[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/19775498/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/19898602/transformed.cor.cli.txt"

nPatients in clinical file=260, in cluster file=245, common to both=244
[1] "Reduce the number of clustering variables from 24 to 23."
[1]  23 244
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            84            160 
  TP53 MUTATED TP53 WILD-TYPE 
            84            160 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            37            207 
  ATRX MUTATED ATRX WILD-TYPE 
            37            207 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           24           220 
  RB1 MUTATED RB1 WILD-TYPE 
           24           220 
[1] "NUMBL MUTATION ANALYSIS"
[1] 3
  NUMBL MUTATED NUMBL WILD-TYPE 
              9             235 
  NUMBL MUTATED NUMBL WILD-TYPE 
              9             235 
[1] "MSH3 MUTATION ANALYSIS"
[1] 3
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            237 
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            237 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
              6             238 
  EOMES MUTATED EOMES WILD-TYPE 
              6             238 
[1] "PKD2 MUTATION ANALYSIS"
[1] 3
  PKD2 MUTATED PKD2 WILD-TYPE 
             6            238 
  PKD2 MUTATED PKD2 WILD-TYPE 
             6            238 
[1] "LTBP3 MUTATION ANALYSIS"
[1] 3
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             239 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             239 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                8               236 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                8               236 
[1] "WNK1 MUTATION ANALYSIS"
[1] 3
  WNK1 MUTATED WNK1 WILD-TYPE 
             6            238 
  WNK1 MUTATED WNK1 WILD-TYPE 
             6            238 
[1] "ANP32E MUTATION ANALYSIS"
[1] 3
  ANP32E MUTATED ANP32E WILD-TYPE 
               4              240 
  ANP32E MUTATED ANP32E WILD-TYPE 
               4              240 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             7            237 
  PTEN MUTATED PTEN WILD-TYPE 
             7            237 
[1] "KRTAP5-5 MUTATION ANALYSIS"
[1] 3
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                237 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                237 
[1] "TRAF7 MUTATION ANALYSIS"
[1] 3
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             240 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             240 
[1] "MEGF9 MUTATION ANALYSIS"
[1] 3
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             241 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             241 
[1] "LOR MUTATION ANALYSIS"
[1] 3
  LOR MUTATED LOR WILD-TYPE 
            6           238 
  LOR MUTATED LOR WILD-TYPE 
            6           238 
[1] "CABLES1 MUTATION ANALYSIS"
[1] 3
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               241 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               241 
[1] "COL18A1 MUTATION ANALYSIS"
[1] 3
  COL18A1 MUTATED COL18A1 WILD-TYPE 
                7               237 
  COL18A1 MUTATED COL18A1 WILD-TYPE 
                7               237 
[1] "LHCGR MUTATION ANALYSIS"
[1] 3
  LHCGR MUTATED LHCGR WILD-TYPE 
              6             238 
  LHCGR MUTATED LHCGR WILD-TYPE 
              6             238 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           10           234 
  NF1 MUTATED NF1 WILD-TYPE 
           10           234 
[1] "FOXD2 MUTATION ANALYSIS"
[1] 3
  FOXD2 MUTATED FOXD2 WILD-TYPE 
              3             241 
  FOXD2 MUTATED FOXD2 WILD-TYPE 
              3             241 
[1] "MMP17 MUTATION ANALYSIS"
[1] 3
  MMP17 MUTATED MMP17 WILD-TYPE 
              3             241 
  MMP17 MUTATED MMP17 WILD-TYPE 
              3             241 
[1] "ASTE1 MUTATION ANALYSIS"
[1] 3
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              3             241 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              3             241 
[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 244 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=87,	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=169,	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 244 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    55  29
  TP53 WILD-TYPE 100  60
  TP53 MUTATED TP53 WILD-TYPE 
            84            160 
  TP53 MUTATED TP53 WILD-TYPE 
            29             60 
$`TP53 MUTATED`
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       53.49        68.55        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KX 
       10.32        38.47        36.03        18.64        26.56        38.24 
TCGA-DX-A1L1 TCGA-DX-A2J1 TCGA-DX-A3M2 TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       54.21        83.38        34.68        34.88        81.90         9.73 
TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6BA 
       40.80       102.41        47.57        25.15        15.95        66.05 
TCGA-DX-A6BB TCGA-DX-A6YU TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EN TCGA-DX-A7ET 
       23.44        23.54        64.21        88.31        15.62        15.22 
TCGA-DX-A7EU TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BP TCGA-DX-A8BU 
       12.20        14.43        61.97        33.07        14.07        36.69 
TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB30 
       60.66         1.15        17.79       106.55        13.28        22.85 
TCGA-DX-AB32 TCGA-FX-A3TO TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IE-A4EI 
      101.98        20.32        12.62        33.30        26.93        19.53 
TCGA-IE-A4EJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF 
        3.22        28.21       143.41        13.58         5.92         1.05 
TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QT TCGA-KF-A41W TCGA-LI-A67I 
       62.17        17.36         5.19        16.41        11.70        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-N1-A6IA TCGA-PC-A5DK TCGA-QC-A6FX 
       13.35         8.28        19.73         7.36       120.20        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VH 
       13.08        46.82        18.08        48.59        37.12        10.52 
TCGA-SG-A6Z4 TCGA-UE-A6QT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 
       18.94        13.22        38.27        65.46        56.61        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-Z4-AAPG 
        9.04        63.35        36.82        25.71        38.96        15.98 

$`TP53 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HR TCGA-3B-A9HS 
       50.01        36.30        19.69        31.53        88.57        44.91 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        14.04        32.71        12.85        36.69        18.54 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J4 
       66.87         6.28        60.30         8.58         9.70        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        43.76        86.83       124.73        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-A48K TCGA-DX-A48L TCGA-DX-A48N 
       61.91        55.07        50.43        31.27        24.26        24.69 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       46.03        26.47        24.59        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ 
       21.63        16.18         3.06        34.55        16.87        74.10 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ 
       21.30        34.49        75.32        48.36       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN 
       48.20        20.05        17.95         9.34        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BX 
       35.77        51.91       124.37        27.95        35.54        19.43 
TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
        6.58        12.00        15.72        15.85        40.60        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2Z 
       12.07        66.74         9.21        77.88       106.45        50.40 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       30.51        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
       31.63        31.13        16.60        21.70        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 
        8.05        48.30        34.88         4.57        15.91         0.72 
TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K8 
       80.48         1.38        19.89        25.22        52.27       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X 
       73.28        22.62        16.41         3.91        53.33       123.78 
TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       23.38        36.36        35.28        25.41         0.49        21.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DN 
       14.99        17.98        22.39        10.45        37.55        38.63 
TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-QQ-A8VD 
       81.01        20.52        17.65         1.84        35.90       130.32 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
       64.77         0.72        16.77         3.88        17.52        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G 
       25.35        32.75         8.61        19.63        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-X6-A7W8 
       12.46        11.93         4.80        72.72        41.49        26.43 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       18.35        15.95        16.83        35.08        17.72        15.58 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       36.43         4.37        13.38        15.95 

  TP53 MUTATED TP53 WILD-TYPE 
          1.05           0.49 
  TP53 MUTATED TP53 WILD-TYPE 
        143.41         135.48 
  TP53 MUTATED TP53 WILD-TYPE 
         25.20          26.45 
[1] "1.1 - 143.4 (25.2)" "0.5 - 135.5 (26.4)"
[1] "hr=" "1.1"
D1V2, continuous
                vv
clus             CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  TP53 MUTATED                1                  3                   0
  TP53 WILD-TYPE              0                  4                   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                     12
  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                                  4
  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                           29
                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                                                 3
  CHEST - LUNG/PLEURA                                                0
  CHEST - MEDIASTINUM                                                1
  CHEST - OTHER (PLEASE SPECIFY                                      1
  GYNECOLOGICAL - OVARY                                              0
  GYNECOLOGICAL - UTERUS                                            12
  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                                   4
  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                                                   4
  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                                        29
  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   47 37
  TP53 WILD-TYPE 84 76
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     47   37
  TP53 WILD-TYPE   84   76
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           47             84
  MALE             37             76
[1] 2 2
[1] FALSE
D1V5, binary
                cls
clus               0   1
  TP53 MUTATED    58  23
  TP53 WILD-TYPE 112  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     58   23
  TP53 WILD-TYPE  112   44
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            58            112
  YES           23             44
[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                     49
  TP53 WILD-TYPE                   48
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  TP53 MUTATED                                                  1
  TP53 WILD-TYPE                                                7
                vv
clus             MYXOFIBROSARCOMA
  TP53 MUTATED                  9
  TP53 WILD-TYPE               12
                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                                            8
  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)                                                               49
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                    1
  MYXOFIBROSARCOMA                                                                    9
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                            12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                       0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          8
                                                                          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                                                                     12
  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   53 19  3  9
  TP53 WILD-TYPE 94 45  6 14
D1V7, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           53             94
  R1           19             45
  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    74
  TP53 WILD-TYPE     4                        11   140
D1V8, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                1              4
  BLACK OR AFRICAN AMERICAN            7             11
  WHITE                               74            140
[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  70
  TP53 WILD-TYPE   5 141
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0   70
  TP53 WILD-TYPE    5  141
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           70            141
[1] 2 2
[1] FALSE

Clustering(2) Variable = ATRX MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  ATRX MUTATED    20  17
  ATRX WILD-TYPE 135  72
  ATRX MUTATED ATRX WILD-TYPE 
            37            207 
  ATRX MUTATED ATRX WILD-TYPE 
            17             72 
$`ATRX MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-DX-A1L2 TCGA-DX-A23Y 
       19.69        44.91        42.84        18.64        59.24         6.28 
TCGA-DX-A3M2 TCGA-DX-A3UD TCGA-DX-A6B8 TCGA-DX-A7EU TCGA-DX-A8BM TCGA-DX-A8BN 
       34.68        50.43        15.95        12.20        44.68        38.17 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2P TCGA-DX-AB2W 
       35.54        36.69        60.66         1.15        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-IE-A4EJ 
       13.28        84.66        32.15        48.30        34.88         3.22 
TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-K1-A42W TCGA-KD-A5QU TCGA-KF-A41W TCGA-PC-A5DN 
       19.89        16.41        62.17        35.28        11.70        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        36.82 
TCGA-X9-A971 
       15.58 

