A41W 
       22.85       101.98        12.62        26.93        28.21        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-VT-A80J TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.75         8.28        20.94        26.17        53.49        68.55 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A2J1 
       36.03        18.64        26.56        68.61        54.21        95.38 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V 
       34.88        85.45         9.73        52.77       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       37.58        15.95        82.68        36.33        64.21       101.23 
TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AATS 
       30.35        61.97        45.14        36.69        60.66         1.15 
TCGA-DX-AB2E TCGA-DX-AB2V TCGA-FX-A3TO TCGA-HS-A5N7 TCGA-IE-A4EI TCGA-IE-A4EJ 
       17.79       106.55        20.32        33.30        19.53         3.22 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42W 
      171.09        13.58         5.92         1.05       101.26        62.17 
TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A8JL TCGA-N1-A6IA 
       17.36         5.19        16.41        30.31        19.73         7.36 
TCGA-PC-A5DK TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
      122.96        13.08        46.82        18.08        48.59        37.12 
TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-UE-A6QT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
       10.52        18.94        13.22        38.27        65.46        56.61 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C5 
       22.62         8.58        63.35        45.34        35.18        50.86 
TCGA-Z4-AAPG 
       15.98 

$`TP53 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        31.53        16.18        34.36        75.32        17.95 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB35 TCGA-DX-AB36 
       15.85        40.60        12.07       106.45        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-IF-A4AK TCGA-IS-A3K8 
       84.66        32.15        16.60        37.02        52.27       159.29 
TCGA-IW-A3M6 TCGA-SG-A849 TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       22.62        17.52        41.49        35.08        50.01        19.69 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY 
       88.57        44.91         0.56        14.04        32.71        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       45.11        18.54        85.02        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87         6.28        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A48K 
       14.99        10.68        73.87        68.55        50.43        45.99 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B9 TCGA-DX-A6BE 
       24.26        35.28        46.03        26.47        37.41        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX 
       31.96        36.85        26.99         3.06        41.00        16.87 
TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ 
       86.30        21.30        34.49        62.20       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       48.20        20.05         9.34        47.87        38.17        40.77 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ 
       51.91       150.35        27.95        40.44        19.43         6.58 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.00        15.72        65.98        86.10        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       77.88        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       21.70        19.89        15.48         8.05        67.63        34.88 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
        4.57         0.72        80.48         1.38        19.89        25.22 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RU 
       85.97        16.41         3.91        53.33       123.78        23.38 
TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H 
       63.81        35.28        25.41         0.49        21.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       17.98        22.39        10.45        37.55        38.63        81.01 
TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VG 
       26.73        17.65         1.84        35.90       130.32        64.77 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
        0.72        16.77         3.88        22.82        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
        8.61        19.63        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-X6-A7W8 TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
        4.80        84.79        26.43        30.84        19.17        20.65 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 

  TP53 MUTATED TP53 WILD-TYPE 
          1.05           0.49 
  TP53 MUTATED TP53 WILD-TYPE 
        171.09         159.29 
  TP53 MUTATED TP53 WILD-TYPE 
         30.31          31.33 
[1] "1.1 - 171.1 (30.3)" "0.5 - 159.3 (31.3)"
[1] "hr=" "1.1"
D1V2, continuous
                vv
clus             CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  TP53 MUTATED                1                  2                   0
  TP53 WILD-TYPE              0                  5                   2
                vv
clus             CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  TP53 MUTATED                     1                             1
  TP53 WILD-TYPE                   0                             0
                vv
clus             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  TP53 MUTATED                       0                     13
  TP53 WILD-TYPE                     1                     13
                vv
clus             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  TP53 MUTATED                      2                    0
  TP53 WILD-TYPE                    0                    1
                vv
clus             HEAD AND NECK - OTHER (PLEASE SPECIFY
  TP53 MUTATED                                       1
  TP53 WILD-TYPE                                     1
                vv
clus             LOWER ABDOMINAL/PELVIC - BLADDER
  TP53 MUTATED                                  0
  TP53 WILD-TYPE                                1
                vv
clus             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  TP53 MUTATED                                                0
  TP53 WILD-TYPE                                              2
                vv
clus             LOWER ABDOMINAL/PELVIC - PELVIC
  TP53 MUTATED                                 5
  TP53 WILD-TYPE                               6
                vv
clus             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  TP53 MUTATED                                         0
  TP53 WILD-TYPE                                       2
                vv
clus             LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  TP53 MUTATED                              1                       1
  TP53 WILD-TYPE                            3                       1
                vv
clus             LOWER EXTREMITY - LOWER LEG/CALF
  TP53 MUTATED                                  5
  TP53 WILD-TYPE                               11
                vv
clus             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  TP53 MUTATED                                         0
  TP53 WILD-TYPE                                       3
                vv
clus             LOWER EXTREMITY - THIGH/KNEE
  TP53 MUTATED                             13
  TP53 WILD-TYPE                           30
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  TP53 MUTATED                                         2
  TP53 WILD-TYPE                                       2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  TP53 MUTATED                                           0
  TP53 WILD-TYPE                                         2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  TP53 MUTATED                                                  0
  TP53 WILD-TYPE                                                5
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  TP53 MUTATED                                          1
  TP53 WILD-TYPE                                        6
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  TP53 MUTATED                                                         0
  TP53 WILD-TYPE                                                       2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  TP53 MUTATED                                            1
  TP53 WILD-TYPE                                          0
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  TP53 MUTATED                                                  25
  TP53 WILD-TYPE                                                46
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  TP53 MUTATED                                                    2
  TP53 WILD-TYPE                                                  1
                vv
clus             SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  TP53 MUTATED                                    2                        3
  TP53 WILD-TYPE                                  0                        2
                vv
clus             SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  TP53 MUTATED                             0                         0
  TP53 WILD-TYPE                           3                         1
                vv
clus             UPPER EXTREMITY - SHOULDER/AXILLA
  TP53 MUTATED                                   3
  TP53 WILD-TYPE                                 4
                vv
clus             UPPER EXTREMITY - UPPER ARM/ELBOW
  TP53 MUTATED                                   0
  TP53 WILD-TYPE                                 5
D1V3, multiclass
                                                         clus
vv                                                        TP53 MUTATED
  CHEST - BREAST                                                     1
  CHEST - CHEST WALL                                                 2
  CHEST - LUNG/PLEURA                                                0
  CHEST - MEDIASTINUM                                                1
  CHEST - OTHER (PLEASE SPECIFY                                      1
  GYNECOLOGICAL - OVARY                                              0
  GYNECOLOGICAL - UTERUS                                            13
  HEAD AND NECK - HEAD                                               2
  HEAD AND NECK - NECK                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                              1
  LOWER ABDOMINAL/PELVIC - BLADDER                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                    5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                            0
  LOWER EXTREMITY - FOOT/ANKLE                                       1
  LOWER EXTREMITY - GROIN                                            1
  LOWER EXTREMITY - LOWER LEG/CALF                                   5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                            0
  LOWER EXTREMITY - THIGH/KNEE                                      13
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                            2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                 25
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                 2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                 2
  SUPERFICIAL TRUNK - BACK                                           3
  SUPERFICIAL TRUNK - BUTTOCK                                        0
  SUPERFICIAL TRUNK - FLANK                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                  3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                  0
                                                         clus
vv                                                        TP53 WILD-TYPE
  CHEST - BREAST                                                       0
  CHEST - CHEST WALL                                                   5
  CHEST - LUNG/PLEURA                                                  2
  CHEST - MEDIASTINUM                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                        0
  GYNECOLOGICAL - OVARY                                                1
  GYNECOLOGICAL - UTERUS                                              13
  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                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                      6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                              2
  LOWER EXTREMITY - FOOT/ANKLE                                         3
  LOWER EXTREMITY - GROIN                                              1
  LOWER EXTREMITY - LOWER LEG/CALF                                    11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                              3
  LOWER EXTREMITY - THIGH/KNEE                                        30
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                              2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   46
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                   0
  SUPERFICIAL TRUNK - BACK                                             2
  SUPERFICIAL TRUNK - BUTTOCK                                          3
  SUPERFICIAL TRUNK - FLANK                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                    4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                    5
[1] 33  2
[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
  TP53 MUTATED   48 37
  TP53 WILD-TYPE 85 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     48   37
  TP53 WILD-TYPE   85   77
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           48             85
  MALE             37             77
[1] 2 2
[1] FALSE
D1V5, binary
                cls
clus               0   1
  TP53 MUTATED    58  24
  TP53 WILD-TYPE 112  47
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     58   24
  TP53 WILD-TYPE  112   47
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            58            112
  YES           24             47
[1] 2 2
[1] FALSE
                vv
clus             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  TP53 MUTATED                              5             0
  TP53 WILD-TYPE                           51             2
                vv
clus             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  TP53 MUTATED                                                                          0
  TP53 WILD-TYPE                                                                        1
                vv
clus             LEIOMYOSARCOMA (LMS)
  TP53 MUTATED                     50
  TP53 WILD-TYPE                   48
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  TP53 MUTATED                                                  1
  TP53 WILD-TYPE                                                7
                vv
clus             MYXOFIBROSARCOMA
  TP53 MUTATED                  8
  TP53 WILD-TYPE               14
                vv
clus             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  TP53 MUTATED                                                         12
  TP53 WILD-TYPE                                                       17
                vv
clus             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  TP53 MUTATED                                          0
  TP53 WILD-TYPE                                        2
                vv
clus             SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  TP53 MUTATED                             0                             0
  TP53 WILD-TYPE                           2                             6
                vv
clus             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  TP53 MUTATED                                            9
  TP53 WILD-TYPE                                         12
D1V6, multiclass
                                                                          clus
vv                                                                         TP53 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                        5
  DESMOID TUMOR                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS            0
  LEIOMYOSARCOMA (LMS)                                                               50
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                    1
  MYXOFIBROSARCOMA                                                                    8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                           12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          9
                                                                          clus
vv                                                                         TP53 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                         51
  DESMOID TUMOR                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS              1
  LEIOMYOSARCOMA (LMS)                                                                 48
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      7
  MYXOFIBROSARCOMA                                                                     14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           12
[1] 11  2
[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
  TP53 MUTATED   54 19  3  9
  TP53 WILD-TYPE 95 46  6 14
D1V7, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           54             95
  R1           19             46
  R2            3              6
  RX            9             14
[1] 4 2
[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
  TP53 MUTATED       1                         7    75
  TP53 WILD-TYPE     4                        11   142
D1V8, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            7             11
  WHITE                               75            142
[1] 3 2
[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
  TP53 MUTATED     0  71
  TP53 WILD-TYPE   5 142
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0   71
  TP53 WILD-TYPE    5  142
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           71            142
[1] 2 2
[1] FALSE

Clustering(2) Variable = RB1 MUTATION ANALYSIS
D2V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    14  10
  RB1 WILD-TYPE 140  83
  RB1 MUTATED RB1 WILD-TYPE 
           24           223 
  RB1 MUTATED RB1 WILD-TYPE 
           10            83 
$`RB1 MUTATED`
TCGA-DX-A8BG TCGA-DX-AB32 TCGA-3B-A9HP TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I3 
       17.95       101.98        53.49        10.32        36.03        26.56 
TCGA-DX-A3UE TCGA-DX-A48L TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BM 
       34.88        24.26       101.23        62.20        30.35        47.87 
TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-AB2T TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-K1-A6RU 
       40.77        27.95        77.88        25.22        13.58        23.38 
TCGA-LI-A67I TCGA-PC-A5DO TCGA-QQ-A5VD TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-X6-A7WD 
       30.31        81.01        37.12        56.61        22.62        30.84 

$`RB1 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J 
       15.22        23.70        14.43        14.07        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
       12.07       106.45        13.28        22.85        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       84.66        32.15        16.60        37.02        12.62        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH 
       52.27        28.21       159.29        22.62        11.70        17.75 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
        8.28        20.94        17.52        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       50.01        19.69        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3R-A8YX 
       25.25        14.37        42.84        38.47        18.64         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-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87         6.28        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF 
       14.99        10.68        73.87        68.55        50.43        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        45.99        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI 
       41.00        16.87        86.30        64.21        21.30        34.49 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU 
       45.14        38.17        51.91       150.35        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        17.79        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V 
       15.72        65.98        86.10        66.74         9.21       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32        19.89        15.48         8.05        67.63        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
        4.57        33.30         0.72        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
        1.38        19.89       171.09        85.97         5.92        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        1.05         3.91       101.26        53.33        62.17       123.78 
TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 
       17.36         5.19        63.81        16.41        35.28        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PT-A8TR 
       10.45         7.36       122.96        37.55        38.63        26.73 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       13.08        17.65         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
       35.90       130.32        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       19.63        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
        4.80        84.79        38.27        65.46         8.58        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       26.43        45.34        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  RB1 MUTATED RB1 WILD-TYPE 
        10.32          0.49 
  RB1 MUTATED RB1 WILD-TYPE 
       101.98        171.09 
  RB1 MUTATED RB1 WILD-TYPE 
        32.86         30.51 
[1] "10.3 - 102.0 (32.9)" "0.5 - 171.1 (30.5)" 
[1] "hr=" "1"  
D2V2, continuous
               vv
clus            CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  RB1 MUTATED                0                  2                   0
  RB1 WILD-TYPE              1                  5                   2
               vv
clus            CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  RB1 MUTATED                     0                             0
  RB1 WILD-TYPE                   1                             1
               vv
clus            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  RB1 MUTATED                       0                      1
  RB1 WILD-TYPE                     1                     25
               vv
clus            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  RB1 MUTATED                      0                    0
  RB1 WILD-TYPE                    2                    1
               vv
clus            HEAD AND NECK - OTHER (PLEASE SPECIFY
  RB1 MUTATED                                       0
  RB1 WILD-TYPE                                     2
               vv
clus            LOWER ABDOMINAL/PELVIC - BLADDER
  RB1 MUTATED                                  0
  RB1 WILD-TYPE                                1
               vv
clus            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  RB1 MUTATED                                                0
  RB1 WILD-TYPE                                              2
               vv
clus            LOWER ABDOMINAL/PELVIC - PELVIC
  RB1 MUTATED                                 0
  RB1 WILD-TYPE                              11
               vv
clus            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  RB1 MUTATED                                         0
  RB1 WILD-TYPE                                       2
               vv
clus            LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  RB1 MUTATED                              1                       0
  RB1 WILD-TYPE                            3                       2
               vv
clus            LOWER EXTREMITY - LOWER LEG/CALF
  RB1 MUTATED                                  4
  RB1 WILD-TYPE                               12
               vv
clus            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  RB1 MUTATED                                         0
  RB1 WILD-TYPE                                       3
               vv
clus            LOWER EXTREMITY - THIGH/KNEE
  RB1 MUTATED                              7
  RB1 WILD-TYPE                           36
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  RB1 MUTATED                                         0
  RB1 WILD-TYPE                                       4
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  RB1 MUTATED                                           0
  RB1 WILD-TYPE                                         2
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  RB1 MUTATED                                                  0
  RB1 WILD-TYPE                                                5
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  RB1 MUTATED                                          0
  RB1 WILD-TYPE                                        7
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  RB1 MUTATED                                                         0
  RB1 WILD-TYPE                                                       2
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  RB1 MUTATED                                            0
  RB1 WILD-TYPE                                          1
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  RB1 MUTATED                                                   8
  RB1 WILD-TYPE                                                63
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  RB1 MUTATED                                                    0
  RB1 WILD-TYPE                                                  3
               vv
clus            SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  RB1 MUTATED                                    0                        1
  RB1 WILD-TYPE                                  2                        4
               vv
clus            SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  RB1 MUTATED                             0                         0
  RB1 WILD-TYPE                           3                         1
               vv
clus            UPPER EXTREMITY - SHOULDER/AXILLA
  RB1 MUTATED                                   0
  RB1 WILD-TYPE                                 7
               vv
clus            UPPER EXTREMITY - UPPER ARM/ELBOW
  RB1 MUTATED                                   0
  RB1 WILD-TYPE                                 5
D2V3, multiclass
                                                         clus
vv                                                        RB1 MUTATED
  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                                              0
  HEAD AND NECK - NECK                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                   0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                           0
  LOWER EXTREMITY - FOOT/ANKLE                                      1
  LOWER EXTREMITY - GROIN                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                  4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                           0
  LOWER EXTREMITY - THIGH/KNEE                                      7
  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 - PANCREAS                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                 8
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                0
  SUPERFICIAL TRUNK - BACK                                          1
  SUPERFICIAL TRUNK - BUTTOCK                                       0
  SUPERFICIAL TRUNK - FLANK                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                 0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                 0
                                                         clus
vv                                                        RB1 WILD-TYPE
  CHEST - BREAST                                                      1
  CHEST - CHEST WALL                                                  5
  CHEST - LUNG/PLEURA                                                 2
  CHEST - MEDIASTINUM                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                       1
  GYNECOLOGICAL - OVARY                                               1
  GYNECOLOGICAL - UTERUS                                             25
  HEAD AND NECK - HEAD                                                2
  HEAD AND NECK - NECK                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                    11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                             2
  LOWER EXTREMITY - FOOT/ANKLE                                        3
  LOWER EXTREMITY - GROIN                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                   12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             3
  LOWER EXTREMITY - THIGH/KNEE                                       36
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                            7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                  63
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                  2
  SUPERFICIAL TRUNK - BACK                                            4
  SUPERFICIAL TRUNK - BUTTOCK                                         3
  SUPERFICIAL TRUNK - FLANK                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                   7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                   5
[1] 33  2
[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
  RB1 MUTATED    16   8
  RB1 WILD-TYPE 117 106
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     16    8
  RB1 WILD-TYPE  117  106
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          16           117
  MALE             8           106
[1] 2 2
[1] FALSE
D2V5, binary
               cls
clus              0   1
  RB1 MUTATED    13  11
  RB1 WILD-TYPE 157  60
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     13   11
  RB1 WILD-TYPE  157   60
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           13           157
  YES          11            60
[1] 2 2
[1] FALSE
               vv
clus            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  RB1 MUTATED                              0             0
  RB1 WILD-TYPE                           56             2
               vv
clus            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  RB1 MUTATED                                                                          0
  RB1 WILD-TYPE                                                                        1
               vv
clus            LEIOMYOSARCOMA (LMS)
  RB1 MUTATED                     15
  RB1 WILD-TYPE                   83
               vv
clus            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  RB1 MUTATED                                                  0
  RB1 WILD-TYPE                                                8
               vv
clus            MYXOFIBROSARCOMA
  RB1 MUTATED                  5
  RB1 WILD-TYPE               17
               vv
clus            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  RB1 MUTATED                                                          3
  RB1 WILD-TYPE                                                       26
               vv
clus            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  RB1 MUTATED                                          0
  RB1 WILD-TYPE                                        2
               vv
clus            SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  RB1 MUTATED                             0                             0
  RB1 WILD-TYPE                           2                             6
               vv
clus            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  RB1 MUTATED                                            1
  RB1 WILD-TYPE                                         20
D2V6, multiclass
                                                                          clus
vv                                                                         RB1 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                       0
  DESMOID TUMOR                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS           0
  LEIOMYOSARCOMA (LMS)                                                              15
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                   0
  MYXOFIBROSARCOMA                                                                   5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                           3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                           0
  SYNOVIAL SARCOMA - BIPHASIC                                                        0
  SYNOVIAL SARCOMA - MONOPHASIC                                                      0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                         1
                                                                          clus
vv                                                                         RB1 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                        56
  DESMOID TUMOR                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             1
  LEIOMYOSARCOMA (LMS)                                                                83
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     8
  MYXOFIBROSARCOMA                                                                    17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                            26
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          20
[1] 11  2
[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
  RB1 MUTATED    18   5   0   1
  RB1 WILD-TYPE 131  60   9  22
D2V7, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          18           131
  R1           5            60
  R2           0             9
  RX           1            22
[1] 4 2
[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
  RB1 MUTATED       0                         2    22
  RB1 WILD-TYPE     5                        16   195
D2V8, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           2            16
  WHITE                              22           195
[1] 3 2
[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
  RB1 MUTATED     0  22
  RB1 WILD-TYPE   5 191
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   22
  RB1 WILD-TYPE    5  191
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO          22           191
[1] 2 2
[1] FALSE

Clustering(3) Variable = ATRX MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  ATRX MUTATED    19  17
  ATRX WILD-TYPE 135  76
  ATRX MUTATED ATRX WILD-TYPE 
            36            211 
  ATRX MUTATED ATRX WILD-TYPE 
            17             76 
$`ATRX MUTATED`
TCGA-DX-A3M2 TCGA-DX-A7EU TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB37 
       34.68        23.70        12.07       106.45        13.28        84.66 
TCGA-DX-AB3A TCGA-KF-A41W TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 
       32.15        11.70        19.69        44.91        42.84        18.64 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3UD TCGA-DX-A6B8 TCGA-DX-A8BM TCGA-DX-A8BN 
       85.02         6.28        50.43        15.95        47.87        38.17 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AATS TCGA-HB-A2OT TCGA-HB-A3L4 
       40.44        36.69        60.66         1.15        67.63        34.88 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-K1-A42W TCGA-KD-A5QU TCGA-PC-A5DN 
        3.22        19.89        16.41        62.17        35.28        38.63 
TCGA-QC-AA9N TCGA-SI-AA8B TCGA-VT-AB3D TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WC 
       17.65         8.61        12.46        22.62        63.35        45.34 

$`ATRX WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        34.36        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 
       17.95        14.43        14.07        15.85        40.60        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
      101.98        30.51        60.00        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH 
       26.93        52.27        28.21       159.29        22.62        17.75 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
        8.28        20.94        17.52        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU 
       50.01        53.49        68.55        88.57        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX 
       14.37        10.32        38.47        36.03        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-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       54.21        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       73.87        68.55        34.88        85.45         9.73        45.99 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       59.84        37.58        37.41        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX 
       31.96        36.85        26.99         3.06        41.00        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM 
       86.30        64.21       101.23        21.30        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       61.97        45.14        40.77        51.91       150.35        27.95 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       19.43         6.58        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        66.74         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
       19.89        15.48         8.05         4.57        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA 
       80.48        19.53         1.38        25.22       171.09        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       85.97         5.92         1.05         3.91       101.26        53.33 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
      123.78        17.36        23.38         5.19        63.81        16.41 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       30.31        25.41         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        22.39        10.45         7.36       122.96        37.55 
TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       81.01        26.73        13.08         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH 
       48.59        35.90        37.12       130.32        64.77        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        16.77        18.94         3.88        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO 
       32.75        19.63        13.22        13.41        10.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WP-A9GB 
        4.80        84.79        38.27        65.46        56.61         8.58 
TCGA-X6-A7W8 TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       26.43        30.84        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  ATRX MUTATED ATRX WILD-TYPE 
          1.15           0.49 
  ATRX MUTATED ATRX WILD-TYPE 
        106.45         171.09 
  ATRX MUTATED ATRX WILD-TYPE 
         34.78          30.35 
[1] "1.1 - 106.5 (34.8)" "0.5 - 171.1 (30.4)"
[1] "hr=" "1.4"
D3V2, continuous
                vv
clus             CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  ATRX MUTATED                0                  1                   0
  ATRX WILD-TYPE              1                  6                   2
                vv
clus             CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  ATRX MUTATED                     0                             0
  ATRX WILD-TYPE                   1                             1
                vv
clus             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  ATRX MUTATED                       0                      5
  ATRX WILD-TYPE                     1                     21
                vv
clus             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  ATRX MUTATED                      0                    0
  ATRX WILD-TYPE                    2                    1
                vv
clus             HEAD AND NECK - OTHER (PLEASE SPECIFY
  ATRX MUTATED                                       0
  ATRX WILD-TYPE                                     2
                vv
clus             LOWER ABDOMINAL/PELVIC - BLADDER
  ATRX MUTATED                                  0
  ATRX WILD-TYPE                                1
                vv
clus             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  ATRX MUTATED                                                0
  ATRX WILD-TYPE                                              2
                vv
clus             LOWER ABDOMINAL/PELVIC - PELVIC
  ATRX MUTATED                                 2
  ATRX WILD-TYPE                               9
                vv
clus             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  ATRX MUTATED                                         0
  ATRX WILD-TYPE                                       2
                vv
clus             LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  ATRX MUTATED                              0                       0
  ATRX WILD-TYPE                            4                       2
                vv
clus             LOWER EXTREMITY - LOWER LEG/CALF
  ATRX MUTATED                                  1
  ATRX WILD-TYPE                               15
                vv
clus             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  ATRX MUTATED                                         0
  ATRX WILD-TYPE                                       3
                vv
clus             LOWER EXTREMITY - THIGH/KNEE
  ATRX MUTATED                             10
  ATRX WILD-TYPE                           33
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  ATRX MUTATED                                         1
  ATRX WILD-TYPE                                       3
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  ATRX MUTATED                                           0
  ATRX WILD-TYPE                                         2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  ATRX MUTATED                                                  0
  ATRX WILD-TYPE                                                5
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  ATRX MUTATED                                          1
  ATRX WILD-TYPE                                        6
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  ATRX MUTATED                                                         0
  ATRX WILD-TYPE                                                       2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  ATRX MUTATED                                            1
  ATRX WILD-TYPE                                          0
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  ATRX MUTATED                                                   9
  ATRX WILD-TYPE                                                62
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  ATRX MUTATED                                                    0
  ATRX WILD-TYPE                                                  3
                vv
clus             SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  ATRX MUTATED                                    0                        0
  ATRX WILD-TYPE                                  2                        5
                vv
clus             SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  ATRX MUTATED                             2                         0
  ATRX WILD-TYPE                           1                         1
                vv
clus             UPPER EXTREMITY - SHOULDER/AXILLA
  ATRX MUTATED                                   2
  ATRX WILD-TYPE                                 5
                vv
clus             UPPER EXTREMITY - UPPER ARM/ELBOW
  ATRX MUTATED                                   1
  ATRX WILD-TYPE                                 4
D3V3, multiclass
                                                         clus
vv                                                        ATRX MUTATED
  CHEST - BREAST                                                     0
  CHEST - CHEST WALL                                                 1
  CHEST - LUNG/PLEURA                                                0
  CHEST - MEDIASTINUM                                                0
  CHEST - OTHER (PLEASE SPECIFY                                      0
  GYNECOLOGICAL - OVARY                                              0
  GYNECOLOGICAL - UTERUS                                             5
  HEAD AND NECK - HEAD                                               0
  HEAD AND NECK - NECK                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                    2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                            0
  LOWER EXTREMITY - FOOT/ANKLE                                       0
  LOWER EXTREMITY - GROIN                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                   1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                            0
  LOWER EXTREMITY - THIGH/KNEE                                      10
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                            1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                         1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                  9
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                 0
  SUPERFICIAL TRUNK - BACK                                           0
  SUPERFICIAL TRUNK - BUTTOCK                                        2
  SUPERFICIAL TRUNK - FLANK                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                  2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                  1
                                                         clus
vv                                                        ATRX WILD-TYPE
  CHEST - BREAST                                                       1
  CHEST - CHEST WALL                                                   6
  CHEST - LUNG/PLEURA                                                  2
  CHEST - MEDIASTINUM                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                        1
  GYNECOLOGICAL - OVARY                                                1
  GYNECOLOGICAL - UTERUS                                              21
  HEAD AND NECK - HEAD                                                 2
  HEAD AND NECK - NECK                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                      9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                              2
  LOWER EXTREMITY - FOOT/ANKLE                                         4
  LOWER EXTREMITY - GROIN                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                    15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                              3
  LOWER EXTREMITY - THIGH/KNEE                                        33
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                              3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   62
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                   2
  SUPERFICIAL TRUNK - BACK                                             5
  SUPERFICIAL TRUNK - BUTTOCK                                          1
  SUPERFICIAL TRUNK - FLANK                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                    5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                    4
[1] 33  2
[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
  ATRX MUTATED    21  15
  ATRX WILD-TYPE 112  99
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     21   15
  ATRX WILD-TYPE  112   99
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  FEMALE           21            112
  MALE             15             99
[1] 2 2
[1] FALSE
D3V5, binary
                cls
clus               0   1
  ATRX MUTATED    22  13
  ATRX WILD-TYPE 148  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     22   13
  ATRX WILD-TYPE  148   58
     clus
vv    ATRX MUTATED ATRX WILD-TYPE
  NO            22            148
  YES           13             58
[1] 2 2
[1] FALSE
                vv
clus             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  ATRX MUTATED                              6             0
  ATRX WILD-TYPE                           50             2
                vv
clus             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  ATRX MUTATED                                                                          0
  ATRX WILD-TYPE                                                                        1
                vv
clus             LEIOMYOSARCOMA (LMS)
  ATRX MUTATED                     13
  ATRX WILD-TYPE                   85
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  ATRX MUTATED                                                  0
  ATRX WILD-TYPE                                                8
                vv
clus             MYXOFIBROSARCOMA
  ATRX MUTATED                  2
  ATRX WILD-TYPE               20
                vv
clus             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  ATRX MUTATED                                                          8
  ATRX WILD-TYPE                                                       21
                vv
clus             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  ATRX MUTATED                                          0
  ATRX WILD-TYPE                                        2
                vv
clus             SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  ATRX MUTATED                             0                             0
  ATRX WILD-TYPE                           2                             6
                vv
clus             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  ATRX MUTATED                                            7
  ATRX WILD-TYPE                                         14
D3V6, multiclass
                                                                          clus
vv                                                                         ATRX MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                        6
  DESMOID TUMOR                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS            0
  LEIOMYOSARCOMA (LMS)                                                               13
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                    0
  MYXOFIBROSARCOMA                                                                    2
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                            8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          7
                                                                          clus
vv                                                                         ATRX WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                         50
  DESMOID TUMOR                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS              1
  LEIOMYOSARCOMA (LMS)                                                                 85
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      8
  MYXOFIBROSARCOMA                                                                     20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           14
[1] 11  2
[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
  ATRX MUTATED    23  10   0   3
  ATRX WILD-TYPE 126  55   9  20
D3V7, multiclass
    clus
vv   ATRX MUTATED ATRX WILD-TYPE
  R0           23            126
  R1           10             55
  R2            0              9
  RX            3             20
[1] 4 2
[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
  ATRX MUTATED       0                         4    32
  ATRX WILD-TYPE     5                        14   185
D3V8, multiclass
                           clus
vv                          ATRX MUTATED ATRX WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            4             14
  WHITE                               32            185
[1] 3 2
[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
  ATRX MUTATED     0  33
  ATRX WILD-TYPE   5 180
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      0   33
  ATRX WILD-TYPE    5  180
                        clus
vv                       ATRX MUTATED ATRX WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           33            180
[1] 2 2
[1] FALSE

Clustering(4) Variable = NUMBL MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  NUMBL MUTATED     6   2
  NUMBL WILD-TYPE 148  91
  NUMBL MUTATED NUMBL WILD-TYPE 
              8             239 
  NUMBL MUTATED NUMBL WILD-TYPE 
              2              91 
$`NUMBL MUTATED`
TCGA-DX-A8BP TCGA-KF-A41W TCGA-FX-A3TO TCGA-FX-A48G TCGA-PC-A5DN TCGA-QQ-A5VC 
       14.07        11.70        20.32        19.89        38.63        35.90 
TCGA-X6-A7WC TCGA-X9-A973 
       45.34        36.43 

$`NUMBL WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J 
       15.22        23.70        17.95        14.43        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       12.07       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH 
       26.93        52.27        28.21       159.29        22.62        17.75 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
        8.28        20.94        17.52        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       50.01        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        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-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
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-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       41.00        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       20.05         9.34        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       40.77        51.91       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        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-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      106.55        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       21.70        15.48         8.05        67.63        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       33.30         0.72        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       19.89        25.22       171.09        13.58        85.97         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       16.41         1.05         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
      123.78        17.36        23.38         5.19        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       35.28        30.31        25.41         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        22.39        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        81.01        26.73        13.08        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
       46.82        18.08        48.59        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       10.52         0.72        16.77        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       25.35        32.75         8.61        19.63        13.22        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX 
       10.72        12.46        11.93         4.80        84.79        38.27 
TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       65.46        56.61        22.62         8.58        63.35        26.43 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       30.84        35.18        19.17        20.65        50.86        29.46 
TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32         4.37        13.38        15.95        15.98 

  NUMBL MUTATED NUMBL WILD-TYPE 
          11.70            0.49 
  NUMBL MUTATED NUMBL WILD-TYPE 
          45.34          171.09 
  NUMBL MUTATED NUMBL WILD-TYPE 
          28.11           30.84 
[1] "11.7 - 45.3 (28.1)" "0.5 - 171.1 (30.8)"
[1] "hr=" "1.2"
D4V2, continuous
                 vv
clus              CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  NUMBL MUTATED                0                  0                   0
  NUMBL WILD-TYPE              1                  7                   2
                 vv
clus              CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  NUMBL MUTATED                     0                             0
  NUMBL WILD-TYPE                   1                             1
                 vv
clus              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  NUMBL MUTATED                       0                      2
  NUMBL WILD-TYPE                     1                     24
                 vv
clus              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  NUMBL MUTATED                      0                    0
  NUMBL WILD-TYPE                    2                    1
                 vv
clus              HEAD AND NECK - OTHER (PLEASE SPECIFY
  NUMBL MUTATED                                       0
  NUMBL WILD-TYPE                                     2
                 vv
clus              LOWER ABDOMINAL/PELVIC - BLADDER
  NUMBL MUTATED                                  0
  NUMBL WILD-TYPE                                1
                 vv
clus              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  NUMBL MUTATED                                                0
  NUMBL WILD-TYPE                                              2
                 vv
clus              LOWER ABDOMINAL/PELVIC - PELVIC
  NUMBL MUTATED                                 1
  NUMBL WILD-TYPE                              10
                 vv
clus              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  NUMBL MUTATED                                         0
  NUMBL WILD-TYPE                                       2
                 vv
clus              LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  NUMBL MUTATED                              0                       0
  NUMBL WILD-TYPE                            4                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  NUMBL MUTATED                                  0
  NUMBL WILD-TYPE                               16
                 vv
clus              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  NUMBL MUTATED                                         0
  NUMBL WILD-TYPE                                       3
                 vv
clus              LOWER EXTREMITY - THIGH/KNEE
  NUMBL MUTATED                              3
  NUMBL WILD-TYPE                           40
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  NUMBL MUTATED                                         0
  NUMBL WILD-TYPE                                       4
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  NUMBL MUTATED                                           0
  NUMBL WILD-TYPE                                         2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  NUMBL MUTATED                                                  0
  NUMBL WILD-TYPE                                                5
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  NUMBL MUTATED                                          0
  NUMBL WILD-TYPE                                        7
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  NUMBL MUTATED                                                         0
  NUMBL WILD-TYPE                                                       2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  NUMBL MUTATED                                            0
  NUMBL WILD-TYPE                                          1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  NUMBL MUTATED                                                   2
  NUMBL WILD-TYPE                                                69
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  NUMBL MUTATED                                                    0
  NUMBL WILD-TYPE                                                  3
                 vv
clus              SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  NUMBL MUTATED                                    0                        0
  NUMBL WILD-TYPE                                  2                        5
                 vv
clus              SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  NUMBL MUTATED                             0                         0
  NUMBL WILD-TYPE                           3                         1
                 vv
clus              UPPER EXTREMITY - SHOULDER/AXILLA
  NUMBL MUTATED                                   0
  NUMBL WILD-TYPE                                 7
                 vv
clus              UPPER EXTREMITY - UPPER ARM/ELBOW
  NUMBL MUTATED                                   0
  NUMBL WILD-TYPE                                 5
D4V3, multiclass
                                                         clus
vv                                                        NUMBL MUTATED
  CHEST - BREAST                                                      0
  CHEST - CHEST WALL                                                  0
  CHEST - LUNG/PLEURA                                                 0
  CHEST - MEDIASTINUM                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                       0
  GYNECOLOGICAL - OVARY                                               0
  GYNECOLOGICAL - UTERUS                                              2
  HEAD AND NECK - HEAD                                                0
  HEAD AND NECK - NECK                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                      0
  LOWER ABDOMINAL/PELVIC - PELVIC                                     1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                             0
  LOWER EXTREMITY - FOOT/ANKLE                                        0
  LOWER EXTREMITY - GROIN                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                    0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             0
  LOWER EXTREMITY - THIGH/KNEE                                        3
  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 - PANCREAS                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   2
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                  0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                  0
  SUPERFICIAL TRUNK - BACK                                            0
  SUPERFICIAL TRUNK - BUTTOCK                                         0
  SUPERFICIAL TRUNK - FLANK                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                   0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                   0
                                                         clus
vv                                                        NUMBL WILD-TYPE
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    7
  CHEST - LUNG/PLEURA                                                   2
  CHEST - MEDIASTINUM                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                               24
  HEAD AND NECK - HEAD                                                  2
  HEAD AND NECK - NECK                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                      10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               2
  LOWER EXTREMITY - FOOT/ANKLE                                          4
  LOWER EXTREMITY - GROIN                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                     16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         40
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    69
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              5
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                     7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     5
[1] 33  2
[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
  NUMBL MUTATED     4   4
  NUMBL WILD-TYPE 129 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMBL MUTATED      4    4
  NUMBL WILD-TYPE  129  110
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  FEMALE             4             129
  MALE               4             110
[1] 2 2
[1] FALSE
D4V5, binary
                 cls
clus                0   1
  NUMBL MUTATED     7   1
  NUMBL WILD-TYPE 163  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMBL MUTATED      7    1
  NUMBL WILD-TYPE  163   70
     clus
vv    NUMBL MUTATED NUMBL WILD-TYPE
  NO              7             163
  YES             1              70
[1] 2 2
[1] FALSE
                 vv
clus              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  NUMBL MUTATED                              0             0
  NUMBL WILD-TYPE                           56             2
                 vv
clus              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  NUMBL MUTATED                                                                          0
  NUMBL WILD-TYPE                                                                        1
                 vv
clus              LEIOMYOSARCOMA (LMS)
  NUMBL MUTATED                      5
  NUMBL WILD-TYPE                   93
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  NUMBL MUTATED                                                  0
  NUMBL WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  NUMBL MUTATED                  0
  NUMBL WILD-TYPE               22
                 vv
clus              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  NUMBL MUTATED                                                          1
  NUMBL WILD-TYPE                                                       28
                 vv
clus              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  NUMBL MUTATED                                          0
  NUMBL WILD-TYPE                                        2
                 vv
clus              SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  NUMBL MUTATED                             0                             0
  NUMBL WILD-TYPE                           2                             6
                 vv
clus              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  NUMBL MUTATED                                            2
  NUMBL WILD-TYPE                                         19
D4V6, multiclass
                                                                          clus
vv                                                                         NUMBL MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                         0
  DESMOID TUMOR                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             0
  LEIOMYOSARCOMA (LMS)                                                                 5
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     0
  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)                                           2
                                                                          clus
vv                                                                         NUMBL WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                          56
  DESMOID TUMOR                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               1
  LEIOMYOSARCOMA (LMS)                                                                  93
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       8
  MYXOFIBROSARCOMA                                                                      22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              28
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            19
[1] 11  2
[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
  NUMBL MUTATED     3   3   0   2
  NUMBL WILD-TYPE 146  62   9  21
D4V7, multiclass
    clus
vv   NUMBL MUTATED NUMBL WILD-TYPE
  R0             3             146
  R1             3              62
  R2             0               9
  RX             2              21
[1] 4 2
[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
  NUMBL MUTATED       0                         0     8
  NUMBL WILD-TYPE     5                        18   209
D4V8, multiclass
                           clus
vv                          NUMBL MUTATED NUMBL WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 8             209
[1] 3 2
[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
  NUMBL MUTATED     0   8
  NUMBL WILD-TYPE   5 205
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMBL MUTATED      0    8
  NUMBL WILD-TYPE    5  205
                        clus
vv                       NUMBL MUTATED NUMBL WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8             205
[1] 2 2
[1] FALSE

Clustering(5) Variable = MSH3 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  MSH3 MUTATED     3   4
  MSH3 WILD-TYPE 151  89
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            240 
  MSH3 MUTATED MSH3 WILD-TYPE 
             4             89 
$`MSH3 MUTATED`
TCGA-DX-AB37 TCGA-DX-A23T TCGA-DX-A48U TCGA-DX-AB2S TCGA-FX-A2QS TCGA-FX-A48G 
       84.66         5.26       108.82         9.21        49.15        19.89 
TCGA-X6-A8C4 
       20.65 