$`ATRX WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       50.01        36.30        31.53        53.49        68.55        88.57 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        14.37        10.32        38.47        36.03 
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        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       36.69        18.54        54.21        33.53        42.54        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
        5.26        76.41        66.87        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       83.38        54.77         9.04        43.76        86.83       124.73 
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-A3UE TCGA-DX-A3UF 
       14.99        10.68        61.91        55.07        34.88        81.90 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        31.27        24.26        24.69        40.80        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47       102.41        47.57        25.15        24.59        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        34.55        23.54        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       88.31        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
      135.48        29.49        48.20        20.05        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BP 
       14.43         9.34        61.97        33.07        35.77        14.07 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E 
       51.91       124.37        27.95        19.43         6.58        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2Q 
       12.00        15.72        15.85        40.60        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
        9.21        77.88       106.55        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       30.51        60.00        50.89        71.31        31.63        31.13 
TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       16.60        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV 
        4.57        15.91        12.62        33.30         0.72        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       26.93        19.53         1.38        25.22        52.27        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
        1.05         3.91        53.33       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
        5.19        36.36        16.41        22.03        13.35        25.41 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         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-A5DO 
       22.39        10.45         7.36       120.20        37.55        81.01 
TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       20.52        20.94        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-SG-A849 TCGA-SI-A71O 
        0.72        16.77        18.94         3.88        17.52        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       25.35        32.75        19.63        13.22        13.41        10.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-WK-A8XZ TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       56.61         9.04        26.43        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB 
       16.83        38.96        35.08        17.72        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  ATRX MUTATED ATRX WILD-TYPE 
          1.15           0.49 
  ATRX MUTATED ATRX WILD-TYPE 
        106.45         143.41 
  ATRX MUTATED ATRX WILD-TYPE 
         34.68          25.35 
[1] "1.1 - 106.5 (34.7)" "0.5 - 143.4 (25.4)"
[1] "hr=" "1.4"
D2V2, 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                     20
                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                               14
                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                           32
                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                                   3
  ATRX WILD-TYPE                                 4
                vv
clus             UPPER EXTREMITY - UPPER ARM/ELBOW
  ATRX MUTATED                                   1
  ATRX WILD-TYPE                                 4
D2V3, 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                                  3
  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                                              20
  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                                    14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                              3
  LOWER EXTREMITY - THIGH/KNEE                                        32
  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                                    4
  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"
D2V4, binary
                cls
clus               0   1
  ATRX MUTATED    22  15
  ATRX WILD-TYPE 109  98
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     22   15
  ATRX WILD-TYPE  109   98
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  FEMALE           22            109
  MALE             15             98
[1] 2 2
[1] FALSE
D2V5, binary
                cls
clus               0   1
  ATRX MUTATED    23  13
  ATRX WILD-TYPE 147  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     23   13
  ATRX WILD-TYPE  147   54
     clus
vv    ATRX MUTATED ATRX WILD-TYPE
  NO            23            147
  YES           13             54
[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                     14
  ATRX WILD-TYPE                   83
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  ATRX MUTATED                                                  0
  ATRX WILD-TYPE                                                8
                vv
clus             MYXOFIBROSARCOMA
  ATRX MUTATED                  2
  ATRX WILD-TYPE               19
                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                                         13
D2V6, multiclass
                                                                          clus
vv                                                                         ATRX MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                        6
  DESMOID TUMOR                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS            0
  LEIOMYOSARCOMA (LMS)                                                               14
  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)                                                                 83
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      8
  MYXOFIBROSARCOMA                                                                     19
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                         6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           13
[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    24  10   0   3
  ATRX WILD-TYPE 123  54   9  20
D2V7, multiclass
    clus
vv   ATRX MUTATED ATRX WILD-TYPE
  R0           24            123
  R1           10             54
  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    33
  ATRX WILD-TYPE     5                        14   181
D2V8, multiclass
                           clus
vv                          ATRX MUTATED ATRX WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            4             14
  WHITE                               33            181
[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
  ATRX MUTATED     0  34
  ATRX WILD-TYPE   5 177
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED      0   34
  ATRX WILD-TYPE    5  177
                        clus
vv                       ATRX MUTATED ATRX WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           34            177
[1] 2 2
[1] FALSE

Clustering(3) Variable = RB1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    14  10
  RB1 WILD-TYPE 141  79
  RB1 MUTATED RB1 WILD-TYPE 
           24           220 
  RB1 MUTATED RB1 WILD-TYPE 
           10            79 
$`RB1 MUTATED`
TCGA-3B-A9HP TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A3UE TCGA-DX-A48L 
       53.49        10.32        36.03        26.56        34.88        24.26 
TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BG TCGA-DX-A8BM TCGA-DX-A8BO 
       88.31        48.36        15.62        17.95        44.68        35.77 
TCGA-DX-A8BS TCGA-DX-AB2T TCGA-DX-AB32 TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-K1-A6RU 
       27.95        77.88       101.98        25.22        13.58        23.38 
TCGA-LI-A67I TCGA-PC-A5DO TCGA-QQ-A5VD TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-X6-A7WD 
       22.03        81.01        37.12        56.61        22.62        18.35 

$`RB1 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HQ TCGA-3B-A9HR 
       50.01        36.30        19.69        31.53        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-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64         0.56        14.04        32.71        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.69        18.54        54.21        59.24        33.53        42.54 
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        83.38        54.77         9.04        43.76 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       86.83       124.73        33.44        44.68        34.68        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        61.91 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       55.07        50.43        81.90         9.73        31.27        24.69 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       40.80        46.03        26.47       102.41        47.57        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        24.59        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU 
       17.79        21.63        16.18         3.06        34.55        23.54 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       16.87        74.10        64.21        21.30        34.49        75.32 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU 
      135.48        29.49        48.20        20.05        15.22        12.20 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BP 
       14.43         9.34        61.97        33.07        38.17        14.07 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
       51.91       124.37        35.54        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
        6.58         1.15        17.79        12.00        15.72        15.85 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V 
       40.60        86.10        12.07        66.74         9.21       106.55 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        50.40        22.85        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31        31.63        31.13 
TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       16.60        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       48.30        34.88         4.57        15.91        12.62        33.30 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.72        80.48        26.93        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       19.89        52.27        28.21       143.41       116.88        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO 
        5.92        22.62        16.41         1.05         3.91        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
       62.17       123.78        17.36         5.19        36.36        16.41 
TCGA-KD-A5QU TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       35.28        11.70        13.35        25.41         8.28         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-PT-A8TR TCGA-QC-A6FX 
        7.36       120.20        37.55        38.63        20.52        20.94 
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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       18.94         3.88        17.52        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-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 
        9.04        63.35        26.43        36.82        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  RB1 MUTATED RB1 WILD-TYPE 
        10.32          0.49 
  RB1 MUTATED RB1 WILD-TYPE 
       101.98        143.41 
  RB1 MUTATED RB1 WILD-TYPE 
       31.415        25.300 
[1] "10.3 - 102.0 (31.4)" "0.5 - 143.4 (25.3)" 
[1] "hr=" "1"  
D3V2, 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                     24
               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                               11
               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                           35
               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
D3V3, 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                                             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                                    11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                             2
  LOWER EXTREMITY - FOOT/ANKLE                                        3
  LOWER EXTREMITY - GROIN                                             2
  LOWER EXTREMITY - LOWER LEG/CALF                                   11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             3
  LOWER EXTREMITY - THIGH/KNEE                                       35
  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"
D3V4, binary
               cls
clus              0   1
  RB1 MUTATED    16   8
  RB1 WILD-TYPE 115 105
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     16    8
  RB1 WILD-TYPE  115  105
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          16           115
  MALE             8           105
[1] 2 2
[1] FALSE
D3V5, binary
               cls
clus              0   1
  RB1 MUTATED    13  11
  RB1 WILD-TYPE 157  56
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     13   11
  RB1 WILD-TYPE  157   56
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           13           157
  YES          11            56
[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                   82
               vv
clus            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  RB1 MUTATED                                                  0
  RB1 WILD-TYPE                                                8
               vv
clus            MYXOFIBROSARCOMA
  RB1 MUTATED                  5
  RB1 WILD-TYPE               16
               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                                         19
D3V6, 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)                                                                82
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     8
  MYXOFIBROSARCOMA                                                                    16
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             26
  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
  RB1 MUTATED    18   5   0   1
  RB1 WILD-TYPE 129  59   9  22
D3V7, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          18           129
  R1           5            59
  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   192
D3V8, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           2            16
  WHITE                              22           192
[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
  RB1 MUTATED     0  22
  RB1 WILD-TYPE   5 189
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      0   22
  RB1 WILD-TYPE    5  189
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO          22           189
[1] 2 2
[1] FALSE

Clustering(4) Variable = NUMBL MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  NUMBL MUTATED     7   2
  NUMBL WILD-TYPE 148  87
  NUMBL MUTATED NUMBL WILD-TYPE 
              9             235 
  NUMBL MUTATED NUMBL WILD-TYPE 
              2              87 
$`NUMBL MUTATED`
TCGA-DX-A48R TCGA-DX-A8BP TCGA-FX-A3TO TCGA-FX-A48G TCGA-KF-A41W TCGA-PC-A5DN 
       26.47        14.07        20.32        19.89        11.70        38.63 
TCGA-QQ-A5VC TCGA-X6-A7WC TCGA-X9-A973 
       35.90        36.82        36.43 

$`NUMBL WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        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 
       83.38        54.77         9.04        43.76        86.83       124.73 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       33.44        44.68        34.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        61.91        55.07        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        81.90         9.73        31.27        24.26        24.69 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       40.80        46.03       102.41        47.57        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       24.59        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX 
       21.63        16.18         3.06        34.55        23.54        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       74.10        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        20.05 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       15.22        12.20        17.95        14.43         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR 
       33.07        44.68        38.17        35.77        51.91       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        35.54        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        17.79        12.00        15.72        15.85        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       86.10        12.07        66.74         9.21        77.88       106.55 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31        31.63 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       31.13        16.60        21.70        15.48         8.05        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        26.93        19.53         3.22         1.38        19.89 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        52.27        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
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-LI-A9QH TCGA-MB-A5Y8 
       36.36        16.41        35.28        22.03        13.35        25.41 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         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-A5DO 
       22.39        10.45         7.36       120.20        37.55        81.01 
TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       20.52        20.94        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH 
       18.08        48.59        37.12       130.32        64.77        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
        0.72        16.77        18.94         3.88        17.52        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-A8XT 
       10.72        12.46        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       38.27        65.46        56.61        22.62         9.04        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       26.43        18.35        25.71        15.95        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       35.08        17.72        15.58         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  NUMBL MUTATED NUMBL WILD-TYPE 
          11.70            0.49 
  NUMBL MUTATED NUMBL WILD-TYPE 
          38.63          143.41 
  NUMBL MUTATED NUMBL WILD-TYPE 
          26.47           25.41 
[1] "11.7 - 38.6 (26.5)" "0.5 - 143.4 (25.4)"
[1] "hr=" "1.3"
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                     23
                 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                               15
                 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                           39
                 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                                                   3
  NUMBL WILD-TYPE                                                68
                 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                   3
  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                                               23
  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                                     15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         39
  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                    68
  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   5
  NUMBL WILD-TYPE 127 108
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMBL MUTATED      4    5
  NUMBL WILD-TYPE  127  108
        clus
vv       NUMBL MUTATED NUMBL WILD-TYPE
  FEMALE             4             127
  MALE               5             108
[1] 2 2
[1] FALSE
D4V5, binary
                 cls
clus                0   1
  NUMBL MUTATED     8   1
  NUMBL WILD-TYPE 162  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMBL MUTATED      8    1
  NUMBL WILD-TYPE  162   66
     clus
vv    NUMBL MUTATED NUMBL WILD-TYPE
  NO              8             162
  YES             1              66
[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                      6
  NUMBL WILD-TYPE                   91
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  NUMBL MUTATED                                                  0
  NUMBL WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  NUMBL MUTATED                  0
  NUMBL WILD-TYPE               21
                 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                                         18
D4V6, multiclass
                                                                          clus
vv                                                                         NUMBL MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                         0
  DESMOID TUMOR                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             0
  LEIOMYOSARCOMA (LMS)                                                                 6
  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)                                                                  91
  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)                                            18
[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   4   0   2
  NUMBL WILD-TYPE 144  60   9  21
D4V7, multiclass
    clus
vv   NUMBL MUTATED NUMBL WILD-TYPE
  R0             3             144
  R1             4              60
  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     9
  NUMBL WILD-TYPE     5                        18   205
D4V8, multiclass
                           clus
vv                          NUMBL MUTATED NUMBL WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 9             205
[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   5 203
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUMBL MUTATED      0    8
  NUMBL WILD-TYPE    5  203
                        clus
vv                       NUMBL MUTATED NUMBL WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8             203
[1] 2 2
[1] FALSE

Clustering(5) Variable = MSH3 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  MSH3 MUTATED     4   3
  MSH3 WILD-TYPE 151  86
  MSH3 MUTATED MSH3 WILD-TYPE 
             7            237 
  MSH3 MUTATED MSH3 WILD-TYPE 
             3             86 
$`MSH3 MUTATED`
TCGA-DX-A23T TCGA-DX-A48U TCGA-DX-AB2S TCGA-DX-AB37 TCGA-FX-A2QS TCGA-FX-A48G 
        5.26       102.41         9.21        84.66        31.63        19.89 
TCGA-X6-A8C4 
       16.83 

$`MSH3 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23U 
       54.21        59.24        33.53        42.54        74.66        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        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        43.76        86.83       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       44.68        34.68        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        61.91        55.07        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       81.90         9.73        31.27        24.26        24.69        40.80 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       46.03        26.47        47.57        25.15        15.95        24.59 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18         3.06        34.55        23.54        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        20.05        15.22 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       12.20        17.95        14.43         9.34        61.97        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR 
       44.68        38.17        35.77        14.07        51.91       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        35.54        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        17.79        12.00        15.72        15.85        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
       86.10        12.07        66.74        77.88       106.55       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       13.28        50.40        22.85       101.98        30.51        60.00 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE 
       32.15        50.89        71.31        31.13        16.60        21.70 
TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       20.32        15.48         8.05        48.30        34.88         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH 
       15.91        12.62        33.30         0.72        80.48        26.93 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       19.53         3.22         1.38        19.89        25.22        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W 
       22.62        16.41         1.05         3.91        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        36.36        16.41 
TCGA-KD-A5QU TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       35.28        11.70        22.03        13.35        25.41         8.28 
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       120.20        37.55        38.63        81.01 
TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       20.52        20.94        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-SG-A849 
       10.52         0.72        16.77        18.94         3.88        17.52 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       22.82        25.35        32.75         8.61        19.63        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.41        10.72        12.46        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB 
       41.49        38.27        65.46        56.61        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        26.43        36.82        18.35        25.71        15.95 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       38.96        35.08        17.72        15.58        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  MSH3 MUTATED MSH3 WILD-TYPE 
          5.26           0.49 
  MSH3 MUTATED MSH3 WILD-TYPE 
        102.41         143.41 
  MSH3 MUTATED MSH3 WILD-TYPE 
         19.89          25.71 
[1] "5.3 - 102.4 (19.9)" "0.5 - 143.4 (25.7)"
[1] "hr=" "1"  
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                     24
                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                               14
                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                           41
                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                                              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                                     11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                              2
  LOWER EXTREMITY - FOOT/ANKLE                                         4
  LOWER EXTREMITY - GROIN                                              2
  LOWER EXTREMITY - LOWER LEG/CALF                                    14
  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              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 125 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH3 MUTATED      6    1
  MSH3 WILD-TYPE  125  112
        clus
vv       MSH3 MUTATED MSH3 WILD-TYPE
  FEMALE            6            125
  MALE              1            112
[1] 2 2
[1] FALSE
D5V5, binary
                cls
clus               0   1
  MSH3 MUTATED     5   2
  MSH3 WILD-TYPE 165  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH3 MUTATED      5    2
  MSH3 WILD-TYPE  165   65
     clus
vv    MSH3 MUTATED MSH3 WILD-TYPE
  NO             5            165
  YES            2             65
[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                   95
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  MSH3 MUTATED                                                  0
  MSH3 WILD-TYPE                                                8
                vv
clus             MYXOFIBROSARCOMA
  MSH3 MUTATED                  1
  MSH3 WILD-TYPE               20
                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                                         19
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)                                                                 95
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      8
  MYXOFIBROSARCOMA                                                                     20
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              29
  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
  MSH3 MUTATED     4   2   0   1
  MSH3 WILD-TYPE 143  62   9  22
D5V7, multiclass
    clus
vv   MSH3 MUTATED MSH3 WILD-TYPE
  R0            4            143
  R1            2             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
  MSH3 MUTATED       0                         0     7
  MSH3 WILD-TYPE     5                        18   207
D5V8, multiclass
                           clus
vv                          MSH3 MUTATED MSH3 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                7            207
[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   4 206
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH3 MUTATED      1    5
  MSH3 WILD-TYPE    4  206
                        clus
vv                       MSH3 MUTATED MSH3 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            5            206
[1] 2 2
[1] FALSE

Clustering(6) Variable = EOMES MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  EOMES MUTATED     4   2
  EOMES WILD-TYPE 151  87
  EOMES MUTATED EOMES WILD-TYPE 
              6             238 
  EOMES MUTATED EOMES WILD-TYPE 
              2              87 
$`EOMES MUTATED`
TCGA-3B-A9HR TCGA-DX-AB2V TCGA-FX-A8OO TCGA-QQ-A5VD TCGA-SG-A849 TCGA-X6-A7WC 
       88.57       106.55         8.05        37.12        17.52        36.82 

$`EOMES WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        53.49        68.55 
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        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        43.76        86.83       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       44.68        34.68        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        61.91        55.07        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       81.90         9.73        31.27        24.26        24.69        40.80 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       102.41        47.57        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       24.59        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX 
       21.63        16.18         3.06        34.55        23.54        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       74.10        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        20.05 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       15.22        12.20        17.95        14.43         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ 
       33.07        44.68        38.17        35.77        14.07        51.91 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      124.37        27.95        35.54        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
        6.58         1.15        17.79        12.00        15.72        15.85 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       40.60        86.10        12.07        66.74         9.21        77.88 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31        31.63 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       31.13        16.60        21.70        20.32        19.89        15.48 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       48.30        34.88         4.57        15.91        12.62        33.30 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.72        80.48        26.93        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       19.89        25.22        52.27        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
        3.91        53.33        62.17       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-KF-A41W TCGA-LI-A67I 
        5.19        36.36        16.41        35.28        11.70        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35        25.41         8.28         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       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 
       37.55        38.63        81.01        20.52        20.94        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-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-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 
       72.72        41.49        38.27        65.46        56.61        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
        9.04        63.35        26.43        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  EOMES MUTATED EOMES WILD-TYPE 
           8.05            0.49 
  EOMES MUTATED EOMES WILD-TYPE 
         106.55          143.41 
  EOMES MUTATED EOMES WILD-TYPE 
          36.97           25.38 
[1] "8.1 - 106.5 (37.0)" "0.5 - 143.4 (25.4)"
[1] "hr=" "1.6"
D6V2, 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                     25
                 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                              1                       0
  EOMES WILD-TYPE                            3                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  EOMES MUTATED                                  0
  EOMES WILD-TYPE                               15
                 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                           40
                 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
D6V3, 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                                        1
  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                                               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                                     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                    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"
D6V4, binary
                 cls
clus                0   1
  EOMES MUTATED     2   4
  EOMES WILD-TYPE 129 109
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      2    4
  EOMES WILD-TYPE  129  109
        clus
vv       EOMES MUTATED EOMES WILD-TYPE
  FEMALE             2             129
  MALE               4             109
[1] 2 2
[1] FALSE
D6V5, binary
                 cls
clus                0   1
  EOMES MUTATED     2   4
  EOMES WILD-TYPE 168  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      2    4
  EOMES WILD-TYPE  168   63
     clus
vv    EOMES MUTATED EOMES WILD-TYPE
  NO              2             168
  YES             4              63
[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                      3
  EOMES WILD-TYPE                   94
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  EOMES MUTATED                                                  0
  EOMES WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  EOMES MUTATED                  1
  EOMES WILD-TYPE               20
                 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                                         19
D6V6, multiclass
                                                                          clus
vv                                                                         EOMES 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                              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)                                                                  94
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       8
  MYXOFIBROSARCOMA                                                                      20
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               29
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  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
  EOMES MUTATED     5   1   0   0
  EOMES WILD-TYPE 142  63   9  23
D6V7, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  R0             5             142
  R1             1              63
  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     5
  EOMES WILD-TYPE     5                        17   209
D6V8, multiclass
                           clus
vv                          EOMES MUTATED EOMES WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              17
  WHITE                                 5             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"
D6V9, binary
                 cls
clus                0   1
  EOMES MUTATED     0   6
  EOMES WILD-TYPE   5 205
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      0    6
  EOMES WILD-TYPE    5  205
                        clus
vv                       EOMES MUTATED EOMES WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6             205
[1] 2 2
[1] FALSE

Clustering(7) Variable = PKD2 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  PKD2 MUTATED     5   1
  PKD2 WILD-TYPE 150  88
  PKD2 MUTATED PKD2 WILD-TYPE 
             6            238 
  PKD2 MUTATED PKD2 WILD-TYPE 
             1             88 
$`PKD2 MUTATED`
TCGA-3B-A9HQ TCGA-DX-A48R TCGA-DX-A8BP TCGA-DX-AB2S TCGA-QQ-A5VC TCGA-WK-A8XT 
       68.55        26.47        14.07         9.21        35.90        41.49 