$`MSH3 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       15.22        23.70        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       40.60        12.07       106.45        13.28        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       30.51        60.00        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
       17.75         8.28        20.94        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       35.08        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       38.47        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        68.61        12.85        45.11        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23U TCGA-DX-A23V 
       85.02        33.53        66.94        74.66        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
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-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        86.30        64.21       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        61.97        45.14        47.87        38.17        40.77 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       51.91       150.35        27.95        40.44        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       19.43         6.58         1.15        17.79        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       65.98        86.10        66.74        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y 
       50.89        71.31        31.13        21.70        20.32        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
        8.05        67.63        34.88         4.57        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
       80.48        19.53         3.22         1.38        19.89        25.22 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
      171.09        13.58        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
       23.38         5.19        63.81        16.41        35.28        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       22.39        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        26.73        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
       18.08        48.59        35.90        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       10.52         0.72        16.77        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       25.35        32.75         8.61        19.63        13.22        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX 
       10.72        12.46        11.93         4.80        84.79        38.27 
TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       65.46        56.61        22.62         8.58        63.35        26.43 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
       45.34        30.84        35.18        19.17        50.86        29.46 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        36.43         4.37        13.38        15.95        15.98 

  MSH3 MUTATED MSH3 WILD-TYPE 
          5.26           0.49 
  MSH3 MUTATED MSH3 WILD-TYPE 
        108.82         171.09 
  MSH3 MUTATED MSH3 WILD-TYPE 
        20.650         30.985 
[1] "5.3 - 108.8 (20.6)" "0.5 - 171.1 (31.0)"
[1] "hr=" "1.4"
D5V2, continuous
                vv
clus             CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  MSH3 MUTATED                0                  0                   0
  MSH3 WILD-TYPE              1                  7                   2
                vv
clus             CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  MSH3 MUTATED                     0                             0
  MSH3 WILD-TYPE                   1                             1
                vv
clus             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  MSH3 MUTATED                       0                      1
  MSH3 WILD-TYPE                     1                     25
                vv
clus             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  MSH3 MUTATED                      0                    0
  MSH3 WILD-TYPE                    2                    1
                vv
clus             HEAD AND NECK - OTHER (PLEASE SPECIFY
  MSH3 MUTATED                                       0
  MSH3 WILD-TYPE                                     2
                vv
clus             LOWER ABDOMINAL/PELVIC - BLADDER
  MSH3 MUTATED                                  0
  MSH3 WILD-TYPE                                1
                vv
clus             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  MSH3 MUTATED                                                0
  MSH3 WILD-TYPE                                              2
                vv
clus             LOWER ABDOMINAL/PELVIC - PELVIC
  MSH3 MUTATED                                 0
  MSH3 WILD-TYPE                              11
                vv
clus             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  MSH3 MUTATED                                         0
  MSH3 WILD-TYPE                                       2
                vv
clus             LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  MSH3 MUTATED                              0                       0
  MSH3 WILD-TYPE                            4                       2
                vv
clus             LOWER EXTREMITY - LOWER LEG/CALF
  MSH3 MUTATED                                  1
  MSH3 WILD-TYPE                               15
                vv
clus             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  MSH3 MUTATED                                         0
  MSH3 WILD-TYPE                                       3
                vv
clus             LOWER EXTREMITY - THIGH/KNEE
  MSH3 MUTATED                              1
  MSH3 WILD-TYPE                           42
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  MSH3 MUTATED                                         0
  MSH3 WILD-TYPE                                       4
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  MSH3 MUTATED                                           0
  MSH3 WILD-TYPE                                         2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  MSH3 MUTATED                                                  0
  MSH3 WILD-TYPE                                                5
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  MSH3 MUTATED                                          0
  MSH3 WILD-TYPE                                        7
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  MSH3 MUTATED                                                         1
  MSH3 WILD-TYPE                                                       1
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  MSH3 MUTATED                                            0
  MSH3 WILD-TYPE                                          1
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  MSH3 MUTATED                                                   2
  MSH3 WILD-TYPE                                                69
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  MSH3 MUTATED                                                    0
  MSH3 WILD-TYPE                                                  3
                vv
clus             SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  MSH3 MUTATED                                    0                        1
  MSH3 WILD-TYPE                                  2                        4
                vv
clus             SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  MSH3 MUTATED                             0                         0
  MSH3 WILD-TYPE                           3                         1
                vv
clus             UPPER EXTREMITY - SHOULDER/AXILLA
  MSH3 MUTATED                                   0
  MSH3 WILD-TYPE                                 7
                vv
clus             UPPER EXTREMITY - UPPER ARM/ELBOW
  MSH3 MUTATED                                   0
  MSH3 WILD-TYPE                                 5
D5V3, multiclass
                                                         clus
vv                                                        MSH3 MUTATED
  CHEST - BREAST                                                     0
  CHEST - CHEST WALL                                                 0
  CHEST - LUNG/PLEURA                                                0
  CHEST - MEDIASTINUM                                                0
  CHEST - OTHER (PLEASE SPECIFY                                      0
  GYNECOLOGICAL - OVARY                                              0
  GYNECOLOGICAL - UTERUS                                             1
  HEAD AND NECK - HEAD                                               0
  HEAD AND NECK - NECK                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                    0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                            0
  LOWER EXTREMITY - FOOT/ANKLE                                       0
  LOWER EXTREMITY - GROIN                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                   1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                            0
  LOWER EXTREMITY - THIGH/KNEE                                       1
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                          0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                           0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY            1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                  2
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                 0
  SUPERFICIAL TRUNK - BACK                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                        0
  SUPERFICIAL TRUNK - FLANK                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                  0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                  0
                                                         clus
vv                                                        MSH3 WILD-TYPE
  CHEST - BREAST                                                       1
  CHEST - CHEST WALL                                                   7
  CHEST - LUNG/PLEURA                                                  2
  CHEST - MEDIASTINUM                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                        1
  GYNECOLOGICAL - OVARY                                                1
  GYNECOLOGICAL - UTERUS                                              25
  HEAD AND NECK - HEAD                                                 2
  HEAD AND NECK - NECK                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                     11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                              2
  LOWER EXTREMITY - FOOT/ANKLE                                         4
  LOWER EXTREMITY - GROIN                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                    15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                              3
  LOWER EXTREMITY - THIGH/KNEE                                        42
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                             7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY              1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   69
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                   2
  SUPERFICIAL TRUNK - BACK                                             4
  SUPERFICIAL TRUNK - BUTTOCK                                          3
  SUPERFICIAL TRUNK - FLANK                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                    7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                    5
[1] 33  2
[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
  MSH3 MUTATED     6   1
  MSH3 WILD-TYPE 127 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH3 MUTATED      6    1
  MSH3 WILD-TYPE  127  113
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  FEMALE            6            127
  MALE              1            113
[1] 2 2
[1] FALSE
D5V5, binary
                cls
clus               0   1
  MSH3 MUTATED     5   2
  MSH3 WILD-TYPE 165  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH3 MUTATED      5    2
  MSH3 WILD-TYPE  165   69
     clus
vv    MSH3 MUTATED MSH3 WILD-TYPE
  NO             5            165
  YES            2             69
[1] 2 2
[1] FALSE
                vv
clus             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  MSH3 MUTATED                              3             0
  MSH3 WILD-TYPE                           53             2
                vv
clus             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  MSH3 MUTATED                                                                          0
  MSH3 WILD-TYPE                                                                        1
                vv
clus             LEIOMYOSARCOMA (LMS)
  MSH3 MUTATED                      2
  MSH3 WILD-TYPE                   96
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  MSH3 MUTATED                                                  0
  MSH3 WILD-TYPE                                                8
                vv
clus             MYXOFIBROSARCOMA
  MSH3 MUTATED                  1
  MSH3 WILD-TYPE               21
                vv
clus             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  MSH3 MUTATED                                                          0
  MSH3 WILD-TYPE                                                       29
                vv
clus             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  MSH3 MUTATED                                          0
  MSH3 WILD-TYPE                                        2
                vv
clus             SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  MSH3 MUTATED                             0                             0
  MSH3 WILD-TYPE                           2                             6
                vv
clus             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  MSH3 MUTATED                                            1
  MSH3 WILD-TYPE                                         20
D5V6, multiclass
                                                                          clus
vv                                                                         MSH3 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                        3
  DESMOID TUMOR                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS            0
  LEIOMYOSARCOMA (LMS)                                                                2
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                    0
  MYXOFIBROSARCOMA                                                                    1
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                            0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          1
                                                                          clus
vv                                                                         MSH3 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                         53
  DESMOID TUMOR                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS              1
  LEIOMYOSARCOMA (LMS)                                                                 96
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      8
  MYXOFIBROSARCOMA                                                                     21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             29
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           20
[1] 11  2
[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
  MSH3 MUTATED     4   2   0   1
  MSH3 WILD-TYPE 145  63   9  22
D5V7, multiclass
    clus
vv   MSH3 MUTATED MSH3 WILD-TYPE
  R0            4            145
  R1            2             63
  R2            0              9
  RX            1             22
[1] 4 2
[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
  MSH3 MUTATED       0                         0     7
  MSH3 WILD-TYPE     5                        18   210
D5V8, multiclass
                           clus
vv                          MSH3 MUTATED MSH3 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                7            210
[1] 3 2
[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
  MSH3 MUTATED     1   5
  MSH3 WILD-TYPE   4 208
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH3 MUTATED      1    5
  MSH3 WILD-TYPE    4  208
                        clus
vv                       MSH3 MUTATED MSH3 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            5            208
[1] 2 2
[1] FALSE

Clustering(6) Variable = LTBP3 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  LTBP3 MUTATED     3   2
  LTBP3 WILD-TYPE 151  91
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             242 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              2              91 
$`LTBP3 MUTATED`
TCGA-DX-A8BP TCGA-3B-A9HY TCGA-3B-A9I1 TCGA-DX-AB2E TCGA-WK-A8XY 
       14.07        10.32        18.64        17.79        65.46 

$`LTBP3 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J 
       15.22        23.70        17.95        14.43        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       12.07       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
       17.75         8.28        20.94        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       35.08        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HZ 
       44.91        54.74        25.25        14.37        42.84        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       36.03        26.56         0.56        14.04        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        45.11        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       66.94        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       35.77        51.02         4.54        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       68.55        50.43        34.88        85.45         9.73        45.99 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        86.30        64.21       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        61.97        45.14        47.87        38.17        40.77 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       51.91       150.35        27.95        40.44        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       19.43         6.58         1.15        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        66.74         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       19.89        15.48         8.05        67.63        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       33.30         0.72        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       19.89        25.22       171.09        13.58        85.97         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       16.41         1.05         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
      123.78        17.36        23.38         5.19        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       35.28        30.31        25.41         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        22.39        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QC-AA9N 
       37.55        38.63        81.01        26.73        13.08        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32        64.77        10.52         0.72        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        3.88        22.82        25.35        32.75         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22        13.41        10.72        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       84.79        38.27        56.61        22.62         8.58        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       26.43        45.34        30.84        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  LTBP3 MUTATED LTBP3 WILD-TYPE 
          10.32            0.49 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
          65.46          171.09 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
          17.79           31.33 
[1] "10.3 - 65.5 (17.8)" "0.5 - 171.1 (31.3)"
[1] "hr=" "1.5"
D6V2, continuous
                 vv
clus              CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  LTBP3 MUTATED                0                  0                   0
  LTBP3 WILD-TYPE              1                  7                   2
                 vv
clus              CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  LTBP3 MUTATED                     0                             0
  LTBP3 WILD-TYPE                   1                             1
                 vv
clus              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  LTBP3 MUTATED                       0                      1
  LTBP3 WILD-TYPE                     1                     25
                 vv
clus              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  LTBP3 MUTATED                      0                    0
  LTBP3 WILD-TYPE                    2                    1
                 vv
clus              HEAD AND NECK - OTHER (PLEASE SPECIFY
  LTBP3 MUTATED                                       0
  LTBP3 WILD-TYPE                                     2
                 vv
clus              LOWER ABDOMINAL/PELVIC - BLADDER
  LTBP3 MUTATED                                  0
  LTBP3 WILD-TYPE                                1
                 vv
clus              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  LTBP3 MUTATED                                                0
  LTBP3 WILD-TYPE                                              2
                 vv
clus              LOWER ABDOMINAL/PELVIC - PELVIC
  LTBP3 MUTATED                                 0
  LTBP3 WILD-TYPE                              11
                 vv
clus              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  LTBP3 MUTATED                                         0
  LTBP3 WILD-TYPE                                       2
                 vv
clus              LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  LTBP3 MUTATED                              0                       0
  LTBP3 WILD-TYPE                            4                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  LTBP3 MUTATED                                  0
  LTBP3 WILD-TYPE                               16
                 vv
clus              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  LTBP3 MUTATED                                         0
  LTBP3 WILD-TYPE                                       3
                 vv
clus              LOWER EXTREMITY - THIGH/KNEE
  LTBP3 MUTATED                              2
  LTBP3 WILD-TYPE                           41
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  LTBP3 MUTATED                                         0
  LTBP3 WILD-TYPE                                       4
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  LTBP3 MUTATED                                           0
  LTBP3 WILD-TYPE                                         2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  LTBP3 MUTATED                                                  0
  LTBP3 WILD-TYPE                                                5
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  LTBP3 MUTATED                                          0
  LTBP3 WILD-TYPE                                        7
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  LTBP3 MUTATED                                                         0
  LTBP3 WILD-TYPE                                                       2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  LTBP3 MUTATED                                            0
  LTBP3 WILD-TYPE                                          1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  LTBP3 MUTATED                                                   0
  LTBP3 WILD-TYPE                                                71
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  LTBP3 MUTATED                                                    1
  LTBP3 WILD-TYPE                                                  2
                 vv
clus              SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  LTBP3 MUTATED                                    0                        0
  LTBP3 WILD-TYPE                                  2                        5
                 vv
clus              SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  LTBP3 MUTATED                             0                         0
  LTBP3 WILD-TYPE                           3                         1
                 vv
clus              UPPER EXTREMITY - SHOULDER/AXILLA
  LTBP3 MUTATED                                   1
  LTBP3 WILD-TYPE                                 6
                 vv
clus              UPPER EXTREMITY - UPPER ARM/ELBOW
  LTBP3 MUTATED                                   0
  LTBP3 WILD-TYPE                                 5
D6V3, multiclass
                                                         clus
vv                                                        LTBP3 MUTATED
  CHEST - BREAST                                                      0
  CHEST - CHEST WALL                                                  0
  CHEST - LUNG/PLEURA                                                 0
  CHEST - MEDIASTINUM                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                       0
  GYNECOLOGICAL - OVARY                                               0
  GYNECOLOGICAL - UTERUS                                              1
  HEAD AND NECK - HEAD                                                0
  HEAD AND NECK - NECK                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                      0
  LOWER ABDOMINAL/PELVIC - PELVIC                                     0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                             0
  LOWER EXTREMITY - FOOT/ANKLE                                        0
  LOWER EXTREMITY - GROIN                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                    0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             0
  LOWER EXTREMITY - THIGH/KNEE                                        2
  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 - PANCREAS                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   0
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                  1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                  0
  SUPERFICIAL TRUNK - BACK                                            0
  SUPERFICIAL TRUNK - BUTTOCK                                         0
  SUPERFICIAL TRUNK - FLANK                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                   1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                   0
                                                         clus
vv                                                        LTBP3 WILD-TYPE
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    7
  CHEST - LUNG/PLEURA                                                   2
  CHEST - MEDIASTINUM                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                               25
  HEAD AND NECK - HEAD                                                  2
  HEAD AND NECK - NECK                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                      11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               2
  LOWER EXTREMITY - FOOT/ANKLE                                          4
  LOWER EXTREMITY - GROIN                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                     16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         41
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    71
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              5
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                     6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     5
[1] 33  2
[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
  LTBP3 MUTATED     2   3
  LTBP3 WILD-TYPE 131 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED      2    3
  LTBP3 WILD-TYPE  131  111
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  FEMALE             2             131
  MALE               3             111
[1] 2 2
[1] FALSE
D6V5, binary
                 cls
clus                0   1
  LTBP3 MUTATED     5   0
  LTBP3 WILD-TYPE 165  71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED      5    0
  LTBP3 WILD-TYPE  165   71
     clus
vv    LTBP3 MUTATED LTBP3 WILD-TYPE
  NO              5             165
  YES             0              71
[1] 2 2
[1] FALSE
                 vv
clus              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  LTBP3 MUTATED                              0             0
  LTBP3 WILD-TYPE                           56             2
                 vv
clus              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  LTBP3 MUTATED                                                                          0
  LTBP3 WILD-TYPE                                                                        1
                 vv
clus              LEIOMYOSARCOMA (LMS)
  LTBP3 MUTATED                      3
  LTBP3 WILD-TYPE                   95
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  LTBP3 MUTATED                                                  0
  LTBP3 WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  LTBP3 MUTATED                  1
  LTBP3 WILD-TYPE               21
                 vv
clus              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  LTBP3 MUTATED                                                          1
  LTBP3 WILD-TYPE                                                       28
                 vv
clus              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  LTBP3 MUTATED                                          0
  LTBP3 WILD-TYPE                                        2
                 vv
clus              SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  LTBP3 MUTATED                             0                             0
  LTBP3 WILD-TYPE                           2                             6
                 vv
clus              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  LTBP3 MUTATED                                            0
  LTBP3 WILD-TYPE                                         21
D6V6, multiclass
                                                                          clus
vv                                                                         LTBP3 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                         0
  DESMOID TUMOR                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             0
  LEIOMYOSARCOMA (LMS)                                                                 3
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     0
  MYXOFIBROSARCOMA                                                                     1
  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                                                                         LTBP3 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                          56
  DESMOID TUMOR                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               1
  LEIOMYOSARCOMA (LMS)                                                                  95
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       8
  MYXOFIBROSARCOMA                                                                      21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              28
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            21
[1] 11  2
[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
  LTBP3 MUTATED     2   2   0   1
  LTBP3 WILD-TYPE 147  63   9  22
D6V7, multiclass
    clus
vv   LTBP3 MUTATED LTBP3 WILD-TYPE
  R0             2             147
  R1             2              63
  R2             0               9
  RX             1              22
[1] 4 2
[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
  LTBP3 MUTATED       0                         1     4
  LTBP3 WILD-TYPE     5                        17   213
D6V8, multiclass
                           clus
vv                          LTBP3 MUTATED LTBP3 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              17
  WHITE                                 4             213
[1] 3 2
[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
  LTBP3 MUTATED     0   5
  LTBP3 WILD-TYPE   5 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED      0    5
  LTBP3 WILD-TYPE    5  208
                        clus
vv                       LTBP3 MUTATED LTBP3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             208
[1] 2 2
[1] FALSE

Clustering(7) Variable = EOMES MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  EOMES MUTATED     3   2
  EOMES WILD-TYPE 151  91
  EOMES MUTATED EOMES WILD-TYPE 
              5             242 
  EOMES MUTATED EOMES WILD-TYPE 
              2              91 
$`EOMES MUTATED`
TCGA-SG-A849 TCGA-3B-A9HR TCGA-DX-AB2V TCGA-FX-A8OO TCGA-X6-A7WC 
       17.52        88.57       106.55         8.05        45.34 