$`PKD2 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HR 
       50.01        36.30        19.69        31.53        53.49        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        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        43.76        86.83       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       44.68        34.68        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        61.91        55.07        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       81.90         9.73        31.27        24.26        24.69        40.80 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       46.03       102.41        47.57        25.15        15.95        24.59 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18         3.06        34.55        23.54        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        20.05        15.22 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       12.20        17.95        14.43         9.34        61.97        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       44.68        38.17        35.77        51.91       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.54        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       17.79        12.00        15.72        15.85        40.60        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       12.07        66.74        77.88       106.55       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       50.40        22.85       101.98        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK 
       32.15        50.89        71.31        31.63        31.13        16.60 
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        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        26.93        19.53         3.22         1.38        19.89 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        52.27        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
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-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       36.36        16.41        35.28        11.70        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       25.41         8.28         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       120.20        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
       38.63        81.01        20.52        20.94        13.08        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD 
        1.84        46.82        18.08        48.59        37.12       130.32 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       64.77        10.52         0.72        16.77        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
       17.52        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 
       72.72        38.27        65.46        56.61        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        26.43        36.82        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  PKD2 MUTATED PKD2 WILD-TYPE 
          9.21           0.49 
  PKD2 MUTATED PKD2 WILD-TYPE 
         68.55         143.41 
  PKD2 MUTATED PKD2 WILD-TYPE 
        31.185         25.380 
[1] "9.2 - 68.5 (31.2)"  "0.5 - 143.4 (25.4)"
[1] "hr=" "2.2"
D7V2, continuous
                vv
clus             CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  PKD2 MUTATED                0                  0                   0
  PKD2 WILD-TYPE              1                  7                   2
                vv
clus             CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  PKD2 MUTATED                     0                             0
  PKD2 WILD-TYPE                   1                             1
                vv
clus             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  PKD2 MUTATED                       0                      0
  PKD2 WILD-TYPE                     1                     25
                vv
clus             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  PKD2 MUTATED                      0                    0
  PKD2 WILD-TYPE                    2                    1
                vv
clus             HEAD AND NECK - OTHER (PLEASE SPECIFY
  PKD2 MUTATED                                       0
  PKD2 WILD-TYPE                                     2
                vv
clus             LOWER ABDOMINAL/PELVIC - BLADDER
  PKD2 MUTATED                                  0
  PKD2 WILD-TYPE                                1
                vv
clus             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  PKD2 MUTATED                                                0
  PKD2 WILD-TYPE                                              2
                vv
clus             LOWER ABDOMINAL/PELVIC - PELVIC
  PKD2 MUTATED                                 0
  PKD2 WILD-TYPE                              11
                vv
clus             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  PKD2 MUTATED                                         0
  PKD2 WILD-TYPE                                       2
                vv
clus             LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  PKD2 MUTATED                              0                       0
  PKD2 WILD-TYPE                            4                       2
                vv
clus             LOWER EXTREMITY - LOWER LEG/CALF
  PKD2 MUTATED                                  0
  PKD2 WILD-TYPE                               15
                vv
clus             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  PKD2 MUTATED                                         0
  PKD2 WILD-TYPE                                       3
                vv
clus             LOWER EXTREMITY - THIGH/KNEE
  PKD2 MUTATED                              2
  PKD2 WILD-TYPE                           40
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  PKD2 MUTATED                                         0
  PKD2 WILD-TYPE                                       4
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  PKD2 MUTATED                                           0
  PKD2 WILD-TYPE                                         2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  PKD2 MUTATED                                                  0
  PKD2 WILD-TYPE                                                5
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  PKD2 MUTATED                                          1
  PKD2 WILD-TYPE                                        6
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  PKD2 MUTATED                                                         0
  PKD2 WILD-TYPE                                                       2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  PKD2 MUTATED                                            0
  PKD2 WILD-TYPE                                          1
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  PKD2 MUTATED                                                   2
  PKD2 WILD-TYPE                                                69
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  PKD2 MUTATED                                                    0
  PKD2 WILD-TYPE                                                  3
                vv
clus             SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  PKD2 MUTATED                                    0                        1
  PKD2 WILD-TYPE                                  2                        4
                vv
clus             SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  PKD2 MUTATED                             0                         0
  PKD2 WILD-TYPE                           3                         1
                vv
clus             UPPER EXTREMITY - SHOULDER/AXILLA
  PKD2 MUTATED                                   0
  PKD2 WILD-TYPE                                 7
                vv
clus             UPPER EXTREMITY - UPPER ARM/ELBOW
  PKD2 MUTATED                                   0
  PKD2 WILD-TYPE                                 5
D7V3, multiclass
                                                         clus
vv                                                        PKD2 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                                   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                           1
  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                                           1
  SUPERFICIAL TRUNK - BUTTOCK                                        0
  SUPERFICIAL TRUNK - FLANK                                          0
  UPPER EXTREMITY - SHOULDER/AXILLA                                  0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                  0
                                                         clus
vv                                                        PKD2 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                                        40
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                              4
  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                           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"
D7V4, binary
                cls
clus               0   1
  PKD2 MUTATED     4   2
  PKD2 WILD-TYPE 127 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      4    2
  PKD2 WILD-TYPE  127  111
        clus
vv       PKD2 MUTATED PKD2 WILD-TYPE
  FEMALE            4            127
  MALE              2            111
[1] 2 2
[1] FALSE
D7V5, binary
                cls
clus               0   1
  PKD2 MUTATED     5   1
  PKD2 WILD-TYPE 165  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      5    1
  PKD2 WILD-TYPE  165   66
     clus
vv    PKD2 MUTATED PKD2 WILD-TYPE
  NO             5            165
  YES            1             66
[1] 2 2
[1] FALSE
                vv
clus             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  PKD2 MUTATED                              0             0
  PKD2 WILD-TYPE                           56             2
                vv
clus             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  PKD2 MUTATED                                                                          0
  PKD2 WILD-TYPE                                                                        1
                vv
clus             LEIOMYOSARCOMA (LMS)
  PKD2 MUTATED                      3
  PKD2 WILD-TYPE                   94
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  PKD2 MUTATED                                                  0
  PKD2 WILD-TYPE                                                8
                vv
clus             MYXOFIBROSARCOMA
  PKD2 MUTATED                  1
  PKD2 WILD-TYPE               20
                vv
clus             PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  PKD2 MUTATED                                                         1
  PKD2 WILD-TYPE                                                      28
                vv
clus             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  PKD2 MUTATED                                          0
  PKD2 WILD-TYPE                                        2
                vv
clus             SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  PKD2 MUTATED                             0                             1
  PKD2 WILD-TYPE                           2                             5
                vv
clus             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  PKD2 MUTATED                                            0
  PKD2 WILD-TYPE                                         20
D7V6, multiclass
                                                                          clus
vv                                                                         PKD2 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                                                       1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          0
                                                                          clus
vv                                                                         PKD2 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                         56
  DESMOID TUMOR                                                                         2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS              1
  LEIOMYOSARCOMA (LMS)                                                                 94
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      8
  MYXOFIBROSARCOMA                                                                     20
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              28
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                         5
  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
  PKD2 MUTATED     4   2   0   0
  PKD2 WILD-TYPE 143  62   9  23
D7V7, multiclass
    clus
vv   PKD2 MUTATED PKD2 WILD-TYPE
  R0            4            143
  R1            2             62
  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
  PKD2 MUTATED       0                         0     6
  PKD2 WILD-TYPE     5                        18   208
D7V8, multiclass
                           clus
vv                          PKD2 MUTATED PKD2 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                6            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"
D7V9, binary
                cls
clus               0   1
  PKD2 MUTATED     1   4
  PKD2 WILD-TYPE   4 207
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKD2 MUTATED      1    4
  PKD2 WILD-TYPE    4  207
                        clus
vv                       PKD2 MUTATED PKD2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4            207
[1] 2 2
[1] FALSE

Clustering(8) Variable = LTBP3 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  LTBP3 MUTATED     3   2
  LTBP3 WILD-TYPE 152  87
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              5             239 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
              2              87 
$`LTBP3 MUTATED`
TCGA-3B-A9HY TCGA-3B-A9I1 TCGA-DX-A8BP TCGA-DX-AB2E TCGA-WK-A8XY 
       10.32        18.64        14.07        17.79        65.46 

$`LTBP3 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       38.47        36.03        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 
       38.24        12.85        36.69        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        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        83.38        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        43.76        86.83       124.73        33.44        44.68 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       34.68        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        61.91        55.07        50.43        34.88        81.90 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        31.27        24.26        24.69        40.80        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       102.41        47.57        25.15        15.95        24.59 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18         3.06        34.55        23.54        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        20.05        15.22 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       12.20        17.95        14.43         9.34        61.97        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       44.68        38.17        35.77        51.91       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.54        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
       12.00        15.72        15.85        40.60        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       66.74         9.21        77.88       106.55       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       50.40        22.85       101.98        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK 
       32.15        50.89        71.31        31.63        31.13        16.60 
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        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        26.93        19.53         3.22         1.38        19.89 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        52.27        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
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-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       36.36        16.41        35.28        11.70        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       25.41         8.28         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       120.20        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
       38.63        81.01        20.52        20.94        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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
        3.88        17.52        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-A8XT TCGA-WK-A8XX TCGA-WK-A8XZ TCGA-WK-A8Y0 
        4.80        72.72        41.49        38.27        56.61        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        9.04        63.35        26.43        36.82        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       15.95        16.83        38.96        35.08        17.72        15.58 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  LTBP3 MUTATED LTBP3 WILD-TYPE 
          10.32            0.49 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
          65.46          143.41 
  LTBP3 MUTATED LTBP3 WILD-TYPE 
          17.79           26.43 
[1] "10.3 - 65.5 (17.8)" "0.5 - 143.4 (26.4)"
[1] "hr=" "1.5"
D8V2, 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                     24
                 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                               15
                 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                           40
                 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
D8V3, 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                                               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                                      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                    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"
D8V4, binary
                 cls
clus                0   1
  LTBP3 MUTATED     2   3
  LTBP3 WILD-TYPE 129 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED      2    3
  LTBP3 WILD-TYPE  129  110
        clus
vv       LTBP3 MUTATED LTBP3 WILD-TYPE
  FEMALE             2             129
  MALE               3             110
[1] 2 2
[1] FALSE
D8V5, binary
                 cls
clus                0   1
  LTBP3 MUTATED     5   0
  LTBP3 WILD-TYPE 165  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED      5    0
  LTBP3 WILD-TYPE  165   67
     clus
vv    LTBP3 MUTATED LTBP3 WILD-TYPE
  NO              5             165
  YES             0              67
[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                   94
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  LTBP3 MUTATED                                                  0
  LTBP3 WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  LTBP3 MUTATED                  1
  LTBP3 WILD-TYPE               20
                 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                                         20
D8V6, 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)                                                                  94
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       8
  MYXOFIBROSARCOMA                                                                      20
  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
  LTBP3 MUTATED     2   2   0   1
  LTBP3 WILD-TYPE 145  62   9  22
D8V7, multiclass
    clus
vv   LTBP3 MUTATED LTBP3 WILD-TYPE
  R0             2             145
  R1             2              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
  LTBP3 MUTATED       0                         1     4
  LTBP3 WILD-TYPE     5                        17   210
D8V8, multiclass
                           clus
vv                          LTBP3 MUTATED LTBP3 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             1              17
  WHITE                                 4             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
  LTBP3 MUTATED     0   5
  LTBP3 WILD-TYPE   5 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LTBP3 MUTATED      0    5
  LTBP3 WILD-TYPE    5  206
                        clus
vv                       LTBP3 MUTATED LTBP3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             206
[1] 2 2
[1] FALSE

Clustering(9) Variable = SHROOM4 MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  SHROOM4 MUTATED     7   1
  SHROOM4 WILD-TYPE 148  88
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                8               236 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                1                88 
$`SHROOM4 MUTATED`
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A7EN TCGA-DX-AB2Z TCGA-IE-A4EJ TCGA-IW-A3M6 
       24.26        24.69        15.62        50.40         3.22        22.62 
TCGA-K1-A42W TCGA-SG-A6Z4 
       62.17        18.94 