$`EOMES WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       15.22        23.70        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       40.60        12.07       106.45        13.28        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
       30.51        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-VT-A80J TCGA-WK-A8XT 
       11.70        17.75         8.28        20.94        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS 
       35.08        50.01        19.69        53.49        68.55        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        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-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
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-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       41.00        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       20.05         9.34        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       40.77        51.91       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        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-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       20.32        19.89        15.48        67.63        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       33.30         0.72        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       19.89        25.22       171.09        13.58        85.97         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       16.41         1.05         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
      123.78        17.36        23.38         5.19        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       35.28        30.31        25.41         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        22.39        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QC-AA9N 
       37.55        38.63        81.01        26.73        13.08        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32        64.77        10.52         0.72        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        3.88        22.82        25.35        32.75         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22        13.41        10.72        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB 
       84.79        38.27        65.46        56.61        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       63.35        26.43        30.84        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  EOMES MUTATED EOMES WILD-TYPE 
           8.05            0.49 
  EOMES MUTATED EOMES WILD-TYPE 
         106.55          171.09 
  EOMES MUTATED EOMES WILD-TYPE 
         45.340          30.675 
[1] "8.1 - 106.5 (45.3)" "0.5 - 171.1 (30.7)"
[1] "hr=" "1.4"
D7V2, continuous
                 vv
clus              CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  EOMES MUTATED                0                  0                   1
  EOMES WILD-TYPE              1                  7                   1
                 vv
clus              CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  EOMES MUTATED                     0                             0
  EOMES WILD-TYPE                   1                             1
                 vv
clus              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  EOMES MUTATED                       0                      0
  EOMES WILD-TYPE                     1                     26
                 vv
clus              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  EOMES MUTATED                      0                    0
  EOMES WILD-TYPE                    2                    1
                 vv
clus              HEAD AND NECK - OTHER (PLEASE SPECIFY
  EOMES MUTATED                                       0
  EOMES WILD-TYPE                                     2
                 vv
clus              LOWER ABDOMINAL/PELVIC - BLADDER
  EOMES MUTATED                                  0
  EOMES WILD-TYPE                                1
                 vv
clus              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  EOMES MUTATED                                                0
  EOMES WILD-TYPE                                              2
                 vv
clus              LOWER ABDOMINAL/PELVIC - PELVIC
  EOMES MUTATED                                 0
  EOMES WILD-TYPE                              11
                 vv
clus              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  EOMES MUTATED                                         0
  EOMES WILD-TYPE                                       2
                 vv
clus              LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  EOMES MUTATED                              0                       0
  EOMES WILD-TYPE                            4                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  EOMES MUTATED                                  0
  EOMES WILD-TYPE                               16
                 vv
clus              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  EOMES MUTATED                                         0
  EOMES WILD-TYPE                                       3
                 vv
clus              LOWER EXTREMITY - THIGH/KNEE
  EOMES MUTATED                              2
  EOMES WILD-TYPE                           41
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  EOMES MUTATED                                         0
  EOMES WILD-TYPE                                       4
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  EOMES MUTATED                                           0
  EOMES WILD-TYPE                                         2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  EOMES MUTATED                                                  0
  EOMES WILD-TYPE                                                5
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  EOMES MUTATED                                          0
  EOMES WILD-TYPE                                        7
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  EOMES MUTATED                                                         0
  EOMES WILD-TYPE                                                       2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  EOMES MUTATED                                            0
  EOMES WILD-TYPE                                          1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  EOMES MUTATED                                                   0
  EOMES WILD-TYPE                                                71
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  EOMES MUTATED                                                    0
  EOMES WILD-TYPE                                                  3
                 vv
clus              SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  EOMES MUTATED                                    0                        1
  EOMES WILD-TYPE                                  2                        4
                 vv
clus              SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  EOMES MUTATED                             0                         0
  EOMES WILD-TYPE                           3                         1
                 vv
clus              UPPER EXTREMITY - SHOULDER/AXILLA
  EOMES MUTATED                                   0
  EOMES WILD-TYPE                                 7
                 vv
clus              UPPER EXTREMITY - UPPER ARM/ELBOW
  EOMES MUTATED                                   1
  EOMES WILD-TYPE                                 4
D7V3, multiclass
                                                         clus
vv                                                        EOMES MUTATED
  CHEST - BREAST                                                      0
  CHEST - CHEST WALL                                                  0
  CHEST - LUNG/PLEURA                                                 1
  CHEST - MEDIASTINUM                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                       0
  GYNECOLOGICAL - OVARY                                               0
  GYNECOLOGICAL - UTERUS                                              0
  HEAD AND NECK - HEAD                                                0
  HEAD AND NECK - NECK                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                      0
  LOWER ABDOMINAL/PELVIC - PELVIC                                     0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                             0
  LOWER EXTREMITY - FOOT/ANKLE                                        0
  LOWER EXTREMITY - GROIN                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                    0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             0
  LOWER EXTREMITY - THIGH/KNEE                                        2
  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 - PANCREAS                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   0
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                  0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                  0
  SUPERFICIAL TRUNK - BACK                                            1
  SUPERFICIAL TRUNK - BUTTOCK                                         0
  SUPERFICIAL TRUNK - FLANK                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                   0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                   1
                                                         clus
vv                                                        EOMES WILD-TYPE
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    7
  CHEST - LUNG/PLEURA                                                   1
  CHEST - MEDIASTINUM                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                               26
  HEAD AND NECK - HEAD                                                  2
  HEAD AND NECK - NECK                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                      11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               2
  LOWER EXTREMITY - FOOT/ANKLE                                          4
  LOWER EXTREMITY - GROIN                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                     16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         41
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    71
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              4
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                     7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     4
[1] 33  2
[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
  EOMES MUTATED     2   3
  EOMES WILD-TYPE 131 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      2    3
  EOMES WILD-TYPE  131  111
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  FEMALE             2             131
  MALE               3             111
[1] 2 2
[1] FALSE
D7V5, binary
                 cls
clus                0   1
  EOMES MUTATED     1   4
  EOMES WILD-TYPE 169  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      1    4
  EOMES WILD-TYPE  169   67
     clus
vv    EOMES MUTATED EOMES WILD-TYPE
  NO              1             169
  YES             4              67
[1] 2 2
[1] FALSE
                 vv
clus              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  EOMES MUTATED                              0             0
  EOMES WILD-TYPE                           56             2
                 vv
clus              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  EOMES MUTATED                                                                          0
  EOMES WILD-TYPE                                                                        1
                 vv
clus              LEIOMYOSARCOMA (LMS)
  EOMES MUTATED                      2
  EOMES WILD-TYPE                   96
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  EOMES MUTATED                                                  0
  EOMES WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  EOMES MUTATED                  1
  EOMES WILD-TYPE               21
                 vv
clus              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  EOMES MUTATED                                                          0
  EOMES WILD-TYPE                                                       29
                 vv
clus              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  EOMES MUTATED                                          1
  EOMES WILD-TYPE                                        1
                 vv
clus              SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  EOMES MUTATED                             0                             0
  EOMES WILD-TYPE                           2                             6
                 vv
clus              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  EOMES MUTATED                                            1
  EOMES WILD-TYPE                                         20
D7V6, multiclass
                                                                          clus
vv                                                                         EOMES MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                         0
  DESMOID TUMOR                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             0
  LEIOMYOSARCOMA (LMS)                                                                 2
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     0
  MYXOFIBROSARCOMA                                                                     1
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                             1
  SYNOVIAL SARCOMA - BIPHASIC                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           1
                                                                          clus
vv                                                                         EOMES WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                          56
  DESMOID TUMOR                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               1
  LEIOMYOSARCOMA (LMS)                                                                  96
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       8
  MYXOFIBROSARCOMA                                                                      21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              29
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            20
[1] 11  2
[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
  EOMES MUTATED     4   1   0   0
  EOMES WILD-TYPE 145  64   9  23
D7V7, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  R0             4             145
  R1             1              64
  R2             0               9
  RX             0              23
[1] 4 2
[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
  EOMES MUTATED       0                         1     4
  EOMES WILD-TYPE     5                        17   213
D7V8, multiclass
                           clus
vv                          EOMES MUTATED EOMES WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              17
  WHITE                                 4             213
[1] 3 2
[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
  EOMES MUTATED     0   5
  EOMES WILD-TYPE   5 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      0    5
  EOMES WILD-TYPE    5  208
                        clus
vv                       EOMES MUTATED EOMES WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             208
[1] 2 2
[1] FALSE

Clustering(8) Variable = PTEN MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     5   2
  PTEN WILD-TYPE 149  91
  PTEN MUTATED PTEN WILD-TYPE 
             7            240 
  PTEN MUTATED PTEN WILD-TYPE 
             2             91 
$`PTEN MUTATED`
TCGA-3B-A9HZ TCGA-IE-A4EK TCGA-LI-A67I TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 
       38.47         1.38        30.31        84.79        65.46        22.62 
TCGA-Z4-A9VC 
       13.38 

$`PTEN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       15.22        23.70        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       40.60        12.07       106.45        13.28        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
       30.51        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
       11.70        17.75         8.28        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       41.49        35.08        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       88.57        44.91        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        68.61        12.85        45.11        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       85.02        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       79.17         9.04        49.05        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       82.68        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
        3.06        41.00        16.87        86.30        64.21       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       21.30        34.49        62.20        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.20        20.05         9.34        61.97        45.14        47.87 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        40.77        51.91       150.35        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       36.69        60.66        19.43         6.58         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.00        15.72        65.98        86.10        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       77.88       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV 
       67.63        34.88         4.57        33.30         0.72        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA 
       19.53         3.22        19.89        25.22       171.09        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       53.33        62.17       123.78        17.36        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       63.81        16.41        35.28        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
       19.73        14.99        17.98        22.39        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 
      122.96        37.55        38.63        81.01        26.73        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       17.65         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
       37.12       130.32        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       19.63        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XZ TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
        4.80        38.27        56.61         8.58        63.35        26.43 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       45.34        30.84        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-AAPF TCGA-Z4-AAPG 
       29.46        27.32        36.43         4.37        15.95        15.98 

  PTEN MUTATED PTEN WILD-TYPE 
          1.38           0.49 
  PTEN MUTATED PTEN WILD-TYPE 
         84.79         171.09 
  PTEN MUTATED PTEN WILD-TYPE 
        30.310         30.985 
[1] "1.4 - 84.8 (30.3)"  "0.5 - 171.1 (31.0)"
[1] "hr=" "1.4"
D8V2, continuous
                vv
clus             CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  PTEN MUTATED                0                  1                   0
  PTEN WILD-TYPE              1                  6                   2
                vv
clus             CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  PTEN MUTATED                     1                             0
  PTEN WILD-TYPE                   0                             1
                vv
clus             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  PTEN MUTATED                       0                      0
  PTEN WILD-TYPE                     1                     26
                vv
clus             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  PTEN MUTATED                      0                    0
  PTEN WILD-TYPE                    2                    1
                vv
clus             HEAD AND NECK - OTHER (PLEASE SPECIFY
  PTEN MUTATED                                       0
  PTEN WILD-TYPE                                     2
                vv
clus             LOWER ABDOMINAL/PELVIC - BLADDER
  PTEN MUTATED                                  0
  PTEN WILD-TYPE                                1
                vv
clus             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  PTEN MUTATED                                                0
  PTEN WILD-TYPE                                              2
                vv
clus             LOWER ABDOMINAL/PELVIC - PELVIC
  PTEN MUTATED                                 0
  PTEN WILD-TYPE                              11
                vv
clus             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  PTEN MUTATED                                         0
  PTEN WILD-TYPE                                       2
                vv
clus             LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  PTEN MUTATED                              0                       0
  PTEN WILD-TYPE                            4                       2
                vv
clus             LOWER EXTREMITY - LOWER LEG/CALF
  PTEN MUTATED                                  0
  PTEN WILD-TYPE                               16
                vv
clus             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  PTEN MUTATED                                         0
  PTEN WILD-TYPE                                       3
                vv
clus             LOWER EXTREMITY - THIGH/KNEE
  PTEN MUTATED                              2
  PTEN WILD-TYPE                           41
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  PTEN MUTATED                                         0
  PTEN WILD-TYPE                                       4
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  PTEN MUTATED                                           1
  PTEN WILD-TYPE                                         1
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  PTEN MUTATED                                                  0
  PTEN WILD-TYPE                                                5
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  PTEN MUTATED                                          1
  PTEN WILD-TYPE                                        6
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  PTEN MUTATED                                                         0
  PTEN WILD-TYPE                                                       2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  PTEN MUTATED                                            0
  PTEN WILD-TYPE                                          1
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  PTEN MUTATED                                                   0
  PTEN WILD-TYPE                                                71
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  PTEN MUTATED                                                    1
  PTEN WILD-TYPE                                                  2
                vv
clus             SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  PTEN MUTATED                                    0                        0
  PTEN WILD-TYPE                                  2                        5
                vv
clus             SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  PTEN MUTATED                             0                         0
  PTEN WILD-TYPE                           3                         1
                vv
clus             UPPER EXTREMITY - SHOULDER/AXILLA
  PTEN MUTATED                                   0
  PTEN WILD-TYPE                                 7
                vv
clus             UPPER EXTREMITY - UPPER ARM/ELBOW
  PTEN MUTATED                                   0
  PTEN WILD-TYPE                                 5
D8V3, multiclass
                                                         clus
vv                                                        PTEN MUTATED
  CHEST - BREAST                                                     0
  CHEST - CHEST WALL                                                 1
  CHEST - LUNG/PLEURA                                                0
  CHEST - MEDIASTINUM                                                1
  CHEST - OTHER (PLEASE SPECIFY                                      0
  GYNECOLOGICAL - OVARY                                              0
  GYNECOLOGICAL - UTERUS                                             0
  HEAD AND NECK - HEAD                                               0
  HEAD AND NECK - NECK                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                    0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                            0
  LOWER EXTREMITY - FOOT/ANKLE                                       0
  LOWER EXTREMITY - GROIN                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                   0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                            0
  LOWER EXTREMITY - THIGH/KNEE                                       2
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                            0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                          1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                   0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                           1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY            0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                  0
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                 1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                 0
  SUPERFICIAL TRUNK - BACK                                           0
  SUPERFICIAL TRUNK - BUTTOCK                                        0
  SUPERFICIAL TRUNK - FLANK                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                  0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                  0
                                                         clus
vv                                                        PTEN WILD-TYPE
  CHEST - BREAST                                                       1
  CHEST - CHEST WALL                                                   6
  CHEST - LUNG/PLEURA                                                  2
  CHEST - MEDIASTINUM                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                        1
  GYNECOLOGICAL - OVARY                                                1
  GYNECOLOGICAL - UTERUS                                              26
  HEAD AND NECK - HEAD                                                 2
  HEAD AND NECK - NECK                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                     11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                              2
  LOWER EXTREMITY - FOOT/ANKLE                                         4
  LOWER EXTREMITY - GROIN                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                    16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                              3
  LOWER EXTREMITY - THIGH/KNEE                                        41
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                            1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                             6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   71
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                   2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                   2
  SUPERFICIAL TRUNK - BACK                                             5
  SUPERFICIAL TRUNK - BUTTOCK                                          3
  SUPERFICIAL TRUNK - FLANK                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                    7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                    5
[1] 33  2
[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
  PTEN MUTATED     4   3
  PTEN WILD-TYPE 129 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    3
  PTEN WILD-TYPE  129  111
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4            129
  MALE              3            111
[1] 2 2
[1] FALSE
D8V5, binary
                cls
clus               0   1
  PTEN MUTATED     3   3
  PTEN WILD-TYPE 167  68
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      3    3
  PTEN WILD-TYPE  167   68
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             3            167
  YES            3             68
[1] 2 2
[1] FALSE
                vv
clus             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  PTEN MUTATED                              1             0
  PTEN WILD-TYPE                           55             2
                vv
clus             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  PTEN MUTATED                                                                          0
  PTEN WILD-TYPE                                                                        1
                vv
clus             LEIOMYOSARCOMA (LMS)
  PTEN MUTATED                      4
  PTEN WILD-TYPE                   94
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  PTEN MUTATED                                                  0
  PTEN WILD-TYPE                                                8
                vv
clus             MYXOFIBROSARCOMA
  PTEN MUTATED                  1
  PTEN WILD-TYPE               21
                vv
clus             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  PTEN MUTATED                                                          0
  PTEN WILD-TYPE                                                       29
                vv
clus             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  PTEN MUTATED                                          0
  PTEN WILD-TYPE                                        2
                vv
clus             SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  PTEN MUTATED                             0                             0
  PTEN WILD-TYPE                           2                             6
                vv
clus             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  PTEN MUTATED                                            1
  PTEN WILD-TYPE                                         20
D8V6, multiclass
                                                                          clus
vv                                                                         PTEN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                        1
  DESMOID TUMOR                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS            0
  LEIOMYOSARCOMA (LMS)                                                                4
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                    0
  MYXOFIBROSARCOMA                                                                    1
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                            0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          1
                                                                          clus
vv                                                                         PTEN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                         55
  DESMOID TUMOR                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS              1
  LEIOMYOSARCOMA (LMS)                                                                 94
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      8
  MYXOFIBROSARCOMA                                                                     21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             29
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           20
[1] 11  2
[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
  PTEN MUTATED     3   3   0   1
  PTEN WILD-TYPE 146  62   9  22
D8V7, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            3            146
  R1            3             62
  R2            0              9
  RX            1             22
[1] 4 2
[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
  PTEN MUTATED       0                         0     7
  PTEN WILD-TYPE     5                        18   210
D8V8, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                7            210
[1] 3 2
[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
  PTEN MUTATED     0   7
  PTEN WILD-TYPE   5 206
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    7
  PTEN WILD-TYPE    5  206
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            7            206
[1] 2 2
[1] FALSE

Clustering(9) Variable = KRTAP5-5 MUTATION ANALYSIS
D9V1, survival
                    sevent
clus2                  0   1
  KRTAP5-5 MUTATED     4   3
  KRTAP5-5 WILD-TYPE 150  90
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                240 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 90 
$`KRTAP5-5 MUTATED`
TCGA-DX-AB30 TCGA-DX-A1KX TCGA-DX-A2J1 TCGA-DX-A48N TCGA-DX-A8BN TCGA-JV-A75J 
       22.85        68.61        95.38        35.28        38.17         3.91 
TCGA-QQ-A8VH 
       10.52 

$`KRTAP5-5 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       15.22        23.70        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB32 TCGA-DX-AB35 
       40.60        12.07       106.45        13.28       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
       17.75         8.28        20.94        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       35.08        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       38.47        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       32.71        12.85        45.11        18.54        54.21        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-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J4 TCGA-DX-A3LS 
        6.28        60.30         8.58         9.70        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       35.77        51.02         4.54        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       68.55        50.43        34.88        85.45         9.73        45.99 
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-A6BE 
       37.58        15.95        37.41        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX 
       31.96        36.85        26.99         3.06        41.00        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM 
       86.30        64.21       101.23        21.30        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR 
       61.97        45.14        47.87        40.77        51.91       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        1.15        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       66.74         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       15.48         8.05        67.63        34.88         4.57        33.30 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
        0.72        80.48        19.53         3.22         1.38        19.89 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       25.22       171.09        13.58        85.97         5.92        16.41 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        1.05       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
       23.38         5.19        63.81        16.41        35.28        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       22.39        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        26.73        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
       18.08        48.59        35.90        37.12       130.32        64.77 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        16.77        18.94         3.88        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       32.75         8.61        19.63        13.22        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       12.46        11.93         4.80        84.79        38.27        65.46 
TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC 
       56.61        22.62         8.58        63.35        26.43        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       30.84        35.18        19.17        20.65        50.86        29.46 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        36.43         4.37        13.38        15.95        15.98 

  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
              3.91               0.49 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             95.38             171.09 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
            35.280             30.675 
[1] "3.9 - 95.4 (35.3)"  "0.5 - 171.1 (30.7)"
[1] "hr=" "1"  
D9V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  KRTAP5-5 MUTATED                0                  0                   0
  KRTAP5-5 WILD-TYPE              1                  7                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  KRTAP5-5 MUTATED                     0                             1
  KRTAP5-5 WILD-TYPE                   1                             0
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  KRTAP5-5 MUTATED                       0                      1
  KRTAP5-5 WILD-TYPE                     1                     25
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  KRTAP5-5 MUTATED                      0                    0
  KRTAP5-5 WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  KRTAP5-5 MUTATED                                       0
  KRTAP5-5 WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  KRTAP5-5 MUTATED                                  0
  KRTAP5-5 WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  KRTAP5-5 MUTATED                                                0
  KRTAP5-5 WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  KRTAP5-5 MUTATED                                 1
  KRTAP5-5 WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  KRTAP5-5 MUTATED                                         0
  KRTAP5-5 WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  KRTAP5-5 MUTATED                              0                       0
  KRTAP5-5 WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  KRTAP5-5 MUTATED                                  0
  KRTAP5-5 WILD-TYPE                               16
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  KRTAP5-5 MUTATED                                         0
  KRTAP5-5 WILD-TYPE                                       3
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  KRTAP5-5 MUTATED                              2
  KRTAP5-5 WILD-TYPE                           41
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  KRTAP5-5 MUTATED                                         0
  KRTAP5-5 WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  KRTAP5-5 MUTATED                                           0
  KRTAP5-5 WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  KRTAP5-5 MUTATED                                                  0
  KRTAP5-5 WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  KRTAP5-5 MUTATED                                          0
  KRTAP5-5 WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  KRTAP5-5 MUTATED                                                         0
  KRTAP5-5 WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  KRTAP5-5 MUTATED                                            0
  KRTAP5-5 WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  KRTAP5-5 MUTATED                                                   2
  KRTAP5-5 WILD-TYPE                                                69
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  KRTAP5-5 MUTATED                                                    0
  KRTAP5-5 WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  KRTAP5-5 MUTATED                                    0
  KRTAP5-5 WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  KRTAP5-5 MUTATED                          0                           0
  KRTAP5-5 WILD-TYPE                        5                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  KRTAP5-5 MUTATED                           0
  KRTAP5-5 WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  KRTAP5-5 MUTATED                                   0
  KRTAP5-5 WILD-TYPE                                 7
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  KRTAP5-5 MUTATED                                   0
  KRTAP5-5 WILD-TYPE                                 5
D9V3, multiclass
                                                         clus
vv                                                        KRTAP5-5 MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     0
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 1
  HEAD AND NECK - HEAD                                                   0
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  0
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         0
  LOWER ABDOMINAL/PELVIC - PELVIC                                        1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                0
  LOWER EXTREMITY - THIGH/KNEE                                           2
  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 - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      2
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               0
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      0
                                                         clus
vv                                                        KRTAP5-5 WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       7
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            0
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  25
  HEAD AND NECK - HEAD                                                     2
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  3
  LOWER EXTREMITY - THIGH/KNEE                                            41
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       69
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       2
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              3
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        5
[1] 33  2
[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
  KRTAP5-5 MUTATED     5   2
  KRTAP5-5 WILD-TYPE 128 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      5    2
  KRTAP5-5 WILD-TYPE  128  112
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  FEMALE                5                128
  MALE                  2                112
[1] 2 2
[1] FALSE
D9V5, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     4   3
  KRTAP5-5 WILD-TYPE 166  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      4    3
  KRTAP5-5 WILD-TYPE  166   68
     clus
vv    KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  NO                 4                166
  YES                3                 68
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  KRTAP5-5 MUTATED                              3             0
  KRTAP5-5 WILD-TYPE                           53             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  KRTAP5-5 MUTATED                                                                          0
  KRTAP5-5 WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  KRTAP5-5 MUTATED                      1
  KRTAP5-5 WILD-TYPE                   97
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  KRTAP5-5 MUTATED                                                  1
  KRTAP5-5 WILD-TYPE                                                7
                    vv
clus                 MYXOFIBROSARCOMA
  KRTAP5-5 MUTATED                  1
  KRTAP5-5 WILD-TYPE               21
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  KRTAP5-5 MUTATED                                                          1
  KRTAP5-5 WILD-TYPE                                                       28
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  KRTAP5-5 MUTATED                                          0
  KRTAP5-5 WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  KRTAP5-5 MUTATED                             0                             0
  KRTAP5-5 WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  KRTAP5-5 MUTATED                                            0
  KRTAP5-5 WILD-TYPE                                         21
D9V6, multiclass
                                                                          clus
vv                                                                         KRTAP5-5 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            3
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                        1
  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                                                                         KRTAP5-5 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             53
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     97
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          7
  MYXOFIBROSARCOMA                                                                         21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 28
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               21
[1] 11  2
[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
  KRTAP5-5 MUTATED     2   3   1   1
  KRTAP5-5 WILD-TYPE 147  62   8  22
D9V7, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  R0                2                147
  R1                3                 62
  R2                1                  8
  RX                1                 22
[1] 4 2
[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
  KRTAP5-5 MUTATED       0                         0     7
  KRTAP5-5 WILD-TYPE     5                        18   210
D9V8, multiclass
                           clus
vv                          KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                    7                210
[1] 3 2
[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
  KRTAP5-5 MUTATED     1   6
  KRTAP5-5 WILD-TYPE   4 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      1    6
  KRTAP5-5 WILD-TYPE    4  207
                        clus
vv                       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                6                207
[1] 2 2
[1] FALSE

Clustering(10) Variable = CABLES1 MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  CABLES1 MUTATED     1   2
  CABLES1 WILD-TYPE 153  91
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               244 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                2                91 
$`CABLES1 MUTATED`
TCGA-DX-AB3A TCGA-DX-A3UB TCGA-DX-A48L 
       32.15        73.87        24.26 

$`CABLES1 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       15.22        23.70        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       40.60        12.07       106.45        13.28        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       30.51        60.00        84.66        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
       17.75         8.28        20.94        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       35.08        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       38.47        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        68.61        12.85        45.11        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       85.02        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       79.17         9.04        49.05        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       10.68        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       45.99        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        86.30        64.21       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        61.97        45.14        47.87        38.17        40.77 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       51.91       150.35        27.95        40.44        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       19.43         6.58         1.15        17.79        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       65.98        86.10        66.74         9.21        77.88       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32        19.89        15.48         8.05        67.63        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
        4.57        33.30         0.72        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        19.89        25.22       171.09        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        16.41         1.05         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS 
       62.17       123.78        17.36        23.38         5.19        63.81 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       16.41        35.28        30.31        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
       19.73        14.99        17.98        22.39        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 
      122.96        37.55        38.63        81.01        26.73        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       17.65         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
       37.12       130.32        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       19.63        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 
        4.80        84.79        38.27        65.46        56.61        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        8.58        63.35        26.43        45.34        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       19.17        20.65        50.86        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  CABLES1 MUTATED CABLES1 WILD-TYPE 
            24.26              0.49 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
            73.87            171.09 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
           32.150            30.675 
[1] "24.3 - 73.9 (32.1)" "0.5 - 171.1 (30.7)"
[1] "hr=" "1.6"
D10V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  CABLES1 MUTATED                0                  0                   0
  CABLES1 WILD-TYPE              1                  7                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  CABLES1 MUTATED                     0                             0
  CABLES1 WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  CABLES1 MUTATED                       0                      0
  CABLES1 WILD-TYPE                     1                     26
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  CABLES1 MUTATED                      0                    0
  CABLES1 WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  CABLES1 MUTATED                                       0
  CABLES1 WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  CABLES1 MUTATED                                  0
  CABLES1 WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  CABLES1 MUTATED                                                0
  CABLES1 WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  CABLES1 MUTATED                                 0
  CABLES1 WILD-TYPE                              11
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  CABLES1 MUTATED                                         0
  CABLES1 WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  CABLES1 MUTATED                              0                       0
  CABLES1 WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  CABLES1 MUTATED                                  1
  CABLES1 WILD-TYPE                               15
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  CABLES1 MUTATED                                         0
  CABLES1 WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  CABLES1 MUTATED                              0
  CABLES1 WILD-TYPE                           43
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  CABLES1 MUTATED                                         0
  CABLES1 WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  CABLES1 MUTATED                                           0
  CABLES1 WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  CABLES1 MUTATED                                                  0
  CABLES1 WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  CABLES1 MUTATED                                          0
  CABLES1 WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  CABLES1 MUTATED                                                         0
  CABLES1 WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  CABLES1 MUTATED                                            0
  CABLES1 WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  CABLES1 MUTATED                                                   1
  CABLES1 WILD-TYPE                                                70
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  CABLES1 MUTATED                                                    1
  CABLES1 WILD-TYPE                                                  2
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  CABLES1 MUTATED                                    0                        0
  CABLES1 WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  CABLES1 MUTATED                             0                         0
  CABLES1 WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  CABLES1 MUTATED                                   0
  CABLES1 WILD-TYPE                                 7
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  CABLES1 MUTATED                                   0
  CABLES1 WILD-TYPE                                 5
D10V3, multiclass
                                                         clus
vv                                                        CABLES1 MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    0
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                0
  HEAD AND NECK - HEAD                                                  0
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                       0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               0
  LOWER EXTREMITY - THIGH/KNEE                                          0
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     1
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           0
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     0
                                                         clus
vv                                                        CABLES1 WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      7
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           1
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 26
  HEAD AND NECK - HEAD                                                    2
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           43
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      70
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       5
[1] 33  2
[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
  CABLES1 MUTATED     1   2
  CABLES1 WILD-TYPE 132 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CABLES1 MUTATED      1    2
  CABLES1 WILD-TYPE  132  112
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  FEMALE               1               132
  MALE                 2               112
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                  0   1
  CABLES1 MUTATED     2   1
  CABLES1 WILD-TYPE 168  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CABLES1 MUTATED      2    1
  CABLES1 WILD-TYPE  168   70
     clus
vv    CABLES1 MUTATED CABLES1 WILD-TYPE
  NO                2               168
  YES               1                70
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  CABLES1 MUTATED                              1             0
  CABLES1 WILD-TYPE                           55             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  CABLES1 MUTATED                                                                          0
  CABLES1 WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  CABLES1 MUTATED                      2
  CABLES1 WILD-TYPE                   96
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  CABLES1 MUTATED                                                  0
  CABLES1 WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  CABLES1 MUTATED                  0
  CABLES1 WILD-TYPE               22
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  CABLES1 MUTATED                                                          0
  CABLES1 WILD-TYPE                                                       29
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  CABLES1 MUTATED                                          0
  CABLES1 WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  CABLES1 MUTATED                             0                             0
  CABLES1 WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  CABLES1 MUTATED                                            0
  CABLES1 WILD-TYPE                                         21
D10V6, multiclass
                                                                          clus
vv                                                                         CABLES1 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           1
  DESMOID TUMOR                                                                          0
  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                               0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             0
                                                                          clus
vv                                                                         CABLES1 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            55
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    96
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                29
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              21
[1] 11  2
[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
  CABLES1 MUTATED     3   0   0   0
  CABLES1 WILD-TYPE 146  65   9  23
D10V7, multiclass
    clus
vv   CABLES1 MUTATED CABLES1 WILD-TYPE
  R0               3               146
  R1               0                65
  R2               0                 9
  RX               0                23
[1] 4 2
[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
  CABLES1 MUTATED       0                         0     3
  CABLES1 WILD-TYPE     5                        18   214
D10V8, multiclass
                           clus
vv                          CABLES1 MUTATED CABLES1 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                18
  WHITE                                   3               214
[1] 3 2
[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
  CABLES1 MUTATED     0   2
  CABLES1 WILD-TYPE   5 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CABLES1 MUTATED      0    2
  CABLES1 WILD-TYPE    5  211
                        clus
vv                       CABLES1 MUTATED CABLES1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2               211
[1] 2 2
[1] FALSE

Clustering(11) Variable = TRAF7 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  TRAF7 MUTATED     3   1
  TRAF7 WILD-TYPE 151  92
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             243 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              1              92 
$`TRAF7 MUTATED`
TCGA-DX-A6YU TCGA-DX-AB35 TCGA-DX-A1L4 TCGA-DX-A8BJ 
       34.36        30.51        66.94         9.34 

$`TRAF7 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        34.68        16.18        75.32        15.22 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J 
       23.70        17.95        14.43        14.07        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       12.07       106.45        13.28        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       84.66        32.15        16.60        37.02        12.62        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH 
       52.27        28.21       159.29        22.62        11.70        17.75 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
        8.28        20.94        17.52        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       50.01        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       35.77        51.02         4.54        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       68.55        50.43        34.88        85.45         9.73        45.99 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        86.30        64.21       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ 
       61.97        45.14        47.87        38.17        40.77        51.91 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      150.35        27.95        40.44        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
        6.58         1.15        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        66.74         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       19.89        15.48         8.05        67.63        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       33.30         0.72        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       19.89        25.22       171.09        13.58        85.97         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       16.41         1.05         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
      123.78        17.36        23.38         5.19        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       35.28        30.31        25.41         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        22.39        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QC-AA9N 
       37.55        38.63        81.01        26.73        13.08        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32        64.77        10.52         0.72        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        3.88        22.82        25.35        32.75         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22        13.41        10.72        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB 
       84.79        38.27        65.46        56.61        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        26.43        45.34        30.84        35.18        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       20.65        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  TRAF7 MUTATED TRAF7 WILD-TYPE 
           9.34            0.49 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
          66.94          171.09 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
         32.435          30.840 
[1] "9.3 - 66.9 (32.4)"  "0.5 - 171.1 (30.8)"
[1] "hr=" "1.4"
D11V2, continuous
                 vv
clus              CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  TRAF7 MUTATED                0                  2                   0
  TRAF7 WILD-TYPE              1                  5                   2
                 vv
clus              CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  TRAF7 MUTATED                     0                             0
  TRAF7 WILD-TYPE                   1                             1
                 vv
clus              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  TRAF7 MUTATED                       0                      0
  TRAF7 WILD-TYPE                     1                     26
                 vv
clus              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  TRAF7 MUTATED                      0                    0
  TRAF7 WILD-TYPE                    2                    1
                 vv
clus              HEAD AND NECK - OTHER (PLEASE SPECIFY
  TRAF7 MUTATED                                       0
  TRAF7 WILD-TYPE                                     2
                 vv
clus              LOWER ABDOMINAL/PELVIC - BLADDER
  TRAF7 MUTATED                                  0
  TRAF7 WILD-TYPE                                1
                 vv
clus              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  TRAF7 MUTATED                                                0
  TRAF7 WILD-TYPE                                              2
                 vv
clus              LOWER ABDOMINAL/PELVIC - PELVIC
  TRAF7 MUTATED                                 0
  TRAF7 WILD-TYPE                              11
                 vv
clus              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  TRAF7 MUTATED                                         0
  TRAF7 WILD-TYPE                                       2
                 vv
clus              LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  TRAF7 MUTATED                              0                       0
  TRAF7 WILD-TYPE                            4                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  TRAF7 MUTATED                                  0
  TRAF7 WILD-TYPE                               16
                 vv
clus              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  TRAF7 MUTATED                                         0
  TRAF7 WILD-TYPE                                       3
                 vv
clus              LOWER EXTREMITY - THIGH/KNEE
  TRAF7 MUTATED                              0
  TRAF7 WILD-TYPE                           43
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  TRAF7 MUTATED                                         0
  TRAF7 WILD-TYPE                                       4
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  TRAF7 MUTATED                                           0
  TRAF7 WILD-TYPE                                         2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  TRAF7 MUTATED                                                  0
  TRAF7 WILD-TYPE                                                5
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  TRAF7 MUTATED                                          0
  TRAF7 WILD-TYPE                                        7
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  TRAF7 MUTATED                                                         0
  TRAF7 WILD-TYPE                                                       2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  TRAF7 MUTATED                                            0
  TRAF7 WILD-TYPE                                          1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  TRAF7 MUTATED                                                   2
  TRAF7 WILD-TYPE                                                69
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  TRAF7 MUTATED                                                    0
  TRAF7 WILD-TYPE                                                  3
                 vv
clus              SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  TRAF7 MUTATED                                    0                        0
  TRAF7 WILD-TYPE                                  2                        5
                 vv
clus              SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  TRAF7 MUTATED                             0                         0
  TRAF7 WILD-TYPE                           3                         1
                 vv
clus              UPPER EXTREMITY - SHOULDER/AXILLA
  TRAF7 MUTATED                                   0
  TRAF7 WILD-TYPE                                 7
                 vv
clus              UPPER EXTREMITY - UPPER ARM/ELBOW
  TRAF7 MUTATED                                   0
  TRAF7 WILD-TYPE                                 5
D11V3, multiclass
                                                         clus
vv                                                        TRAF7 MUTATED
  CHEST - BREAST                                                      0
  CHEST - CHEST WALL                                                  2
  CHEST - LUNG/PLEURA                                                 0
  CHEST - MEDIASTINUM                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                       0
  GYNECOLOGICAL - OVARY                                               0
  GYNECOLOGICAL - UTERUS                                              0
  HEAD AND NECK - HEAD                                                0
  HEAD AND NECK - NECK                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                      0
  LOWER ABDOMINAL/PELVIC - PELVIC                                     0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                             0
  LOWER EXTREMITY - FOOT/ANKLE                                        0
  LOWER EXTREMITY - GROIN                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                    0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             0
  LOWER EXTREMITY - THIGH/KNEE                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                             0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                           0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                    0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY             0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   2
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                  0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                  0
  SUPERFICIAL TRUNK - BACK                                            0
  SUPERFICIAL TRUNK - BUTTOCK                                         0
  SUPERFICIAL TRUNK - FLANK                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                   0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                   0
                                                         clus
vv                                                        TRAF7 WILD-TYPE
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    5
  CHEST - LUNG/PLEURA                                                   2
  CHEST - MEDIASTINUM                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                               26
  HEAD AND NECK - HEAD                                                  2
  HEAD AND NECK - NECK                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                      11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               2
  LOWER EXTREMITY - FOOT/ANKLE                                          4
  LOWER EXTREMITY - GROIN                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                     16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         43
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    69
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              5
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                     7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                 cls
clus                0   1
  TRAF7 MUTATED     1   3
  TRAF7 WILD-TYPE 132 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF7 MUTATED      1    3
  TRAF7 WILD-TYPE  132  111
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  FEMALE             1             132
  MALE               3             111
[1] 2 2
[1] FALSE
D11V5, binary
                 cls
clus                0   1
  TRAF7 MUTATED     3   1
  TRAF7 WILD-TYPE 167  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF7 MUTATED      3    1
  TRAF7 WILD-TYPE  167   70
     clus
vv    TRAF7 MUTATED TRAF7 WILD-TYPE
  NO              3             167
  YES             1              70
[1] 2 2
[1] FALSE
                 vv
clus              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  TRAF7 MUTATED                              2             0
  TRAF7 WILD-TYPE                           54             2
                 vv
clus              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  TRAF7 MUTATED                                                                          0
  TRAF7 WILD-TYPE                                                                        1
                 vv
clus              LEIOMYOSARCOMA (LMS)
  TRAF7 MUTATED                      0
  TRAF7 WILD-TYPE                   98
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  TRAF7 MUTATED                                                  0
  TRAF7 WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  TRAF7 MUTATED                  1
  TRAF7 WILD-TYPE               21
                 vv
clus              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  TRAF7 MUTATED                                                          1
  TRAF7 WILD-TYPE                                                       28
                 vv
clus              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  TRAF7 MUTATED                                          0
  TRAF7 WILD-TYPE                                        2
                 vv
clus              SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  TRAF7 MUTATED                             0                             0
  TRAF7 WILD-TYPE                           2                             6
                 vv
clus              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  TRAF7 MUTATED                                            0
  TRAF7 WILD-TYPE                                         21
D11V6, multiclass
                                                                          clus
vv                                                                         TRAF7 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                         2
  DESMOID TUMOR                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             0
  LEIOMYOSARCOMA (LMS)                                                                 0
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     0
  MYXOFIBROSARCOMA                                                                     1
  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                                                                         TRAF7 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                          54
  DESMOID TUMOR                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               1
  LEIOMYOSARCOMA (LMS)                                                                  98
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       8
  MYXOFIBROSARCOMA                                                                      21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              28
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            21
[1] 11  2
[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
  TRAF7 MUTATED     4   0   0   0
  TRAF7 WILD-TYPE 145  65   9  23
D11V7, multiclass
    clus
vv   TRAF7 MUTATED TRAF7 WILD-TYPE
  R0             4             145
  R1             0              65
  R2             0               9
  RX             0              23
[1] 4 2
[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
  TRAF7 MUTATED       0                         0     4
  TRAF7 WILD-TYPE     5                        18   213
D11V8, multiclass
                           clus
vv                          TRAF7 MUTATED TRAF7 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 4             213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                 cls
clus                0   1
  TRAF7 MUTATED     0   4
  TRAF7 WILD-TYPE   5 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF7 MUTATED      0    4
  TRAF7 WILD-TYPE    5  209
                        clus
vv                       TRAF7 MUTATED TRAF7 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             209
[1] 2 2
[1] FALSE

Clustering(12) Variable = LOR MUTATION ANALYSIS
D12V1, survival
               sevent
clus2             0   1
  LOR MUTATED     4   2
  LOR WILD-TYPE 150  91
  LOR MUTATED LOR WILD-TYPE 
            6           241 
  LOR MUTATED LOR WILD-TYPE 
            2            91 
$`LOR MUTATED`
TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A6BG TCGA-DX-A7ER TCGA-DX-AB2F TCGA-FX-A48G 
       79.17        49.05        36.85        48.20        12.00        19.89 