$`SHROOM4 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        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 
       83.38        54.77         9.04        43.76        86.83       124.73 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       33.44        44.68        34.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        61.91        55.07        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48O TCGA-DX-A48P 
       34.88        81.90         9.73        31.27        40.80        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       102.41        47.57        25.15        15.95        24.59 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18         3.06        34.55        23.54        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU 
      135.48        29.49        48.20        20.05        15.22        12.20 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        61.97        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       38.17        35.77        14.07        51.91       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.54        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       17.79        12.00        15.72        15.85        40.60        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
       12.07        66.74         9.21        77.88       106.55       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       13.28        22.85       101.98        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK 
       32.15        50.89        71.31        31.63        31.13        16.60 
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        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
       80.48        26.93        19.53         1.38        19.89        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       52.27        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X 
        5.92        16.41         1.05         3.91        53.33       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        36.36        16.41        35.28 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       11.70        22.03        13.35        25.41         8.28         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       120.20        37.55        38.63        81.01        20.52 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       20.94        13.08        17.65         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-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        16.77         3.88        17.52        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-A8XT TCGA-WK-A8XX 
       12.46        11.93         4.80        72.72        41.49        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         9.04        63.35        26.43 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       36.82        18.35        25.71        15.95        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       35.08        17.72        15.58        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             3.22              0.49 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            62.17            143.41 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            23.44             26.45 
[1] "3.2 - 62.2 (23.4)"  "0.5 - 143.4 (26.4)"
[1] "hr=" "2.4"
D9V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  SHROOM4 MUTATED                0                  0                   0
  SHROOM4 WILD-TYPE              1                  7                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  SHROOM4 MUTATED                     0                             0
  SHROOM4 WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  SHROOM4 MUTATED                       0                      1
  SHROOM4 WILD-TYPE                     1                     24
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  SHROOM4 MUTATED                      0                    0
  SHROOM4 WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  SHROOM4 MUTATED                                       0
  SHROOM4 WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  SHROOM4 MUTATED                                  0
  SHROOM4 WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  SHROOM4 MUTATED                                                0
  SHROOM4 WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  SHROOM4 MUTATED                                 0
  SHROOM4 WILD-TYPE                              11
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  SHROOM4 MUTATED                                         0
  SHROOM4 WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  SHROOM4 MUTATED                              0                       0
  SHROOM4 WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  SHROOM4 MUTATED                                  1
  SHROOM4 WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  SHROOM4 MUTATED                                         0
  SHROOM4 WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  SHROOM4 MUTATED                              3
  SHROOM4 WILD-TYPE                           39
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  SHROOM4 MUTATED                                         0
  SHROOM4 WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  SHROOM4 MUTATED                                           0
  SHROOM4 WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  SHROOM4 MUTATED                                                  0
  SHROOM4 WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  SHROOM4 MUTATED                                          0
  SHROOM4 WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  SHROOM4 MUTATED                                                         0
  SHROOM4 WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  SHROOM4 MUTATED                                            1
  SHROOM4 WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  SHROOM4 MUTATED                                                   2
  SHROOM4 WILD-TYPE                                                69
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  SHROOM4 MUTATED                                                    0
  SHROOM4 WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  SHROOM4 MUTATED                                    0                        0
  SHROOM4 WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  SHROOM4 MUTATED                             0                         0
  SHROOM4 WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  SHROOM4 MUTATED                                   0
  SHROOM4 WILD-TYPE                                 7
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  SHROOM4 MUTATED                                   0
  SHROOM4 WILD-TYPE                                 5
D9V3, multiclass
                                                         clus
vv                                                        SHROOM4 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                                          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                            1
  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                                                        SHROOM4 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                                        11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           39
  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                              0
  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
  SHROOM4 MUTATED     6   2
  SHROOM4 WILD-TYPE 125 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      6    2
  SHROOM4 WILD-TYPE  125  111
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  FEMALE               6               125
  MALE                 2               111
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED     5   2
  SHROOM4 WILD-TYPE 165  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      5    2
  SHROOM4 WILD-TYPE  165   65
     clus
vv    SHROOM4 MUTATED SHROOM4 WILD-TYPE
  NO                5               165
  YES               2                65
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  SHROOM4 MUTATED                              1             0
  SHROOM4 WILD-TYPE                           55             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  SHROOM4 MUTATED                                                                          0
  SHROOM4 WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  SHROOM4 MUTATED                      4
  SHROOM4 WILD-TYPE                   93
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  SHROOM4 MUTATED                                                  0
  SHROOM4 WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  SHROOM4 MUTATED                  0
  SHROOM4 WILD-TYPE               21
                   vv
clus                PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  SHROOM4 MUTATED                                                         2
  SHROOM4 WILD-TYPE                                                      27
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  SHROOM4 MUTATED                                          0
  SHROOM4 WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  SHROOM4 MUTATED                             0                             0
  SHROOM4 WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  SHROOM4 MUTATED                                            1
  SHROOM4 WILD-TYPE                                         19
D9V6, multiclass
                                                                          clus
vv                                                                         SHROOM4 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                                                                       0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             1
                                                                          clus
vv                                                                         SHROOM4 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            55
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    93
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  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)                                              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
  SHROOM4 MUTATED     5   3   0   0
  SHROOM4 WILD-TYPE 142  61   9  23
D9V7, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  R0               5               142
  R1               3                61
  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
  SHROOM4 MUTATED       1                         0     7
  SHROOM4 WILD-TYPE     4                        18   207
D9V8, multiclass
                           clus
vv                          SHROOM4 MUTATED SHROOM4 WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                18
  WHITE                                   7               207
[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
  SHROOM4 MUTATED     0   8
  SHROOM4 WILD-TYPE   5 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      0    8
  SHROOM4 WILD-TYPE    5  203
                        clus
vv                       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               8               203
[1] 2 2
[1] FALSE

Clustering(10) Variable = WNK1 MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  WNK1 MUTATED     3   3
  WNK1 WILD-TYPE 152  86
  WNK1 MUTATED WNK1 WILD-TYPE 
             6            238 
  WNK1 MUTATED WNK1 WILD-TYPE 
             3             86 
$`WNK1 MUTATED`
TCGA-3B-A9HL TCGA-DX-A3U8 TCGA-DX-A48U TCGA-DX-AB3B TCGA-RN-A68Q TCGA-WK-A8XX 
       19.69         4.54       102.41        50.89         0.72        38.27 

$`WNK1 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       50.01        36.30        31.53        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        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        43.76        86.83       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U9 
       44.68        34.68        31.86        35.77        51.02        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        61.91        55.07        50.43        34.88        81.90 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        31.27        24.26        24.69        40.80        46.03 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        47.57        25.15        15.95        24.59        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        34.55        23.54        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       88.31        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU 
      135.48        29.49        48.20        20.05        15.22        12.20 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        61.97        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       38.17        35.77        14.07        51.91       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.54        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       17.79        12.00        15.72        15.85        40.60        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
       12.07        66.74         9.21        77.88       106.55       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       13.28        50.40        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK 
       84.66        32.15        71.31        31.63        31.13        16.60 
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        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        26.93        19.53         3.22         1.38        19.89 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        52.27        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
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-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       36.36        16.41        35.28        11.70        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       25.41         8.28         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       120.20        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
       38.63        81.01        20.52        20.94        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-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
      130.32        64.77        10.52        16.77        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
       17.52        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-A8XT TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB 
       72.72        41.49        65.46        56.61        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        26.43        36.82        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  WNK1 MUTATED WNK1 WILD-TYPE 
          0.72           0.49 
  WNK1 MUTATED WNK1 WILD-TYPE 
        102.41         143.41 
  WNK1 MUTATED WNK1 WILD-TYPE 
         28.98          25.56 
[1] "0.7 - 102.4 (29.0)" "0.5 - 143.4 (25.6)"
[1] "hr=" "1.3"
D10V2, continuous
                vv
clus             CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  WNK1 MUTATED                0                  0                   0
  WNK1 WILD-TYPE              1                  7                   2
                vv
clus             CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  WNK1 MUTATED                     0                             0
  WNK1 WILD-TYPE                   1                             1
                vv
clus             GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  WNK1 MUTATED                       0                      0
  WNK1 WILD-TYPE                     1                     25
                vv
clus             HEAD AND NECK - HEAD HEAD AND NECK - NECK
  WNK1 MUTATED                      0                    0
  WNK1 WILD-TYPE                    2                    1
                vv
clus             HEAD AND NECK - OTHER (PLEASE SPECIFY
  WNK1 MUTATED                                       1
  WNK1 WILD-TYPE                                     1
                vv
clus             LOWER ABDOMINAL/PELVIC - BLADDER
  WNK1 MUTATED                                  0
  WNK1 WILD-TYPE                                1
                vv
clus             LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  WNK1 MUTATED                                                0
  WNK1 WILD-TYPE                                              2
                vv
clus             LOWER ABDOMINAL/PELVIC - PELVIC
  WNK1 MUTATED                                 0
  WNK1 WILD-TYPE                              11
                vv
clus             LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  WNK1 MUTATED                                         1
  WNK1 WILD-TYPE                                       1
                vv
clus             LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  WNK1 MUTATED                              1                       0
  WNK1 WILD-TYPE                            3                       2
                vv
clus             LOWER EXTREMITY - LOWER LEG/CALF
  WNK1 MUTATED                                  0
  WNK1 WILD-TYPE                               15
                vv
clus             LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  WNK1 MUTATED                                         0
  WNK1 WILD-TYPE                                       3
                vv
clus             LOWER EXTREMITY - THIGH/KNEE
  WNK1 MUTATED                              0
  WNK1 WILD-TYPE                           42
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - COLON
  WNK1 MUTATED                                         0
  WNK1 WILD-TYPE                                       4
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  WNK1 MUTATED                                           0
  WNK1 WILD-TYPE                                         2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  WNK1 MUTATED                                                  0
  WNK1 WILD-TYPE                                                5
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  WNK1 MUTATED                                          0
  WNK1 WILD-TYPE                                        7
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  WNK1 MUTATED                                                         0
  WNK1 WILD-TYPE                                                       2
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  WNK1 MUTATED                                            0
  WNK1 WILD-TYPE                                          1
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  WNK1 MUTATED                                                   3
  WNK1 WILD-TYPE                                                68
                vv
clus             RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  WNK1 MUTATED                                                    0
  WNK1 WILD-TYPE                                                  3
                vv
clus             SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  WNK1 MUTATED                                    0                        0
  WNK1 WILD-TYPE                                  2                        5
                vv
clus             SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  WNK1 MUTATED                             0                         0
  WNK1 WILD-TYPE                           3                         1
                vv
clus             UPPER EXTREMITY - SHOULDER/AXILLA
  WNK1 MUTATED                                   0
  WNK1 WILD-TYPE                                 7
                vv
clus             UPPER EXTREMITY - UPPER ARM/ELBOW
  WNK1 MUTATED                                   0
  WNK1 WILD-TYPE                                 5
D10V3, multiclass
                                                         clus
vv                                                        WNK1 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                              1
  LOWER ABDOMINAL/PELVIC - BLADDER                                   0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                     0
  LOWER ABDOMINAL/PELVIC - PELVIC                                    0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                            1
  LOWER EXTREMITY - FOOT/ANKLE                                       1
  LOWER EXTREMITY - GROIN                                            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                  3
  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                                                        WNK1 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                                1
  LOWER ABDOMINAL/PELVIC - BLADDER                                     1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                       2
  LOWER ABDOMINAL/PELVIC - PELVIC                                     11
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                              1
  LOWER EXTREMITY - FOOT/ANKLE                                         3
  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              2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                           1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                   68
  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"
D10V4, binary
                cls
clus               0   1
  WNK1 MUTATED     2   4
  WNK1 WILD-TYPE 129 109
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED      2    4
  WNK1 WILD-TYPE  129  109
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  FEMALE            2            129
  MALE              4            109
[1] 2 2
[1] FALSE
D10V5, binary
                cls
clus               0   1
  WNK1 MUTATED     6   0
  WNK1 WILD-TYPE 164  67
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED      6    0
  WNK1 WILD-TYPE  164   67
     clus
vv    WNK1 MUTATED WNK1 WILD-TYPE
  NO             6            164
  YES            0             67
[1] 2 2
[1] FALSE
                vv
clus             DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  WNK1 MUTATED                              1             0
  WNK1 WILD-TYPE                           55             2
                vv
clus             GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  WNK1 MUTATED                                                                          0
  WNK1 WILD-TYPE                                                                        1
                vv
clus             LEIOMYOSARCOMA (LMS)
  WNK1 MUTATED                      3
  WNK1 WILD-TYPE                   94
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  WNK1 MUTATED                                                  1
  WNK1 WILD-TYPE                                                7
                vv
clus             MYXOFIBROSARCOMA
  WNK1 MUTATED                  0
  WNK1 WILD-TYPE               21
                vv
clus             PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  WNK1 MUTATED                                                         0
  WNK1 WILD-TYPE                                                      29
                vv
clus             SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  WNK1 MUTATED                                          0
  WNK1 WILD-TYPE                                        2
                vv
clus             SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  WNK1 MUTATED                             0                             1
  WNK1 WILD-TYPE                           2                             5
                vv
clus             UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  WNK1 MUTATED                                            0
  WNK1 WILD-TYPE                                         20
D10V6, multiclass
                                                                          clus
vv                                                                         WNK1 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                        1
  DESMOID TUMOR                                                                       0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS            0
  LEIOMYOSARCOMA (LMS)                                                                3
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                    1
  MYXOFIBROSARCOMA                                                                    0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                            0
  SYNOVIAL SARCOMA - BIPHASIC                                                         0
  SYNOVIAL SARCOMA - MONOPHASIC                                                       1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                          0
                                                                          clus
vv                                                                         WNK1 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)                                      7
  MYXOFIBROSARCOMA                                                                     21
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              29
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                              2
  SYNOVIAL SARCOMA - BIPHASIC                                                           2
  SYNOVIAL SARCOMA - MONOPHASIC                                                         5
  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
  WNK1 MUTATED     4   1   0   1
  WNK1 WILD-TYPE 143  63   9  22
D10V7, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  R0            4            143
  R1            1             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
  WNK1 MUTATED       0                         0     5
  WNK1 WILD-TYPE     5                        18   209
D10V8, multiclass
                           clus
vv                          WNK1 MUTATED WNK1 WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                5            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"
D10V9, binary
                cls
clus               0   1
  WNK1 MUTATED     0   4
  WNK1 WILD-TYPE   5 207
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED      0    4
  WNK1 WILD-TYPE    5  207
                        clus
vv                       WNK1 MUTATED WNK1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            207
[1] 2 2
[1] FALSE

Clustering(11) Variable = ANP32E MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  ANP32E MUTATED     2   2
  ANP32E WILD-TYPE 153  87
  ANP32E MUTATED ANP32E WILD-TYPE 
               4              240 
  ANP32E MUTATED ANP32E WILD-TYPE 
               2               87 
$`ANP32E MUTATED`
TCGA-DX-A3UB TCGA-DX-A3UE TCGA-FX-A48G TCGA-UE-A6QU 
       61.91        34.88        19.89        13.41 

$`ANP32E WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        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 
       83.38        54.77         9.04        43.76        86.83       124.73 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       33.44        44.68        34.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF 
        4.54        14.99        10.68        55.07        50.43        81.90 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        31.27        24.26        24.69        40.80        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       102.41        47.57        25.15        15.95        24.59 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18         3.06        34.55        23.54        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        20.05        15.22 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       12.20        17.95        14.43         9.34        61.97        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR 
       44.68        38.17        35.77        14.07        51.91       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        35.54        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        17.79        12.00        15.72        15.85        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       86.10        12.07        66.74         9.21        77.88       106.55 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31        31.63 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        16.60        21.70        20.32        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       48.30        34.88         4.57        15.91        12.62        33.30 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.72        80.48        26.93        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       19.89        25.22        52.27        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
        3.91        53.33        62.17       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-KF-A41W TCGA-LI-A67I 
        5.19        36.36        16.41        35.28        11.70        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35        25.41         8.28         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       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 
       37.55        38.63        81.01        20.52        20.94        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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       18.94         3.88        17.52        22.82        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
        8.61        19.63        13.22        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
        4.80        72.72        41.49        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         9.04        63.35        26.43        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       25.71        15.95        16.83        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.58        36.43         4.37        13.38        15.95        15.98 

  ANP32E MUTATED ANP32E WILD-TYPE 
           13.41             0.49 
  ANP32E MUTATED ANP32E WILD-TYPE 
           61.91           143.41 
  ANP32E MUTATED ANP32E WILD-TYPE 
          27.385           25.560 
[1] "13.4 - 61.9 (27.4)" "0.5 - 143.4 (25.6)"
[1] "hr=" "1.5"
D11V2, continuous
                  vv
clus               CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  ANP32E MUTATED                0                  0                   0
  ANP32E WILD-TYPE              1                  7                   2
                  vv
clus               CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  ANP32E MUTATED                     0                             0
  ANP32E WILD-TYPE                   1                             1
                  vv
clus               GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  ANP32E MUTATED                       0                      1
  ANP32E WILD-TYPE                     1                     24
                  vv
clus               HEAD AND NECK - HEAD HEAD AND NECK - NECK
  ANP32E MUTATED                      0                    0
  ANP32E WILD-TYPE                    2                    1
                  vv
clus               HEAD AND NECK - OTHER (PLEASE SPECIFY
  ANP32E MUTATED                                       0
  ANP32E WILD-TYPE                                     2
                  vv
clus               LOWER ABDOMINAL/PELVIC - BLADDER
  ANP32E MUTATED                                  0
  ANP32E WILD-TYPE                                1
                  vv
clus               LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  ANP32E MUTATED                                                0
  ANP32E WILD-TYPE                                              2
                  vv
clus               LOWER ABDOMINAL/PELVIC - PELVIC
  ANP32E MUTATED                                 0
  ANP32E WILD-TYPE                              11
                  vv
clus               LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  ANP32E MUTATED                                         0
  ANP32E WILD-TYPE                                       2
                  vv
clus               LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  ANP32E MUTATED                              0                       0
  ANP32E WILD-TYPE                            4                       2
                  vv
clus               LOWER EXTREMITY - LOWER LEG/CALF
  ANP32E MUTATED                                  0
  ANP32E WILD-TYPE                               15
                  vv
clus               LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  ANP32E MUTATED                                         0
  ANP32E WILD-TYPE                                       3
                  vv
clus               LOWER EXTREMITY - THIGH/KNEE
  ANP32E MUTATED                              0
  ANP32E WILD-TYPE                           42
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - COLON
  ANP32E MUTATED                                         0
  ANP32E WILD-TYPE                                       4
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  ANP32E MUTATED                                           0
  ANP32E WILD-TYPE                                         2
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  ANP32E MUTATED                                                  0
  ANP32E WILD-TYPE                                                5
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  ANP32E MUTATED                                          0
  ANP32E WILD-TYPE                                        7
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  ANP32E MUTATED                                                         0
  ANP32E WILD-TYPE                                                       2
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  ANP32E MUTATED                                            0
  ANP32E WILD-TYPE                                          1
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  ANP32E MUTATED                                                   0
  ANP32E WILD-TYPE                                                71
                  vv
clus               RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  ANP32E MUTATED                                                    1
  ANP32E WILD-TYPE                                                  2
                  vv
clus               SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  ANP32E MUTATED                                    0                        1
  ANP32E WILD-TYPE                                  2                        4
                  vv
clus               SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  ANP32E MUTATED                             0                         0
  ANP32E WILD-TYPE                           3                         1
                  vv
clus               UPPER EXTREMITY - SHOULDER/AXILLA
  ANP32E MUTATED                                   1
  ANP32E WILD-TYPE                                 6
                  vv
clus               UPPER EXTREMITY - UPPER ARM/ELBOW
  ANP32E MUTATED                                   0
  ANP32E WILD-TYPE                                 5
D11V3, multiclass
                                                         clus
vv                                                        ANP32E 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                                         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                    0
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                   1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                   0
  SUPERFICIAL TRUNK - BACK                                             1
  SUPERFICIAL TRUNK - BUTTOCK                                          0
  SUPERFICIAL TRUNK - FLANK                                            0
  UPPER EXTREMITY - SHOULDER/AXILLA                                    1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                    0
                                                         clus
vv                                                        ANP32E 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                                       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                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                                               4
  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"
D11V4, binary
                  cls
clus                 0   1
  ANP32E MUTATED     3   1
  ANP32E WILD-TYPE 128 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANP32E MUTATED      3    1
  ANP32E WILD-TYPE  128  112
        clus
vv       ANP32E MUTATED ANP32E WILD-TYPE
  FEMALE              3              128
  MALE                1              112
[1] 2 2
[1] FALSE
D11V5, binary
                  cls
clus                 0   1
  ANP32E MUTATED     3   1
  ANP32E WILD-TYPE 167  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANP32E MUTATED      3    1
  ANP32E WILD-TYPE  167   66
     clus
vv    ANP32E MUTATED ANP32E WILD-TYPE
  NO               3              167
  YES              1               66
[1] 2 2
[1] FALSE
                  vv
clus               DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  ANP32E MUTATED                              0             0
  ANP32E WILD-TYPE                           56             2
                  vv
clus               GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  ANP32E MUTATED                                                                          0
  ANP32E WILD-TYPE                                                                        1
                  vv
clus               LEIOMYOSARCOMA (LMS)
  ANP32E MUTATED                      3
  ANP32E WILD-TYPE                   94
                  vv
clus               MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  ANP32E MUTATED                                                  0
  ANP32E WILD-TYPE                                                8
                  vv
clus               MYXOFIBROSARCOMA
  ANP32E MUTATED                  0
  ANP32E WILD-TYPE               21
                  vv
clus               PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  ANP32E MUTATED                                                         0
  ANP32E WILD-TYPE                                                      29
                  vv
clus               SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  ANP32E MUTATED                                          0
  ANP32E WILD-TYPE                                        2
                  vv
clus               SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  ANP32E MUTATED                             0                             0
  ANP32E WILD-TYPE                           2                             6
                  vv
clus               UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  ANP32E MUTATED                                            1
  ANP32E WILD-TYPE                                         19
D11V6, multiclass
                                                                          clus
vv                                                                         ANP32E 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                                                                      0
  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                                                                         ANP32E WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                           56
  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)                                             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
  ANP32E MUTATED     3   0   0   1
  ANP32E WILD-TYPE 144  64   9  22
D11V7, multiclass
    clus
vv   ANP32E MUTATED ANP32E WILD-TYPE
  R0              3              144
  R1              0               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
  ANP32E MUTATED       1                         0     3
  ANP32E WILD-TYPE     4                        18   211
D11V8, multiclass
                           clus
vv                          ANP32E MUTATED ANP32E WILD-TYPE
  ASIAN                                  1                4
  BLACK OR AFRICAN AMERICAN              0               18
  WHITE                                  3              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"
D11V9, binary
                  cls
clus                 0   1
  ANP32E MUTATED     0   3
  ANP32E WILD-TYPE   5 208
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANP32E MUTATED      0    3
  ANP32E WILD-TYPE    5  208
                        clus
vv                       ANP32E MUTATED ANP32E WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              208
[1] 2 2
[1] FALSE

Clustering(12) Variable = PTEN MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     5   2
  PTEN WILD-TYPE 150  87
  PTEN MUTATED PTEN WILD-TYPE 
             7            237 
  PTEN MUTATED PTEN WILD-TYPE 
             2             87 
$`PTEN MUTATED`
TCGA-3B-A9HZ TCGA-IE-A4EK TCGA-LI-A67I TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 
       38.47         1.38        22.03        72.72        65.46        22.62 
TCGA-Z4-A9VC 
       13.38 