$`LOR WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       15.22        23.70        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       40.60        12.07       106.45        13.28        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
       30.51        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
       11.70        17.75         8.28        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       41.49        35.08        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       88.57        44.91        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       10.32        38.47        36.03        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-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87         6.28        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       95.38         9.04        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
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-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       36.33        28.96        31.96        26.99         3.06        41.00 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        86.30        64.21       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ES TCGA-DX-A8BJ 
       62.20        30.35       152.12        29.49        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ 
       61.97        45.14        47.87        38.17        40.77        51.91 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      150.35        27.95        40.44        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        6.58         1.15        17.79        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       66.74         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y 
       71.31        49.15        31.13        21.70        20.32        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
        8.05        67.63        34.88         4.57        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
       80.48        19.53         3.22         1.38        19.89        25.22 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
      171.09        13.58        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
       23.38         5.19        63.81        16.41        35.28        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       22.39        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        26.73        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
       18.08        48.59        35.90        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       10.52         0.72        16.77        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       25.35        32.75         8.61        19.63        13.22        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX 
       10.72        12.46        11.93         4.80        84.79        38.27 
TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       65.46        56.61        22.62         8.58        63.35        26.43 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       45.34        30.84        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  LOR MUTATED LOR WILD-TYPE 
        12.00          0.49 
  LOR MUTATED LOR WILD-TYPE 
        79.17        171.09 
  LOR MUTATED LOR WILD-TYPE 
       42.525        30.510 
[1] "12.0 - 79.2 (42.5)" "0.5 - 171.1 (30.5)"
[1] "hr=" "1.2"
D12V2, continuous
               vv
clus            CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  LOR MUTATED                0                  0                   1
  LOR WILD-TYPE              1                  7                   1
               vv
clus            CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  LOR MUTATED                     0                             0
  LOR WILD-TYPE                   1                             1
               vv
clus            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  LOR MUTATED                       0                      1
  LOR WILD-TYPE                     1                     25
               vv
clus            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  LOR MUTATED                      0                    0
  LOR WILD-TYPE                    2                    1
               vv
clus            HEAD AND NECK - OTHER (PLEASE SPECIFY
  LOR MUTATED                                       0
  LOR WILD-TYPE                                     2
               vv
clus            LOWER ABDOMINAL/PELVIC - BLADDER
  LOR MUTATED                                  0
  LOR WILD-TYPE                                1
               vv
clus            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  LOR MUTATED                                                0
  LOR WILD-TYPE                                              2
               vv
clus            LOWER ABDOMINAL/PELVIC - PELVIC
  LOR MUTATED                                 0
  LOR WILD-TYPE                              11
               vv
clus            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  LOR MUTATED                                         0
  LOR WILD-TYPE                                       2
               vv
clus            LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  LOR MUTATED                              0                       0
  LOR WILD-TYPE                            4                       2
               vv
clus            LOWER EXTREMITY - LOWER LEG/CALF
  LOR MUTATED                                  0
  LOR WILD-TYPE                               16
               vv
clus            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  LOR MUTATED                                         0
  LOR WILD-TYPE                                       3
               vv
clus            LOWER EXTREMITY - THIGH/KNEE
  LOR MUTATED                              0
  LOR WILD-TYPE                           43
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  LOR MUTATED                                         0
  LOR WILD-TYPE                                       4
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  LOR MUTATED                                           0
  LOR WILD-TYPE                                         2
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  LOR MUTATED                                                  1
  LOR WILD-TYPE                                                4
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  LOR MUTATED                                          0
  LOR WILD-TYPE                                        7
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  LOR MUTATED                                                         0
  LOR WILD-TYPE                                                       2
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  LOR MUTATED                                            0
  LOR WILD-TYPE                                          1
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  LOR MUTATED                                                   2
  LOR WILD-TYPE                                                69
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  LOR MUTATED                                                    0
  LOR WILD-TYPE                                                  3
               vv
clus            SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  LOR MUTATED                                    0                        0
  LOR WILD-TYPE                                  2                        5
               vv
clus            SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  LOR MUTATED                             0                         0
  LOR WILD-TYPE                           3                         1
               vv
clus            UPPER EXTREMITY - SHOULDER/AXILLA
  LOR MUTATED                                   0
  LOR WILD-TYPE                                 7
               vv
clus            UPPER EXTREMITY - UPPER ARM/ELBOW
  LOR MUTATED                                   1
  LOR WILD-TYPE                                 4
D12V3, multiclass
                                                         clus
vv                                                        LOR MUTATED
  CHEST - BREAST                                                    0
  CHEST - CHEST WALL                                                0
  CHEST - LUNG/PLEURA                                               1
  CHEST - MEDIASTINUM                                               0
  CHEST - OTHER (PLEASE SPECIFY                                     0
  GYNECOLOGICAL - OVARY                                             0
  GYNECOLOGICAL - UTERUS                                            1
  HEAD AND NECK - HEAD                                              0
  HEAD AND NECK - NECK                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                             0
  LOWER ABDOMINAL/PELVIC - BLADDER                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                   0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                           0
  LOWER EXTREMITY - FOOT/ANKLE                                      0
  LOWER EXTREMITY - GROIN                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                  0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                           0
  LOWER EXTREMITY - THIGH/KNEE                                      0
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                           0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                         0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                  1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                          0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY           0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                 2
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                0
  SUPERFICIAL TRUNK - BACK                                          0
  SUPERFICIAL TRUNK - BUTTOCK                                       0
  SUPERFICIAL TRUNK - FLANK                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                 0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                 1
                                                         clus
vv                                                        LOR WILD-TYPE
  CHEST - BREAST                                                      1
  CHEST - CHEST WALL                                                  7
  CHEST - LUNG/PLEURA                                                 1
  CHEST - MEDIASTINUM                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                       1
  GYNECOLOGICAL - OVARY                                               1
  GYNECOLOGICAL - UTERUS                                             25
  HEAD AND NECK - HEAD                                                2
  HEAD AND NECK - NECK                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                               2
  LOWER ABDOMINAL/PELVIC - BLADDER                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                    11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                             2
  LOWER EXTREMITY - FOOT/ANKLE                                        4
  LOWER EXTREMITY - GROIN                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                   16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             3
  LOWER EXTREMITY - THIGH/KNEE                                       43
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                    4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                            7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                  69
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                  2
  SUPERFICIAL TRUNK - BACK                                            5
  SUPERFICIAL TRUNK - BUTTOCK                                         3
  SUPERFICIAL TRUNK - FLANK                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                   7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                   4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
               cls
clus              0   1
  LOR MUTATED     2   4
  LOR WILD-TYPE 131 110
[1] "tbl2"
               cls
clus            [,1] [,2]
  LOR MUTATED      2    4
  LOR WILD-TYPE  131  110
        clus
vv       LOR MUTATED LOR WILD-TYPE
  FEMALE           2           131
  MALE             4           110
[1] 2 2
[1] FALSE
D12V5, binary
               cls
clus              0   1
  LOR MUTATED     5   1
  LOR WILD-TYPE 165  70
[1] "tbl2"
               cls
clus            [,1] [,2]
  LOR MUTATED      5    1
  LOR WILD-TYPE  165   70
     clus
vv    LOR MUTATED LOR WILD-TYPE
  NO            5           165
  YES           1            70
[1] 2 2
[1] FALSE
               vv
clus            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  LOR MUTATED                              4             0
  LOR WILD-TYPE                           52             2
               vv
clus            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  LOR MUTATED                                                                          0
  LOR WILD-TYPE                                                                        1
               vv
clus            LEIOMYOSARCOMA (LMS)
  LOR MUTATED                      1
  LOR WILD-TYPE                   97
               vv
clus            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  LOR MUTATED                                                  0
  LOR WILD-TYPE                                                8
               vv
clus            MYXOFIBROSARCOMA
  LOR MUTATED                  0
  LOR WILD-TYPE               22
               vv
clus            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  LOR MUTATED                                                          0
  LOR WILD-TYPE                                                       29
               vv
clus            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  LOR MUTATED                                          0
  LOR WILD-TYPE                                        2
               vv
clus            SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  LOR MUTATED                             0                             1
  LOR WILD-TYPE                           2                             5
               vv
clus            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  LOR MUTATED                                            0
  LOR WILD-TYPE                                         21
D12V6, multiclass
                                                                          clus
vv                                                                         LOR MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                       4
  DESMOID TUMOR                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS           0
  LEIOMYOSARCOMA (LMS)                                                               1
  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                                                      1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                         0
                                                                          clus
vv                                                                         LOR WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                        52
  DESMOID TUMOR                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             1
  LEIOMYOSARCOMA (LMS)                                                                97
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     8
  MYXOFIBROSARCOMA                                                                    22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                            29
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                        5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          21
[1] 11  2
[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
  LOR MUTATED     5   0   0   1
  LOR WILD-TYPE 144  65   9  22
D12V7, multiclass
    clus
vv   LOR MUTATED LOR WILD-TYPE
  R0           5           144
  R1           0            65
  R2           0             9
  RX           1            22
[1] 4 2
[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
  LOR MUTATED       0                         0     6
  LOR WILD-TYPE     5                        18   211
D12V8, multiclass
                           clus
vv                          LOR MUTATED LOR WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            18
  WHITE                               6           211
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
               cls
clus              0   1
  LOR MUTATED     0   5
  LOR WILD-TYPE   5 208
[1] "tbl2"
               cls
clus            [,1] [,2]
  LOR MUTATED      0    5
  LOR WILD-TYPE    5  208
                        clus
vv                       LOR MUTATED LOR WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           5           208
[1] 2 2
[1] FALSE

Clustering(13) Variable = R3HDM1 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  R3HDM1 MUTATED     3   1
  R3HDM1 WILD-TYPE 151  92
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               4              243 
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
               1               92 
$`R3HDM1 MUTATED`
TCGA-DX-AB2H TCGA-3B-A9HT TCGA-QC-A7B5 TCGA-X6-A8C4 
       15.85        54.74        13.08        20.65 

$`R3HDM1 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2J 
       15.22        23.70        17.95        14.43        14.07        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       12.07       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
       17.75         8.28        20.94        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       35.08        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       44.91        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        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-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
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-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       41.00        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       20.05         9.34        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       40.77        51.91       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        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-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      106.55        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI 
       34.88         4.57        33.30         0.72        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA 
        3.22         1.38        19.89        25.22       171.09        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       53.33        62.17       123.78        17.36        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       63.81        16.41        35.28        30.31        25.41         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
       21.73        19.73        14.99        17.98        22.39        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR 
        7.36       122.96        37.55        38.63        81.01        26.73 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       17.65         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
       37.12       130.32        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       19.63        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 
        4.80        84.79        38.27        65.46        56.61        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        8.58        63.35        26.43        45.34        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
           13.08             0.49 
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
           54.74           171.09 
  R3HDM1 MUTATED R3HDM1 WILD-TYPE 
           18.25            31.13 
[1] "13.1 - 54.7 (18.2)" "0.5 - 171.1 (31.1)"
[1] "hr=" "1.1"
D13V2, continuous
                  vv
clus               CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  R3HDM1 MUTATED                0                  0                   0
  R3HDM1 WILD-TYPE              1                  7                   2
                  vv
clus               CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  R3HDM1 MUTATED                     0                             0
  R3HDM1 WILD-TYPE                   1                             1
                  vv
clus               GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  R3HDM1 MUTATED                       0                      0
  R3HDM1 WILD-TYPE                     1                     26
                  vv
clus               HEAD AND NECK - HEAD HEAD AND NECK - NECK
  R3HDM1 MUTATED                      1                    0
  R3HDM1 WILD-TYPE                    1                    1
                  vv
clus               HEAD AND NECK - OTHER (PLEASE SPECIFY
  R3HDM1 MUTATED                                       1
  R3HDM1 WILD-TYPE                                     1
                  vv
clus               LOWER ABDOMINAL/PELVIC - BLADDER
  R3HDM1 MUTATED                                  0
  R3HDM1 WILD-TYPE                                1
                  vv
clus               LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  R3HDM1 MUTATED                                                0
  R3HDM1 WILD-TYPE                                              2
                  vv
clus               LOWER ABDOMINAL/PELVIC - PELVIC
  R3HDM1 MUTATED                                 0
  R3HDM1 WILD-TYPE                              11
                  vv
clus               LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  R3HDM1 MUTATED                                         0
  R3HDM1 WILD-TYPE                                       2
                  vv
clus               LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  R3HDM1 MUTATED                              0                       0
  R3HDM1 WILD-TYPE                            4                       2
                  vv
clus               LOWER EXTREMITY - LOWER LEG/CALF
  R3HDM1 MUTATED                                  1
  R3HDM1 WILD-TYPE                               15
                  vv
clus               LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  R3HDM1 MUTATED                                         0
  R3HDM1 WILD-TYPE                                       3
                  vv
clus               LOWER EXTREMITY - THIGH/KNEE
  R3HDM1 MUTATED                              0
  R3HDM1 WILD-TYPE                           43
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - COLON
  R3HDM1 MUTATED                                         0
  R3HDM1 WILD-TYPE                                       4
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  R3HDM1 MUTATED                                           0
  R3HDM1 WILD-TYPE                                         2
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  R3HDM1 MUTATED                                                  0
  R3HDM1 WILD-TYPE                                                5
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  R3HDM1 MUTATED                                          0
  R3HDM1 WILD-TYPE                                        7
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  R3HDM1 MUTATED                                                         0
  R3HDM1 WILD-TYPE                                                       2
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  R3HDM1 MUTATED                                            0
  R3HDM1 WILD-TYPE                                          1
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  R3HDM1 MUTATED                                                   1
  R3HDM1 WILD-TYPE                                                70
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  R3HDM1 MUTATED                                                    0
  R3HDM1 WILD-TYPE                                                  3
                  vv
clus               SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  R3HDM1 MUTATED                                    0                        0
  R3HDM1 WILD-TYPE                                  2                        5
                  vv
clus               SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  R3HDM1 MUTATED                             0                         0
  R3HDM1 WILD-TYPE                           3                         1
                  vv
clus               UPPER EXTREMITY - SHOULDER/AXILLA
  R3HDM1 MUTATED                                   0
  R3HDM1 WILD-TYPE                                 7
                  vv
clus               UPPER EXTREMITY - UPPER ARM/ELBOW
  R3HDM1 MUTATED                                   0
  R3HDM1 WILD-TYPE                                 5
D13V3, multiclass
                                                         clus
vv                                                        R3HDM1 MUTATED
  CHEST - BREAST                                                       0
  CHEST - CHEST WALL                                                   0
  CHEST - LUNG/PLEURA                                                  0
  CHEST - MEDIASTINUM                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                        0
  GYNECOLOGICAL - OVARY                                                0
  GYNECOLOGICAL - UTERUS                                               0
  HEAD AND NECK - HEAD                                                 1
  HEAD AND NECK - NECK                                                 0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                1
  LOWER ABDOMINAL/PELVIC - BLADDER                                     0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                      0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                              0
  LOWER EXTREMITY - FOOT/ANKLE                                         0
  LOWER EXTREMITY - GROIN                                              0
  LOWER EXTREMITY - LOWER LEG/CALF                                     1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                              0
  LOWER EXTREMITY - THIGH/KNEE                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                              0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                            0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                     0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                             0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY              0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    1
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                   0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                   0
  SUPERFICIAL TRUNK - BACK                                             0
  SUPERFICIAL TRUNK - BUTTOCK                                          0
  SUPERFICIAL TRUNK - FLANK                                            0
  UPPER EXTREMITY - SHOULDER/AXILLA                                    0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                    0
                                                         clus
vv                                                        R3HDM1 WILD-TYPE
  CHEST - BREAST                                                         1
  CHEST - CHEST WALL                                                     7
  CHEST - LUNG/PLEURA                                                    2
  CHEST - MEDIASTINUM                                                    1
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                26
  HEAD AND NECK - HEAD                                                   1
  HEAD AND NECK - NECK                                                   1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  1
  LOWER ABDOMINAL/PELVIC - BLADDER                                       1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                       11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                2
  LOWER EXTREMITY - FOOT/ANKLE                                           4
  LOWER EXTREMITY - GROIN                                                2
  LOWER EXTREMITY - LOWER LEG/CALF                                      15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                3
  LOWER EXTREMITY - THIGH/KNEE                                          43
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     70
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               5
  SUPERFICIAL TRUNK - BUTTOCK                                            3
  SUPERFICIAL TRUNK - FLANK                                              1
  UPPER EXTREMITY - SHOULDER/AXILLA                                      7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                  cls
clus                 0   1
  R3HDM1 MUTATED     2   2
  R3HDM1 WILD-TYPE 131 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM1 MUTATED      2    2
  R3HDM1 WILD-TYPE  131  112
        clus
vv       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  FEMALE              2              131
  MALE                2              112
[1] 2 2
[1] FALSE
D13V5, binary
                  cls
clus                 0   1
  R3HDM1 MUTATED     2   2
  R3HDM1 WILD-TYPE 168  69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM1 MUTATED      2    2
  R3HDM1 WILD-TYPE  168   69
     clus
vv    R3HDM1 MUTATED R3HDM1 WILD-TYPE
  NO               2              168
  YES              2               69
[1] 2 2
[1] FALSE
                  vv
clus               DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  R3HDM1 MUTATED                              1             0
  R3HDM1 WILD-TYPE                           55             2
                  vv
clus               GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  R3HDM1 MUTATED                                                                          0
  R3HDM1 WILD-TYPE                                                                        1
                  vv
clus               LEIOMYOSARCOMA (LMS)
  R3HDM1 MUTATED                      1
  R3HDM1 WILD-TYPE                   97
                  vv
clus               MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  R3HDM1 MUTATED                                                  0
  R3HDM1 WILD-TYPE                                                8
                  vv
clus               MYXOFIBROSARCOMA
  R3HDM1 MUTATED                  0
  R3HDM1 WILD-TYPE               22
                  vv
clus               PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  R3HDM1 MUTATED                                                          1
  R3HDM1 WILD-TYPE                                                       28
                  vv
clus               SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  R3HDM1 MUTATED                                          0
  R3HDM1 WILD-TYPE                                        2
                  vv
clus               SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  R3HDM1 MUTATED                             0                             0
  R3HDM1 WILD-TYPE                           2                             6
                  vv
clus               UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  R3HDM1 MUTATED                                            1
  R3HDM1 WILD-TYPE                                         20
D13V6, multiclass
                                                                          clus
vv                                                                         R3HDM1 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          1
  DESMOID TUMOR                                                                         0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS              0
  LEIOMYOSARCOMA (LMS)                                                                  1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      0
  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)                                            1
                                                                          clus
vv                                                                         R3HDM1 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                           55
  DESMOID TUMOR                                                                           2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                1
  LEIOMYOSARCOMA (LMS)                                                                   97
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        8
  MYXOFIBROSARCOMA                                                                       22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               28
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                2
  SYNOVIAL SARCOMA - BIPHASIC                                                             2
  SYNOVIAL SARCOMA - MONOPHASIC                                                           6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             20
[1] 11  2
[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
  R3HDM1 MUTATED     2   1   0   1
  R3HDM1 WILD-TYPE 147  64   9  22
D13V7, multiclass
    clus
vv   R3HDM1 MUTATED R3HDM1 WILD-TYPE
  R0              2              147
  R1              1               64
  R2              0                9
  RX              1               22
[1] 4 2
[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
  R3HDM1 MUTATED       0                         0     4
  R3HDM1 WILD-TYPE     5                        18   213
D13V8, multiclass
                           clus
vv                          R3HDM1 MUTATED R3HDM1 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0               18
  WHITE                                  4              213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                  cls
clus                 0   1
  R3HDM1 MUTATED     0   4
  R3HDM1 WILD-TYPE   5 209
[1] "tbl2"
                  cls
clus               [,1] [,2]
  R3HDM1 MUTATED      0    4
  R3HDM1 WILD-TYPE    5  209
                        clus
vv                       R3HDM1 MUTATED R3HDM1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              209
[1] 2 2
[1] FALSE

Clustering(14) Variable = NF1 MUTATION ANALYSIS
D14V1, survival
               sevent
clus2             0   1
  NF1 MUTATED     5   4
  NF1 WILD-TYPE 149  89
  NF1 MUTATED NF1 WILD-TYPE 
            9           238 
  NF1 MUTATED NF1 WILD-TYPE 
            4            89 
$`NF1 MUTATED`
TCGA-DX-A8BP TCGA-DX-AB2X TCGA-DX-AB30 TCGA-3B-A9HT TCGA-DX-A6BG TCGA-QQ-A5VC 
       14.07        13.28        22.85        54.74        36.85        35.90 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-SI-A71P 
       64.77        10.52        25.35 