$`PTEN WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        43.76        86.83       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       44.68        34.68        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        61.91        55.07        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       81.90         9.73        31.27        24.26        24.69        40.80 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       102.41        47.57        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       24.59        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX 
       21.63        16.18         3.06        34.55        23.54        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       74.10        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        20.05 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       15.22        12.20        17.95        14.43         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ 
       33.07        44.68        38.17        35.77        14.07        51.91 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      124.37        27.95        35.54        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
        6.58         1.15        17.79        12.00        15.72        15.85 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       40.60        86.10        12.07        66.74         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
      106.55       106.45        13.28        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       30.51        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       31.63        31.13        16.60        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
       15.48         8.05        48.30        34.88         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       12.62        33.30         0.72        80.48        26.93        19.53 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        3.22        19.89        25.22        52.27        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-KF-A41W 
       23.38         5.19        36.36        16.41        35.28        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35        25.41         8.28         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       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 
       37.55        38.63        81.01        20.52        20.94        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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       18.94         3.88        17.52        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-A8XT TCGA-WK-A8XX TCGA-WK-A8XZ TCGA-WP-A9GB 
       11.93         4.80        41.49        38.27        56.61         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        26.43        36.82        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 
TCGA-Z4-A8JB TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        15.95        15.98 

  PTEN MUTATED PTEN WILD-TYPE 
          1.38           0.49 
  PTEN MUTATED PTEN WILD-TYPE 
         72.72         143.41 
  PTEN MUTATED PTEN WILD-TYPE 
         22.62          25.71 
[1] "1.4 - 72.7 (22.6)"  "0.5 - 143.4 (25.7)"
[1] "hr=" "1.3"
D12V2, 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                     25
                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                               15
                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                           40
                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
D12V3, 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                                              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                                        40
  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"
D12V4, binary
                cls
clus               0   1
  PTEN MUTATED     4   3
  PTEN WILD-TYPE 127 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    3
  PTEN WILD-TYPE  127  110
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4            127
  MALE              3            110
[1] 2 2
[1] FALSE
D12V5, binary
                cls
clus               0   1
  PTEN MUTATED     3   3
  PTEN WILD-TYPE 167  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      3    3
  PTEN WILD-TYPE  167   64
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             3            167
  YES            3             64
[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                   93
                vv
clus             MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  PTEN MUTATED                                                  0
  PTEN WILD-TYPE                                                8
                vv
clus             MYXOFIBROSARCOMA
  PTEN MUTATED                  1
  PTEN WILD-TYPE               20
                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                                         19
D12V6, 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)                                                                 93
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                      8
  MYXOFIBROSARCOMA                                                                     20
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              29
  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
  PTEN MUTATED     3   3   0   1
  PTEN WILD-TYPE 144  61   9  22
D12V7, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            3            144
  R1            3             61
  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   207
D12V8, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              5
  BLACK OR AFRICAN AMERICAN            0             18
  WHITE                                7            207
[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
  PTEN MUTATED     0   7
  PTEN WILD-TYPE   5 204
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    7
  PTEN WILD-TYPE    5  204
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            7            204
[1] 2 2
[1] FALSE

Clustering(13) Variable = KRTAP5-5 MUTATION ANALYSIS
D13V1, survival
                    sevent
clus2                  0   1
  KRTAP5-5 MUTATED     4   3
  KRTAP5-5 WILD-TYPE 151  86
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 7                237 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
                 3                 86 
$`KRTAP5-5 MUTATED`
TCGA-DX-A1KX TCGA-DX-A2J1 TCGA-DX-A48N TCGA-DX-A8BN TCGA-DX-AB30 TCGA-JV-A75J 
       38.24        83.38        24.69        38.17        22.85         3.91 
TCGA-QQ-A8VH 
       10.52 

$`KRTAP5-5 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        32.71        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J4 
       66.87         6.28        60.30         8.58         9.70        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        43.76        86.83       124.73        33.44        44.68 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       34.68        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        61.91        55.07        50.43        34.88        81.90 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        31.27        24.26        40.80        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      102.41        47.57        25.15        15.95        24.59        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        34.55        23.54        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       88.31        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU 
      135.48        29.49        48.20        20.05        15.22        12.20 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        61.97        33.07        44.68 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       35.77        14.07        51.91       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       36.69        60.66        19.43         6.58         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
       12.00        15.72        15.85        40.60        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       66.74         9.21        77.88       106.55       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       50.40       101.98        30.51        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE 
       50.89        71.31        31.63        31.13        16.60        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        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV 
        4.57        15.91        12.62        33.30         0.72        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
       26.93        19.53         3.22         1.38        19.89        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       52.27        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42W 
        5.92        22.62        16.41         1.05        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        36.36        16.41 
TCGA-KD-A5QU TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       35.28        11.70        22.03        13.35        25.41         8.28 
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       120.20        37.55        38.63        81.01 
TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       20.52        20.94        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-SG-A849 TCGA-SI-A71O 
        0.72        16.77        18.94         3.88        17.52        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-A8XT 
       10.72        12.46        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       38.27        65.46        56.61        22.62         9.04        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       26.43        36.82        18.35        25.71        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       38.96        35.08        17.72        15.58        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
              3.91               0.49 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             83.38             143.41 
  KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE 
             24.69              25.71 
[1] "3.9 - 83.4 (24.7)"  "0.5 - 143.4 (25.7)"
[1] "hr=" "1.3"
D13V2, 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                     24
                    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                               15
                    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                           40
                    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
D13V3, 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                                                  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                                        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                       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"
D13V4, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     5   2
  KRTAP5-5 WILD-TYPE 126 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      5    2
  KRTAP5-5 WILD-TYPE  126  111
        clus
vv       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  FEMALE                5                126
  MALE                  2                111
[1] 2 2
[1] FALSE
D13V5, binary
                    cls
clus                   0   1
  KRTAP5-5 MUTATED     4   3
  KRTAP5-5 WILD-TYPE 166  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      4    3
  KRTAP5-5 WILD-TYPE  166   64
     clus
vv    KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  NO                 4                166
  YES                3                 64
[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                   96
                    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               20
                    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                                         20
D13V6, 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)                                                                     96
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          7
  MYXOFIBROSARCOMA                                                                         20
  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
  KRTAP5-5 MUTATED     2   3   1   1
  KRTAP5-5 WILD-TYPE 145  61   8  22
D13V7, multiclass
    clus
vv   KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  R0                2                145
  R1                3                 61
  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   207
D13V8, multiclass
                           clus
vv                          KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                    7                207
[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
  KRTAP5-5 MUTATED     1   6
  KRTAP5-5 WILD-TYPE   4 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-5 MUTATED      1    6
  KRTAP5-5 WILD-TYPE    4  205
                        clus
vv                       KRTAP5-5 MUTATED KRTAP5-5 WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO                6                205
[1] 2 2
[1] FALSE

Clustering(14) Variable = TRAF7 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  TRAF7 MUTATED     3   1
  TRAF7 WILD-TYPE 152  88
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              4             240 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
              1              88 
$`TRAF7 MUTATED`
TCGA-DX-A1L4 TCGA-DX-A6YU TCGA-DX-A8BJ TCGA-DX-AB35 
       42.54        23.54         9.34        30.51 

$`TRAF7 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       54.21        59.24        33.53        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        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        43.76        86.83       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       44.68        34.68        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        61.91        55.07        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       81.90         9.73        31.27        24.26        24.69        40.80 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       102.41        47.57        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       24.59        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ 
       21.63        16.18         3.06        34.55        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        20.05        15.22 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       12.20        17.95        14.43        61.97        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       38.17        35.77        14.07        51.91       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.54        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       17.79        12.00        15.72        15.85        40.60        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
       12.07        66.74         9.21        77.88       106.55       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 
       13.28        50.40        22.85       101.98        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK 
       32.15        50.89        71.31        31.63        31.13        16.60 
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        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        26.93        19.53         3.22         1.38        19.89 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        52.27        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
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-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       36.36        16.41        35.28        11.70        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       25.41         8.28         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       120.20        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
       38.63        81.01        20.52        20.94        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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
        3.88        17.52        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-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
        4.80        72.72        41.49        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         9.04        63.35        26.43        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       25.71        15.95        16.83        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.58        36.43         4.37        13.38        15.95        15.98 

  TRAF7 MUTATED TRAF7 WILD-TYPE 
           9.34            0.49 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
          42.54          143.41 
  TRAF7 MUTATED TRAF7 WILD-TYPE 
         27.025          25.560 
[1] "9.3 - 42.5 (27.0)"  "0.5 - 143.4 (25.6)"
[1] "hr=" "1.1"
D14V2, 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                     25
                 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                               15
                 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                           42
                 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
D14V3, 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                                               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               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"
D14V4, binary
                 cls
clus                0   1
  TRAF7 MUTATED     1   3
  TRAF7 WILD-TYPE 130 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF7 MUTATED      1    3
  TRAF7 WILD-TYPE  130  110
        clus
vv       TRAF7 MUTATED TRAF7 WILD-TYPE
  FEMALE             1             130
  MALE               3             110
[1] 2 2
[1] FALSE
D14V5, binary
                 cls
clus                0   1
  TRAF7 MUTATED     3   1
  TRAF7 WILD-TYPE 167  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF7 MUTATED      3    1
  TRAF7 WILD-TYPE  167   66
     clus
vv    TRAF7 MUTATED TRAF7 WILD-TYPE
  NO              3             167
  YES             1              66
[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                   97
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  TRAF7 MUTATED                                                  0
  TRAF7 WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  TRAF7 MUTATED                  1
  TRAF7 WILD-TYPE               20
                 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                                         20
D14V6, 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)                                                                  97
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       8
  MYXOFIBROSARCOMA                                                                      20
  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
  TRAF7 MUTATED     4   0   0   0
  TRAF7 WILD-TYPE 143  64   9  23
D14V7, multiclass
    clus
vv   TRAF7 MUTATED TRAF7 WILD-TYPE
  R0             4             143
  R1             0              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
  TRAF7 MUTATED       0                         0     4
  TRAF7 WILD-TYPE     5                        18   210
D14V8, multiclass
                           clus
vv                          TRAF7 MUTATED TRAF7 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 4             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"
D14V9, binary
                 cls
clus                0   1
  TRAF7 MUTATED     0   4
  TRAF7 WILD-TYPE   5 207
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF7 MUTATED      0    4
  TRAF7 WILD-TYPE    5  207
                        clus
vv                       TRAF7 MUTATED TRAF7 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             207
[1] 2 2
[1] FALSE

Clustering(15) Variable = MEGF9 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  MEGF9 MUTATED     3   0
  MEGF9 WILD-TYPE 152  89
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              3             241 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
              0              89 
$`MEGF9 MUTATED`
TCGA-DX-A6YR TCGA-QC-A7B5 TCGA-WK-A8XS 
       34.55        13.08        72.72 