$`NF1 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J 
       15.22        23.70        17.95        14.43        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       12.07       106.45       101.98        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK 
       32.15        16.60        37.02        12.62        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       28.21       159.29        22.62        11.70        17.75         8.28 
TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
       20.94        17.52        26.17        41.49        35.08        50.01 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU 
       19.69        53.49        68.55        88.57        44.91        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       14.37        42.84        10.32        38.47        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       26.56         0.56        14.04        32.71        68.61        12.85 
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-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 
       74.66         5.26        76.41        66.87         6.28        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-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       51.02         4.54        14.99        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       50.43        34.88        85.45         9.73        45.99        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       35.28        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-A6BE 
       37.58        15.95        37.41        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ 
       31.96        26.99         3.06        41.00        16.87        86.30 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN 
       64.21       101.23        21.30        34.49        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR 
       45.14        47.87        38.17        40.77        51.91       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        1.15        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       66.74         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       15.48         8.05        67.63        34.88         4.57        33.30 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
        0.72        80.48        19.53         3.22         1.38        19.89 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       25.22       171.09        13.58        85.97         5.92        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        1.05         3.91       101.26        53.33        62.17       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
       17.36        23.38         5.19        63.81        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       30.31        25.41         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        22.39        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       38.63        81.01        26.73        13.08        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-RN-A68Q 
       46.82        18.08        48.59        37.12       130.32         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B 
       16.77        18.94         3.88        22.82        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       19.63        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 
        4.80        84.79        38.27        65.46        56.61        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        8.58        63.35        26.43        45.34        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       19.17        20.65        50.86        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  NF1 MUTATED NF1 WILD-TYPE 
        10.52          0.49 
  NF1 MUTATED NF1 WILD-TYPE 
        64.77        171.09 
  NF1 MUTATED NF1 WILD-TYPE 
       25.350        30.985 
[1] "10.5 - 64.8 (25.4)" "0.5 - 171.1 (31.0)"
[1] "hr=" "1.4"
D14V2, continuous
               vv
clus            CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  NF1 MUTATED                0                  0                   0
  NF1 WILD-TYPE              1                  7                   2
               vv
clus            CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  NF1 MUTATED                     0                             1
  NF1 WILD-TYPE                   1                             0
               vv
clus            GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  NF1 MUTATED                       0                      0
  NF1 WILD-TYPE                     1                     26
               vv
clus            HEAD AND NECK - HEAD HEAD AND NECK - NECK
  NF1 MUTATED                      0                    0
  NF1 WILD-TYPE                    2                    1
               vv
clus            HEAD AND NECK - OTHER (PLEASE SPECIFY
  NF1 MUTATED                                       1
  NF1 WILD-TYPE                                     1
               vv
clus            LOWER ABDOMINAL/PELVIC - BLADDER
  NF1 MUTATED                                  0
  NF1 WILD-TYPE                                1
               vv
clus            LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  NF1 MUTATED                                                0
  NF1 WILD-TYPE                                              2
               vv
clus            LOWER ABDOMINAL/PELVIC - PELVIC
  NF1 MUTATED                                 0
  NF1 WILD-TYPE                              11
               vv
clus            LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  NF1 MUTATED                                         0
  NF1 WILD-TYPE                                       2
               vv
clus            LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  NF1 MUTATED                              0                       0
  NF1 WILD-TYPE                            4                       2
               vv
clus            LOWER EXTREMITY - LOWER LEG/CALF
  NF1 MUTATED                                  1
  NF1 WILD-TYPE                               15
               vv
clus            LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  NF1 MUTATED                                         0
  NF1 WILD-TYPE                                       3
               vv
clus            LOWER EXTREMITY - THIGH/KNEE
  NF1 MUTATED                              3
  NF1 WILD-TYPE                           40
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - COLON
  NF1 MUTATED                                         0
  NF1 WILD-TYPE                                       4
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  NF1 MUTATED                                           0
  NF1 WILD-TYPE                                         2
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  NF1 MUTATED                                                  0
  NF1 WILD-TYPE                                                5
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  NF1 MUTATED                                          0
  NF1 WILD-TYPE                                        7
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  NF1 MUTATED                                                         0
  NF1 WILD-TYPE                                                       2
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  NF1 MUTATED                                            0
  NF1 WILD-TYPE                                          1
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  NF1 MUTATED                                                   1
  NF1 WILD-TYPE                                                70
               vv
clus            RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  NF1 MUTATED                                                    0
  NF1 WILD-TYPE                                                  3
               vv
clus            SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  NF1 MUTATED                                    0                        1
  NF1 WILD-TYPE                                  2                        4
               vv
clus            SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  NF1 MUTATED                             0                         0
  NF1 WILD-TYPE                           3                         1
               vv
clus            UPPER EXTREMITY - SHOULDER/AXILLA
  NF1 MUTATED                                   0
  NF1 WILD-TYPE                                 7
               vv
clus            UPPER EXTREMITY - UPPER ARM/ELBOW
  NF1 MUTATED                                   0
  NF1 WILD-TYPE                                 5
D14V3, multiclass
                                                         clus
vv                                                        NF1 MUTATED
  CHEST - BREAST                                                    0
  CHEST - CHEST WALL                                                0
  CHEST - LUNG/PLEURA                                               0
  CHEST - MEDIASTINUM                                               0
  CHEST - OTHER (PLEASE SPECIFY                                     1
  GYNECOLOGICAL - OVARY                                             0
  GYNECOLOGICAL - UTERUS                                            0
  HEAD AND NECK - HEAD                                              0
  HEAD AND NECK - NECK                                              0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                             1
  LOWER ABDOMINAL/PELVIC - BLADDER                                  0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                    0
  LOWER ABDOMINAL/PELVIC - PELVIC                                   0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                           0
  LOWER EXTREMITY - FOOT/ANKLE                                      0
  LOWER EXTREMITY - GROIN                                           0
  LOWER EXTREMITY - LOWER LEG/CALF                                  1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                           0
  LOWER EXTREMITY - THIGH/KNEE                                      3
  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 - PANCREAS                        0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                 1
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                0
  SUPERFICIAL TRUNK - BACK                                          1
  SUPERFICIAL TRUNK - BUTTOCK                                       0
  SUPERFICIAL TRUNK - FLANK                                         0
  UPPER EXTREMITY - SHOULDER/AXILLA                                 0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                 0
                                                         clus
vv                                                        NF1 WILD-TYPE
  CHEST - BREAST                                                      1
  CHEST - CHEST WALL                                                  7
  CHEST - LUNG/PLEURA                                                 2
  CHEST - MEDIASTINUM                                                 1
  CHEST - OTHER (PLEASE SPECIFY                                       0
  GYNECOLOGICAL - OVARY                                               1
  GYNECOLOGICAL - UTERUS                                             26
  HEAD AND NECK - HEAD                                                2
  HEAD AND NECK - NECK                                                1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                               1
  LOWER ABDOMINAL/PELVIC - BLADDER                                    1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                      2
  LOWER ABDOMINAL/PELVIC - PELVIC                                    11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                             2
  LOWER EXTREMITY - FOOT/ANKLE                                        4
  LOWER EXTREMITY - GROIN                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                   15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             3
  LOWER EXTREMITY - THIGH/KNEE                                       40
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                             4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                           2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                    5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                            7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY             2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                          1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                  70
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                  3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                  2
  SUPERFICIAL TRUNK - BACK                                            4
  SUPERFICIAL TRUNK - BUTTOCK                                         3
  SUPERFICIAL TRUNK - FLANK                                           1
  UPPER EXTREMITY - SHOULDER/AXILLA                                   7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                   5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
               cls
clus              0   1
  NF1 MUTATED     4   5
  NF1 WILD-TYPE 129 109
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      4    5
  NF1 WILD-TYPE  129  109
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE           4           129
  MALE             5           109
[1] 2 2
[1] FALSE
D14V5, binary
               cls
clus              0   1
  NF1 MUTATED     5   4
  NF1 WILD-TYPE 165  67
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      5    4
  NF1 WILD-TYPE  165   67
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            5           165
  YES           4            67
[1] 2 2
[1] FALSE
               vv
clus            DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  NF1 MUTATED                              1             0
  NF1 WILD-TYPE                           55             2
               vv
clus            GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  NF1 MUTATED                                                                          0
  NF1 WILD-TYPE                                                                        1
               vv
clus            LEIOMYOSARCOMA (LMS)
  NF1 MUTATED                      2
  NF1 WILD-TYPE                   96
               vv
clus            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  NF1 MUTATED                                                  3
  NF1 WILD-TYPE                                                5
               vv
clus            MYXOFIBROSARCOMA
  NF1 MUTATED                  1
  NF1 WILD-TYPE               21
               vv
clus            PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  NF1 MUTATED                                                          2
  NF1 WILD-TYPE                                                       27
               vv
clus            SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  NF1 MUTATED                                          0
  NF1 WILD-TYPE                                        2
               vv
clus            SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  NF1 MUTATED                             0                             0
  NF1 WILD-TYPE                           2                             6
               vv
clus            UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  NF1 MUTATED                                            0
  NF1 WILD-TYPE                                         21
D14V6, multiclass
                                                                          clus
vv                                                                         NF1 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                       1
  DESMOID TUMOR                                                                      0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS           0
  LEIOMYOSARCOMA (LMS)                                                               2
  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)                                         0
                                                                          clus
vv                                                                         NF1 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                        55
  DESMOID TUMOR                                                                        2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             1
  LEIOMYOSARCOMA (LMS)                                                                96
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     5
  MYXOFIBROSARCOMA                                                                    21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                            27
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                             2
  SYNOVIAL SARCOMA - BIPHASIC                                                          2
  SYNOVIAL SARCOMA - MONOPHASIC                                                        6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          21
[1] 11  2
[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
  NF1 MUTATED     5   1   0   3
  NF1 WILD-TYPE 144  64   9  20
D14V7, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0           5           144
  R1           1            64
  R2           0             9
  RX           3            20
[1] 4 2
[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
  NF1 MUTATED       0                         0     9
  NF1 WILD-TYPE     5                        18   208
D14V8, multiclass
                           clus
vv                          NF1 MUTATED NF1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            18
  WHITE                               9           208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
               cls
clus              0   1
  NF1 MUTATED     0   9
  NF1 WILD-TYPE   5 204
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      0    9
  NF1 WILD-TYPE    5  204
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           9           204
[1] 2 2
[1] FALSE

Clustering(15) Variable = COL4A3 MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  COL4A3 MUTATED     4   0
  COL4A3 WILD-TYPE 150  93
  COL4A3 MUTATED COL4A3 WILD-TYPE 
               4              243 
  COL4A3 MUTATED COL4A3 WILD-TYPE 
               0               93 
$`COL4A3 MUTATED`
TCGA-DX-AB2H TCGA-DX-A6BA TCGA-QC-A7B5 TCGA-QQ-A8VD 
       15.85        82.68        13.08       130.32 

$`COL4A3 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2J 
       15.22        23.70        17.95        14.43        14.07        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       12.07       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
       17.75         8.28        20.94        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       35.08        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       38.47        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        68.61        12.85        45.11        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       85.02        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       79.17         9.04        49.05        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       41.00        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       20.05         9.34        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       40.77        51.91       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        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-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      106.55        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI 
       34.88         4.57        33.30         0.72        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA 
        3.22         1.38        19.89        25.22       171.09        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       53.33        62.17       123.78        17.36        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       63.81        16.41        35.28        30.31        25.41         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
       21.73        19.73        14.99        17.98        22.39        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR 
        7.36       122.96        37.55        38.63        81.01        26.73 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       17.65         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
       37.12        64.77        10.52         0.72        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        3.88        22.82        25.35        32.75         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22        13.41        10.72        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB 
       84.79        38.27        65.46        56.61        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        26.43        45.34        30.84        35.18        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       20.65        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  COL4A3 MUTATED COL4A3 WILD-TYPE 
           13.08             0.49 
  COL4A3 MUTATED COL4A3 WILD-TYPE 
          130.32           171.09 
  COL4A3 MUTATED COL4A3 WILD-TYPE 
          49.265           30.840 
[1] "13.1 - 130.3 (49.3)" "0.5 - 171.1 (30.8)" 
[1] "hr="     "9300000"
D15V2, continuous
                  vv
clus               CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  COL4A3 MUTATED                0                  0                   0
  COL4A3 WILD-TYPE              1                  7                   2
                  vv
clus               CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  COL4A3 MUTATED                     0                             0
  COL4A3 WILD-TYPE                   1                             1
                  vv
clus               GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  COL4A3 MUTATED                       0                      0
  COL4A3 WILD-TYPE                     1                     26
                  vv
clus               HEAD AND NECK - HEAD HEAD AND NECK - NECK
  COL4A3 MUTATED                      1                    0
  COL4A3 WILD-TYPE                    1                    1
                  vv
clus               HEAD AND NECK - OTHER (PLEASE SPECIFY
  COL4A3 MUTATED                                       0
  COL4A3 WILD-TYPE                                     2
                  vv
clus               LOWER ABDOMINAL/PELVIC - BLADDER
  COL4A3 MUTATED                                  0
  COL4A3 WILD-TYPE                                1
                  vv
clus               LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  COL4A3 MUTATED                                                0
  COL4A3 WILD-TYPE                                              2
                  vv
clus               LOWER ABDOMINAL/PELVIC - PELVIC
  COL4A3 MUTATED                                 1
  COL4A3 WILD-TYPE                              10
                  vv
clus               LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  COL4A3 MUTATED                                         0
  COL4A3 WILD-TYPE                                       2
                  vv
clus               LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  COL4A3 MUTATED                              0                       0
  COL4A3 WILD-TYPE                            4                       2
                  vv
clus               LOWER EXTREMITY - LOWER LEG/CALF
  COL4A3 MUTATED                                  0
  COL4A3 WILD-TYPE                               16
                  vv
clus               LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  COL4A3 MUTATED                                         0
  COL4A3 WILD-TYPE                                       3
                  vv
clus               LOWER EXTREMITY - THIGH/KNEE
  COL4A3 MUTATED                              0
  COL4A3 WILD-TYPE                           43
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - COLON
  COL4A3 MUTATED                                         0
  COL4A3 WILD-TYPE                                       4
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  COL4A3 MUTATED                                           0
  COL4A3 WILD-TYPE                                         2
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  COL4A3 MUTATED                                                  1
  COL4A3 WILD-TYPE                                                4
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  COL4A3 MUTATED                                          0
  COL4A3 WILD-TYPE                                        7
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  COL4A3 MUTATED                                                         0
  COL4A3 WILD-TYPE                                                       2
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  COL4A3 MUTATED                                            0
  COL4A3 WILD-TYPE                                          1
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  COL4A3 MUTATED                                                   1
  COL4A3 WILD-TYPE                                                70
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  COL4A3 MUTATED                                                    0
  COL4A3 WILD-TYPE                                                  3
                  vv
clus               SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  COL4A3 MUTATED                                    0                        0
  COL4A3 WILD-TYPE                                  2                        5
                  vv
clus               SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  COL4A3 MUTATED                             0                         0
  COL4A3 WILD-TYPE                           3                         1
                  vv
clus               UPPER EXTREMITY - SHOULDER/AXILLA
  COL4A3 MUTATED                                   0
  COL4A3 WILD-TYPE                                 7
                  vv
clus               UPPER EXTREMITY - UPPER ARM/ELBOW
  COL4A3 MUTATED                                   0
  COL4A3 WILD-TYPE                                 5
D15V3, multiclass
                                                         clus
vv                                                        COL4A3 MUTATED
  CHEST - BREAST                                                       0
  CHEST - CHEST WALL                                                   0
  CHEST - LUNG/PLEURA                                                  0
  CHEST - MEDIASTINUM                                                  0
  CHEST - OTHER (PLEASE SPECIFY                                        0
  GYNECOLOGICAL - OVARY                                                0
  GYNECOLOGICAL - UTERUS                                               0
  HEAD AND NECK - HEAD                                                 1
  HEAD AND NECK - NECK                                                 0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                0
  LOWER ABDOMINAL/PELVIC - BLADDER                                     0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                       0
  LOWER ABDOMINAL/PELVIC - PELVIC                                      1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                              0
  LOWER EXTREMITY - FOOT/ANKLE                                         0
  LOWER EXTREMITY - GROIN                                              0
  LOWER EXTREMITY - LOWER LEG/CALF                                     0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                              0
  LOWER EXTREMITY - THIGH/KNEE                                         0
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                              0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                            0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                     1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                             0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY              0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                           0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    1
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                   0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                   0
  SUPERFICIAL TRUNK - BACK                                             0
  SUPERFICIAL TRUNK - BUTTOCK                                          0
  SUPERFICIAL TRUNK - FLANK                                            0
  UPPER EXTREMITY - SHOULDER/AXILLA                                    0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                    0
                                                         clus
vv                                                        COL4A3 WILD-TYPE
  CHEST - BREAST                                                         1
  CHEST - CHEST WALL                                                     7
  CHEST - LUNG/PLEURA                                                    2
  CHEST - MEDIASTINUM                                                    1
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                26
  HEAD AND NECK - HEAD                                                   1
  HEAD AND NECK - NECK                                                   1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  2
  LOWER ABDOMINAL/PELVIC - BLADDER                                       1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                       10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                2
  LOWER EXTREMITY - FOOT/ANKLE                                           4
  LOWER EXTREMITY - GROIN                                                2
  LOWER EXTREMITY - LOWER LEG/CALF                                      16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                3
  LOWER EXTREMITY - THIGH/KNEE                                          43
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     70
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               5
  SUPERFICIAL TRUNK - BUTTOCK                                            3
  SUPERFICIAL TRUNK - FLANK                                              1
  UPPER EXTREMITY - SHOULDER/AXILLA                                      7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                  cls
clus                 0   1
  COL4A3 MUTATED     2   2
  COL4A3 WILD-TYPE 131 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A3 MUTATED      2    2
  COL4A3 WILD-TYPE  131  112
        clus
vv       COL4A3 MUTATED COL4A3 WILD-TYPE
  FEMALE              2              131
  MALE                2              112
[1] 2 2
[1] FALSE
D15V5, binary
                  cls
clus                 0   1
  COL4A3 MUTATED     4   0
  COL4A3 WILD-TYPE 166  71
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A3 MUTATED      4    0
  COL4A3 WILD-TYPE  166   71
     clus
vv    COL4A3 MUTATED COL4A3 WILD-TYPE
  NO               4              166
  YES              0               71
[1] 2 2
[1] FALSE
                  vv
clus               DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  COL4A3 MUTATED                              1             1
  COL4A3 WILD-TYPE                           55             1
                  vv
clus               GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  COL4A3 MUTATED                                                                          0
  COL4A3 WILD-TYPE                                                                        1
                  vv
clus               LEIOMYOSARCOMA (LMS)
  COL4A3 MUTATED                      1
  COL4A3 WILD-TYPE                   97
                  vv
clus               MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  COL4A3 MUTATED                                                  0
  COL4A3 WILD-TYPE                                                8
                  vv
clus               MYXOFIBROSARCOMA
  COL4A3 MUTATED                  0
  COL4A3 WILD-TYPE               22
                  vv
clus               PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  COL4A3 MUTATED                                                          1
  COL4A3 WILD-TYPE                                                       28
                  vv
clus               SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  COL4A3 MUTATED                                          0
  COL4A3 WILD-TYPE                                        2
                  vv
clus               SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  COL4A3 MUTATED                             0                             0
  COL4A3 WILD-TYPE                           2                             6
                  vv
clus               UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  COL4A3 MUTATED                                            0
  COL4A3 WILD-TYPE                                         21
D15V6, multiclass
                                                                          clus
vv                                                                         COL4A3 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          1
  DESMOID TUMOR                                                                         1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS              0
  LEIOMYOSARCOMA (LMS)                                                                  1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      0
  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                                                                         COL4A3 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                           55
  DESMOID TUMOR                                                                           1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                1
  LEIOMYOSARCOMA (LMS)                                                                   97
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        8
  MYXOFIBROSARCOMA                                                                       22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               28
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                2
  SYNOVIAL SARCOMA - BIPHASIC                                                             2
  SYNOVIAL SARCOMA - MONOPHASIC                                                           6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             21
[1] 11  2
[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
  COL4A3 MUTATED     2   0   0   2
  COL4A3 WILD-TYPE 147  65   9  21
D15V7, multiclass
    clus
vv   COL4A3 MUTATED COL4A3 WILD-TYPE
  R0              2              147
  R1              0               65
  R2              0                9
  RX              2               21
[1] 4 2
[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
  COL4A3 MUTATED       0                         0     4
  COL4A3 WILD-TYPE     5                        18   213
D15V8, multiclass
                           clus
vv                          COL4A3 MUTATED COL4A3 WILD-TYPE
  ASIAN                                  0                5
  BLACK OR AFRICAN AMERICAN              0               18
  WHITE                                  4              213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                  cls
clus                 0   1
  COL4A3 MUTATED     0   4
  COL4A3 WILD-TYPE   5 209
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A3 MUTATED      0    4
  COL4A3 WILD-TYPE    5  209
                        clus
vv                       COL4A3 MUTATED COL4A3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              209
[1] 2 2
[1] FALSE

Clustering(16) Variable = MEGF9 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  MEGF9 MUTATED     3   0
  MEGF9 WILD-TYPE 151  93
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             244 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              0              93 
$`MEGF9 MUTATED`
TCGA-DX-A6YR TCGA-QC-A7B5 TCGA-WK-A8XS 
       41.00        13.08        84.79 

$`MEGF9 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       15.22        23.70        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       40.60        12.07       106.45        13.28        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
       30.51        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
       11.70        17.75         8.28        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       41.49        35.08        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       88.57        44.91        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       10.32        38.47        36.03        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-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87         6.28        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        73.87        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       85.45         9.73        45.99        24.26        35.28        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-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       26.99         3.06        16.87        86.30        64.21       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       21.30        34.49        62.20        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.20        20.05         9.34        61.97        45.14        47.87 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        40.77        51.91       150.35        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       36.69        60.66        19.43         6.58         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.00        15.72        65.98        86.10        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       77.88       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV 
       67.63        34.88         4.57        33.30         0.72        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 
       19.53         3.22         1.38        19.89        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        85.97         5.92        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
      101.26        53.33        62.17       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
        5.19        63.81        16.41        35.28        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       10.45         7.36       122.96        37.55        38.63        81.01 
TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       26.73        17.65         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       35.90        37.12       130.32        64.77        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       16.77        18.94         3.88        22.82        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D 
        8.61        19.63        13.22        13.41        10.72        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 
       11.93         4.80        38.27        65.46        56.61        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        8.58        63.35        26.43        45.34        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       19.17        20.65        50.86        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  MEGF9 MUTATED MEGF9 WILD-TYPE 
          13.08            0.49 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
          84.79          171.09 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
         41.000          30.675 
[1] "13.1 - 84.8 (41.0)" "0.5 - 171.1 (30.7)"
[1] "hr="     "9100000"
D16V2, continuous
                 vv
clus              CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  MEGF9 MUTATED                0                  1                   0
  MEGF9 WILD-TYPE              1                  6                   2
                 vv
clus              CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  MEGF9 MUTATED                     0                             0
  MEGF9 WILD-TYPE                   1                             1
                 vv
clus              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  MEGF9 MUTATED                       0                      0
  MEGF9 WILD-TYPE                     1                     26
                 vv
clus              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  MEGF9 MUTATED                      1                    0
  MEGF9 WILD-TYPE                    1                    1
                 vv
clus              HEAD AND NECK - OTHER (PLEASE SPECIFY
  MEGF9 MUTATED                                       0
  MEGF9 WILD-TYPE                                     2
                 vv
clus              LOWER ABDOMINAL/PELVIC - BLADDER
  MEGF9 MUTATED                                  0
  MEGF9 WILD-TYPE                                1
                 vv
clus              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  MEGF9 MUTATED                                                0
  MEGF9 WILD-TYPE                                              2
                 vv
clus              LOWER ABDOMINAL/PELVIC - PELVIC
  MEGF9 MUTATED                                 0
  MEGF9 WILD-TYPE                              11
                 vv
clus              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  MEGF9 MUTATED                                         0
  MEGF9 WILD-TYPE                                       2
                 vv
clus              LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  MEGF9 MUTATED                              0                       0
  MEGF9 WILD-TYPE                            4                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  MEGF9 MUTATED                                  0
  MEGF9 WILD-TYPE                               16
                 vv
clus              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  MEGF9 MUTATED                                         0
  MEGF9 WILD-TYPE                                       3
                 vv
clus              LOWER EXTREMITY - THIGH/KNEE
  MEGF9 MUTATED                              0
  MEGF9 WILD-TYPE                           43
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  MEGF9 MUTATED                                         0
  MEGF9 WILD-TYPE                                       4
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  MEGF9 MUTATED                                           1
  MEGF9 WILD-TYPE                                         1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  MEGF9 MUTATED                                                  0
  MEGF9 WILD-TYPE                                                5
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  MEGF9 MUTATED                                          0
  MEGF9 WILD-TYPE                                        7
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  MEGF9 MUTATED                                                         0
  MEGF9 WILD-TYPE                                                       2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  MEGF9 MUTATED                                            0
  MEGF9 WILD-TYPE                                          1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  MEGF9 MUTATED                                                   0
  MEGF9 WILD-TYPE                                                71
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  MEGF9 MUTATED                                                    0
  MEGF9 WILD-TYPE                                                  3
                 vv
clus              SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  MEGF9 MUTATED                                    0                        0
  MEGF9 WILD-TYPE                                  2                        5
                 vv
clus              SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  MEGF9 MUTATED                             0                         0
  MEGF9 WILD-TYPE                           3                         1
                 vv
clus              UPPER EXTREMITY - SHOULDER/AXILLA
  MEGF9 MUTATED                                   0
  MEGF9 WILD-TYPE                                 7
                 vv
clus              UPPER EXTREMITY - UPPER ARM/ELBOW
  MEGF9 MUTATED                                   0
  MEGF9 WILD-TYPE                                 5
D16V3, multiclass
                                                         clus
vv                                                        MEGF9 MUTATED
  CHEST - BREAST                                                      0
  CHEST - CHEST WALL                                                  1
  CHEST - LUNG/PLEURA                                                 0
  CHEST - MEDIASTINUM                                                 0
  CHEST - OTHER (PLEASE SPECIFY                                       0
  GYNECOLOGICAL - OVARY                                               0
  GYNECOLOGICAL - UTERUS                                              0
  HEAD AND NECK - HEAD                                                1
  HEAD AND NECK - NECK                                                0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                               0
  LOWER ABDOMINAL/PELVIC - BLADDER                                    0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                      0
  LOWER ABDOMINAL/PELVIC - PELVIC                                     0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                             0
  LOWER EXTREMITY - FOOT/ANKLE                                        0
  LOWER EXTREMITY - GROIN                                             0
  LOWER EXTREMITY - LOWER LEG/CALF                                    0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             0
  LOWER EXTREMITY - THIGH/KNEE                                        0
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                             0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                           1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                    0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                            0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY             0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                          0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   0
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                  0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                  0
  SUPERFICIAL TRUNK - BACK                                            0
  SUPERFICIAL TRUNK - BUTTOCK                                         0
  SUPERFICIAL TRUNK - FLANK                                           0
  UPPER EXTREMITY - SHOULDER/AXILLA                                   0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                   0
                                                         clus
vv                                                        MEGF9 WILD-TYPE
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    6
  CHEST - LUNG/PLEURA                                                   2
  CHEST - MEDIASTINUM                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                               26
  HEAD AND NECK - HEAD                                                  1
  HEAD AND NECK - NECK                                                  1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 2
  LOWER ABDOMINAL/PELVIC - BLADDER                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                      11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               2
  LOWER EXTREMITY - FOOT/ANKLE                                          4
  LOWER EXTREMITY - GROIN                                               2
  LOWER EXTREMITY - LOWER LEG/CALF                                     16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         43
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    71
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              5
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                     7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                 cls
clus                0   1
  MEGF9 MUTATED     1   2
  MEGF9 WILD-TYPE 132 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF9 MUTATED      1    2
  MEGF9 WILD-TYPE  132  112
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  FEMALE             1             132
  MALE               2             112
[1] 2 2
[1] FALSE
D16V5, binary
                 cls
clus                0   1
  MEGF9 MUTATED     2   1
  MEGF9 WILD-TYPE 168  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF9 MUTATED      2    1
  MEGF9 WILD-TYPE  168   70
     clus
vv    MEGF9 MUTATED MEGF9 WILD-TYPE
  NO              2             168
  YES             1              70
[1] 2 2
[1] FALSE
                 vv
clus              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  MEGF9 MUTATED                              0             0
  MEGF9 WILD-TYPE                           56             2
                 vv
clus              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  MEGF9 MUTATED                                                                          0
  MEGF9 WILD-TYPE                                                                        1
                 vv
clus              LEIOMYOSARCOMA (LMS)
  MEGF9 MUTATED                      1
  MEGF9 WILD-TYPE                   97
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  MEGF9 MUTATED                                                  0
  MEGF9 WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  MEGF9 MUTATED                  1
  MEGF9 WILD-TYPE               21
                 vv
clus              PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  MEGF9 MUTATED                                                          1
  MEGF9 WILD-TYPE                                                       28
                 vv
clus              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  MEGF9 MUTATED                                          0
  MEGF9 WILD-TYPE                                        2
                 vv
clus              SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  MEGF9 MUTATED                             0                             0
  MEGF9 WILD-TYPE                           2                             6
                 vv
clus              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  MEGF9 MUTATED                                            0
  MEGF9 WILD-TYPE                                         21
D16V6, multiclass
                                                                          clus
vv                                                                         MEGF9 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                         0
  DESMOID TUMOR                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             0
  LEIOMYOSARCOMA (LMS)                                                                 1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     0
  MYXOFIBROSARCOMA                                                                     1
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                             0
  SYNOVIAL SARCOMA - BIPHASIC                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                        0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           0
                                                                          clus
vv                                                                         MEGF9 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                          56
  DESMOID TUMOR                                                                          2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               1
  LEIOMYOSARCOMA (LMS)                                                                  97
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       8
  MYXOFIBROSARCOMA                                                                      21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              28
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                          6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            21
[1] 11  2
[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
  MEGF9 MUTATED     2   0   0   1
  MEGF9 WILD-TYPE 147  65   9  22
D16V7, multiclass
    clus
vv   MEGF9 MUTATED MEGF9 WILD-TYPE
  R0             2             147
  R1             0              65
  R2             0               9
  RX             1              22
[1] 4 2
[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
  MEGF9 MUTATED       0                         0     3
  MEGF9 WILD-TYPE     5                        18   214
D16V8, multiclass
                           clus
vv                          MEGF9 MUTATED MEGF9 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                 cls
clus                0   1
  MEGF9 MUTATED     0   3
  MEGF9 WILD-TYPE   5 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF9 MUTATED      0    3
  MEGF9 WILD-TYPE    5  210
                        clus
vv                       MEGF9 MUTATED MEGF9 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             210
[1] 2 2
[1] FALSE

Clustering(17) Variable = SCAP MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  SCAP MUTATED     3   0
  SCAP WILD-TYPE 151  93
  SCAP MUTATED SCAP WILD-TYPE 
             3            244 
  SCAP MUTATED SCAP WILD-TYPE 
             0             93 
$`SCAP MUTATED`
TCGA-K1-A6RT TCGA-QC-A7B5 TCGA-Z4-A9VC 
       17.36        13.08        13.38 

$`SCAP WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       15.22        23.70        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       40.60        12.07       106.45        13.28        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
       30.51        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
       11.70        17.75         8.28        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       41.49        35.08        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       88.57        44.91        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       10.32        38.47        36.03        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-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87         6.28        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        73.87        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       85.45         9.73        45.99        24.26        35.28        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-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       26.99         3.06        41.00        16.87        86.30        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
      101.23        21.30        34.49        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       29.49        48.20        20.05         9.34        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-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       40.44        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
        9.21        77.88       106.55        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       49.15        31.13        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
        8.05        67.63        34.88         4.57        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
       80.48        19.53         3.22         1.38        19.89        25.22 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
      171.09        13.58        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RU 
        3.91       101.26        53.33        62.17       123.78        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
        5.19        63.81        16.41        35.28        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       10.45         7.36       122.96        37.55        38.63        81.01 
TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       26.73        17.65         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       35.90        37.12       130.32        64.77        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       16.77        18.94         3.88        22.82        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D 
        8.61        19.63        13.22        13.41        10.72        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
       11.93         4.80        84.79        38.27        65.46        56.61 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD 
       22.62         8.58        63.35        26.43        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       35.18        19.17        20.65        50.86        29.46        27.32 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        15.95        15.98 

  SCAP MUTATED SCAP WILD-TYPE 
         13.08           0.49 
  SCAP MUTATED SCAP WILD-TYPE 
         17.36         171.09 
  SCAP MUTATED SCAP WILD-TYPE 
         13.38          31.33 
[1] "13.1 - 17.4 (13.4)" "0.5 - 171.1 (31.3)"
[1] "hr="     "3300000"
D17V2, continuous
                vv
clus             CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  SCAP MUTATED                0                  0                   0
  SCAP WILD-TYPE              1                  7                   2
                vv
clus             CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  SCAP MUTATED                     0                             0
  SCAP WILD-TYPE                   1                             1
                vv
clus             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  SCAP MUTATED                       0                      0
  SCAP WILD-TYPE                     1                     26
                vv
clus             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  SCAP MUTATED                      1                    0
  SCAP WILD-TYPE                    1                    1
                vv
clus             HEAD AND NECK - OTHER (PLEASE SPECIFY
  SCAP MUTATED                                       0
  SCAP WILD-TYPE                                     2
                vv
clus             LOWER ABDOMINAL/PELVIC - BLADDER
  SCAP MUTATED                                  0
  SCAP WILD-TYPE                                1
                vv
clus             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  SCAP MUTATED                                                0
  SCAP WILD-TYPE                                              2
                vv
clus             LOWER ABDOMINAL/PELVIC - PELVIC
  SCAP MUTATED                                 0
  SCAP WILD-TYPE                              11
                vv
clus             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  SCAP MUTATED                                         0
  SCAP WILD-TYPE                                       2
                vv
clus             LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  SCAP MUTATED                              0                       0
  SCAP WILD-TYPE                            4                       2
                vv
clus             LOWER EXTREMITY - LOWER LEG/CALF
  SCAP MUTATED                                  0
  SCAP WILD-TYPE                               16
                vv
clus             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  SCAP MUTATED                                         0
  SCAP WILD-TYPE                                       3
                vv
clus             LOWER EXTREMITY - THIGH/KNEE
  SCAP MUTATED                              2
  SCAP WILD-TYPE                           41
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  SCAP MUTATED                                         0
  SCAP WILD-TYPE                                       4
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  SCAP MUTATED                                           0
  SCAP WILD-TYPE                                         2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  SCAP MUTATED                                                  0
  SCAP WILD-TYPE                                                5
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  SCAP MUTATED                                          0
  SCAP WILD-TYPE                                        7
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  SCAP MUTATED                                                         0
  SCAP WILD-TYPE                                                       2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  SCAP MUTATED                                            0
  SCAP WILD-TYPE                                          1
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  SCAP MUTATED                                                   0
  SCAP WILD-TYPE                                                71
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  SCAP MUTATED                                                    0
  SCAP WILD-TYPE                                                  3
                vv
clus             SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  SCAP MUTATED                                    0                        0
  SCAP WILD-TYPE                                  2                        5
                vv
clus             SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  SCAP MUTATED                             0                         0
  SCAP WILD-TYPE                           3                         1
                vv
clus             UPPER EXTREMITY - SHOULDER/AXILLA
  SCAP MUTATED                                   0
  SCAP WILD-TYPE                                 7
                vv
clus             UPPER EXTREMITY - UPPER ARM/ELBOW
  SCAP MUTATED                                   0
  SCAP WILD-TYPE                                 5
D17V3, multiclass
                                                         clus
vv                                                        SCAP MUTATED
  CHEST - BREAST                                                     0
  CHEST - CHEST WALL                                                 0
  CHEST - LUNG/PLEURA                                                0
  CHEST - MEDIASTINUM                                                0
  CHEST - OTHER (PLEASE SPECIFY                                      0
  GYNECOLOGICAL - OVARY                                              0
  GYNECOLOGICAL - UTERUS                                             0
  HEAD AND NECK - HEAD                                               1
  HEAD AND NECK - NECK                                               0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                              0
  LOWER ABDOMINAL/PELVIC - BLADDER                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                    0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                            0
  LOWER EXTREMITY - FOOT/ANKLE                                       0
  LOWER EXTREMITY - GROIN                                            0
  LOWER EXTREMITY - LOWER LEG/CALF                                   0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                            0
  LOWER EXTREMITY - THIGH/KNEE                                       2
  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 - PANCREAS                         0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                  0
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                 0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                 0
  SUPERFICIAL TRUNK - BACK                                           0
  SUPERFICIAL TRUNK - BUTTOCK                                        0
  SUPERFICIAL TRUNK - FLANK                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                  0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                  0
                                                         clus
vv                                                        SCAP WILD-TYPE
  CHEST - BREAST                                                       1
  CHEST - CHEST WALL                                                   7
  CHEST - LUNG/PLEURA                                                  2
  CHEST - MEDIASTINUM                                                  1
  CHEST - OTHER (PLEASE SPECIFY                                        1
  GYNECOLOGICAL - OVARY                                                1
  GYNECOLOGICAL - UTERUS                                              26
  HEAD AND NECK - HEAD                                                 1
  HEAD AND NECK - NECK                                                 1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                2
  LOWER ABDOMINAL/PELVIC - BLADDER                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                     11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                              2
  LOWER EXTREMITY - FOOT/ANKLE                                         4
  LOWER EXTREMITY - GROIN                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                    16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                              3
  LOWER EXTREMITY - THIGH/KNEE                                        41
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                              4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                            2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                     5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                             7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   71
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                   3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                   2
  SUPERFICIAL TRUNK - BACK                                             5
  SUPERFICIAL TRUNK - BUTTOCK                                          3
  SUPERFICIAL TRUNK - FLANK                                            1
  UPPER EXTREMITY - SHOULDER/AXILLA                                    7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                    5
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                cls
clus               0   1
  SCAP MUTATED     0   3
  SCAP WILD-TYPE 133 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAP MUTATED      0    3
  SCAP WILD-TYPE  133  111
        clus
vv       SCAP MUTATED SCAP WILD-TYPE
  FEMALE            0            133
  MALE              3            111
[1] 2 2
[1] FALSE
D17V5, binary
                cls
clus               0   1
  SCAP MUTATED     3   0
  SCAP WILD-TYPE 167  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAP MUTATED      3    0
  SCAP WILD-TYPE  167   71
     clus
vv    SCAP MUTATED SCAP WILD-TYPE
  NO             3            167
  YES            0             71
[1] 2 2
[1] FALSE
                vv
clus             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  SCAP MUTATED                              1             0
  SCAP WILD-TYPE                           55             2
                vv
clus             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  SCAP MUTATED                                                                          0
  SCAP WILD-TYPE                                                                        1
                vv
clus             LEIOMYOSARCOMA (LMS)
  SCAP MUTATED                      1
  SCAP WILD-TYPE                   97
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  SCAP MUTATED                                                  0
  SCAP WILD-TYPE                                                8
                vv
clus             MYXOFIBROSARCOMA
  SCAP MUTATED                  0
  SCAP WILD-TYPE               22
                vv
clus             PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  SCAP MUTATED                                                          1
  SCAP WILD-TYPE                                                       28
                vv
clus             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  SCAP MUTATED                                          0
  SCAP WILD-TYPE                                        2
                vv
clus             SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  SCAP MUTATED                             0                             0
  SCAP WILD-TYPE                           2                             6
                vv
clus             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  SCAP MUTATED                                            0
  SCAP WILD-TYPE                                         21
D17V6, multiclass
                                                                          clus
vv                                                                         SCAP MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                        1
  DESMOID TUMOR                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS            0
  LEIOMYOSARCOMA (LMS)                                                                1
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                    0
  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                                                                         SCAP WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                         55
  DESMOID TUMOR                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS              1
  LEIOMYOSARCOMA (LMS)                                                                 97
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      8
  MYXOFIBROSARCOMA                                                                     22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             28
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           21
[1] 11  2
[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
  SCAP MUTATED     2   0   0   1
  SCAP WILD-TYPE 147  65   9  22
D17V7, multiclass
    clus
vv   SCAP MUTATED SCAP WILD-TYPE
  R0            2            147
  R1            0             65
  R2            0              9
  RX            1             22
[1] 4 2
[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
  SCAP MUTATED       0                         0     3
  SCAP WILD-TYPE     5                        18   214
D17V8, multiclass
                           clus
vv                          SCAP MUTATED SCAP WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                3            214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                cls
clus               0   1
  SCAP MUTATED     0   3
  SCAP WILD-TYPE   5 210
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAP MUTATED      0    3
  SCAP WILD-TYPE    5  210
                        clus
vv                       SCAP MUTATED SCAP WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            210
[1] 2 2
[1] FALSE