$`MEGF9 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        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 
       83.38        54.77         9.04        43.76        86.83       124.73 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       33.44        44.68        34.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        61.91        55.07        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        81.90         9.73        31.27        24.26        24.69 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       40.80        46.03        26.47       102.41        47.57        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        24.59        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A6YX 
       17.79        21.63        16.18         3.06        23.54        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       74.10        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        20.05 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       15.22        12.20        17.95        14.43         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ 
       33.07        44.68        38.17        35.77        14.07        51.91 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      124.37        27.95        35.54        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
        6.58         1.15        17.79        12.00        15.72        15.85 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       40.60        86.10        12.07        66.74         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
      106.55       106.45        13.28        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       30.51        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       31.63        31.13        16.60        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
       15.48         8.05        48.30        34.88         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       12.62        33.30         0.72        80.48        26.93        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        3.22         1.38        19.89        25.22        52.27        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       16.41         1.05         3.91        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        36.36        16.41        35.28 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       11.70        22.03        13.35        25.41         8.28         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       120.20        37.55        38.63        81.01        20.52 
TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       20.94        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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       16.77        18.94         3.88        17.52        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-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       12.46        11.93         4.80        41.49        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         9.04        63.35        26.43        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.35        25.71        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       17.72        15.58        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  MEGF9 MUTATED MEGF9 WILD-TYPE 
          13.08            0.49 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
          72.72          143.41 
  MEGF9 MUTATED MEGF9 WILD-TYPE 
          34.55           25.41 
[1] "13.1 - 72.7 (34.5)" "0.5 - 143.4 (25.4)"
[1] "hr="     "9100000"
D15V2, 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                     25
                 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                               15
                 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                           42
                 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
D15V3, 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                                               25
  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                                     15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         42
  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"
D15V4, binary
                 cls
clus                0   1
  MEGF9 MUTATED     1   2
  MEGF9 WILD-TYPE 130 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF9 MUTATED      1    2
  MEGF9 WILD-TYPE  130  111
        clus
vv       MEGF9 MUTATED MEGF9 WILD-TYPE
  FEMALE             1             130
  MALE               2             111
[1] 2 2
[1] FALSE
D15V5, binary
                 cls
clus                0   1
  MEGF9 MUTATED     2   1
  MEGF9 WILD-TYPE 168  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF9 MUTATED      2    1
  MEGF9 WILD-TYPE  168   66
     clus
vv    MEGF9 MUTATED MEGF9 WILD-TYPE
  NO              2             168
  YES             1              66
[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                   96
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  MEGF9 MUTATED                                                  0
  MEGF9 WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  MEGF9 MUTATED                  1
  MEGF9 WILD-TYPE               20
                 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                                         20
D15V6, 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)                                                                  96
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       8
  MYXOFIBROSARCOMA                                                                      20
  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
  MEGF9 MUTATED     2   0   0   1
  MEGF9 WILD-TYPE 145  64   9  22
D15V7, multiclass
    clus
vv   MEGF9 MUTATED MEGF9 WILD-TYPE
  R0             2             145
  R1             0              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
  MEGF9 MUTATED       0                         0     3
  MEGF9 WILD-TYPE     5                        18   211
D15V8, multiclass
                           clus
vv                          MEGF9 MUTATED MEGF9 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             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"
D15V9, binary
                 cls
clus                0   1
  MEGF9 MUTATED     0   3
  MEGF9 WILD-TYPE   5 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF9 MUTATED      0    3
  MEGF9 WILD-TYPE    5  208
                        clus
vv                       MEGF9 MUTATED MEGF9 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             208
[1] 2 2
[1] FALSE

Clustering(16) Variable = LOR MUTATION ANALYSIS
D16V1, survival
               sevent
clus2             0   1
  LOR MUTATED     4   2
  LOR WILD-TYPE 151  87
  LOR MUTATED LOR WILD-TYPE 
            6           238 
  LOR MUTATED LOR WILD-TYPE 
            2            87 
$`LOR MUTATED`
TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A6BG TCGA-DX-A7ER TCGA-DX-AB2F TCGA-FX-A48G 
       54.77        43.76        17.79        48.20        12.00        19.89 

$`LOR WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        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 
       83.38         9.04        86.83       124.73        33.44        44.68 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       34.68        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        61.91        55.07        50.43        34.88        81.90 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        31.27        24.26        24.69        40.80        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       102.41        47.57        25.15        15.95        24.59 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6BK 
       66.05        23.44        28.96         9.11        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        34.55        23.54        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       88.31        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG 
      135.48        29.49        20.05        15.22        12.20        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       14.43         9.34        61.97        33.07        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       35.77        14.07        51.91       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       36.69        60.66        19.43         6.58         1.15        17.79 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
       15.72        15.85        40.60        86.10        12.07        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
        9.21        77.88       106.55       106.45        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        30.51        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE 
       50.89        71.31        31.63        31.13        16.60        21.70 
TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       20.32        15.48         8.05        48.30        34.88         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH 
       15.91        12.62        33.30         0.72        80.48        26.93 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       19.53         3.22         1.38        19.89        25.22        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W 
       22.62        16.41         1.05         3.91        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        36.36        16.41 
TCGA-KD-A5QU TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       35.28        11.70        22.03        13.35        25.41         8.28 
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       120.20        37.55        38.63        81.01 
TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       20.52        20.94        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-SG-A849 
       10.52         0.72        16.77        18.94         3.88        17.52 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       22.82        25.35        32.75         8.61        19.63        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.41        10.72        12.46        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB 
       41.49        38.27        65.46        56.61        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        26.43        36.82        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  LOR MUTATED LOR WILD-TYPE 
        12.00          0.49 
  LOR MUTATED LOR WILD-TYPE 
        54.77        143.41 
  LOR MUTATED LOR WILD-TYPE 
       31.825        25.560 
[1] "12.0 - 54.8 (31.8)" "0.5 - 143.4 (25.6)"
[1] "hr=" "1.1"
D16V2, 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                     24
               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                               15
               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                           42
               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
D16V3, 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                                             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                                    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                    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"
D16V4, binary
               cls
clus              0   1
  LOR MUTATED     2   4
  LOR WILD-TYPE 129 109
[1] "tbl2"
               cls
clus            [,1] [,2]
  LOR MUTATED      2    4
  LOR WILD-TYPE  129  109
        clus
vv       LOR MUTATED LOR WILD-TYPE
  FEMALE           2           129
  MALE             4           109
[1] 2 2
[1] FALSE
D16V5, binary
               cls
clus              0   1
  LOR MUTATED     5   1
  LOR WILD-TYPE 165  66
[1] "tbl2"
               cls
clus            [,1] [,2]
  LOR MUTATED      5    1
  LOR WILD-TYPE  165   66
     clus
vv    LOR MUTATED LOR WILD-TYPE
  NO            5           165
  YES           1            66
[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                   96
               vv
clus            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  LOR MUTATED                                                  0
  LOR WILD-TYPE                                                8
               vv
clus            MYXOFIBROSARCOMA
  LOR MUTATED                  0
  LOR WILD-TYPE               21
               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                                         20
D16V6, 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)                                                                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                                                        5
  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
  LOR MUTATED     5   0   0   1
  LOR WILD-TYPE 142  64   9  22
D16V7, multiclass
    clus
vv   LOR MUTATED LOR WILD-TYPE
  R0           5           142
  R1           0            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
  LOR MUTATED       0                         0     6
  LOR WILD-TYPE     5                        18   208
D16V8, multiclass
                           clus
vv                          LOR MUTATED LOR WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            18
  WHITE                               6           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"
D16V9, binary
               cls
clus              0   1
  LOR MUTATED     0   5
  LOR WILD-TYPE   5 206
[1] "tbl2"
               cls
clus            [,1] [,2]
  LOR MUTATED      0    5
  LOR WILD-TYPE    5  206
                        clus
vv                       LOR MUTATED LOR WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           5           206
[1] 2 2
[1] FALSE

Clustering(17) Variable = CABLES1 MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  CABLES1 MUTATED     1   2
  CABLES1 WILD-TYPE 154  87
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                3               241 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
                2                87 
$`CABLES1 MUTATED`
TCGA-DX-A3UB TCGA-DX-A48L TCGA-DX-AB3A 
       61.91        24.26        32.15 

$`CABLES1 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        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 
       83.38        54.77         9.04        43.76        86.83       124.73 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       33.44        44.68        34.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        14.99        10.68        55.07        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       81.90         9.73        31.27        24.69        40.80        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       102.41        47.57        25.15        15.95        24.59 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18         3.06        34.55        23.54        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        20.05        15.22 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       12.20        17.95        14.43         9.34        61.97        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR 
       44.68        38.17        35.77        14.07        51.91       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        35.54        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        17.79        12.00        15.72        15.85        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       86.10        12.07        66.74         9.21        77.88       106.55 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       60.00        84.66        50.89        71.31        31.63        31.13 
TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       16.60        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       48.30        34.88         4.57        15.91        12.62        33.30 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.72        80.48        26.93        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       19.89        25.22        52.27        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
        3.91        53.33        62.17       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-KF-A41W TCGA-LI-A67I 
        5.19        36.36        16.41        35.28        11.70        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35        25.41         8.28         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       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 
       37.55        38.63        81.01        20.52        20.94        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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       18.94         3.88        17.52        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-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        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         9.04        63.35        26.43        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.35        25.71        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       17.72        15.58        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  CABLES1 MUTATED CABLES1 WILD-TYPE 
            24.26              0.49 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
            61.91            143.41 
  CABLES1 MUTATED CABLES1 WILD-TYPE 
            32.15             25.41 
[1] "24.3 - 61.9 (32.1)" "0.5 - 143.4 (25.4)"
[1] "hr=" "1.6"
D17V2, 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                     25
                   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                               14
                   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                           42
                   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
D17V3, 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                                                 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                                       14
  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                 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"
D17V4, binary
                   cls
clus                  0   1
  CABLES1 MUTATED     1   2
  CABLES1 WILD-TYPE 130 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CABLES1 MUTATED      1    2
  CABLES1 WILD-TYPE  130  111
        clus
vv       CABLES1 MUTATED CABLES1 WILD-TYPE
  FEMALE               1               130
  MALE                 2               111
[1] 2 2
[1] FALSE
D17V5, binary
                   cls
clus                  0   1
  CABLES1 MUTATED     2   1
  CABLES1 WILD-TYPE 168  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CABLES1 MUTATED      2    1
  CABLES1 WILD-TYPE  168   66
     clus
vv    CABLES1 MUTATED CABLES1 WILD-TYPE
  NO                2               168
  YES               1                66
[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                   95
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  CABLES1 MUTATED                                                  0
  CABLES1 WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  CABLES1 MUTATED                  0
  CABLES1 WILD-TYPE               21
                   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                                         20
D17V6, 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)                                                                    95
  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
  CABLES1 MUTATED     3   0   0   0
  CABLES1 WILD-TYPE 144  64   9  23
D17V7, multiclass
    clus
vv   CABLES1 MUTATED CABLES1 WILD-TYPE
  R0               3               144
  R1               0                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
  CABLES1 MUTATED       0                         0     3
  CABLES1 WILD-TYPE     5                        18   211
D17V8, multiclass
                           clus
vv                          CABLES1 MUTATED CABLES1 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               0                18
  WHITE                                   3               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"
D17V9, binary
                   cls
clus                  0   1
  CABLES1 MUTATED     0   2
  CABLES1 WILD-TYPE   5 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CABLES1 MUTATED      0    2
  CABLES1 WILD-TYPE    5  209
                        clus
vv                       CABLES1 MUTATED CABLES1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2               209
[1] 2 2
[1] FALSE

Clustering(18) Variable = COL18A1 MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  COL18A1 MUTATED     5   2
  COL18A1 WILD-TYPE 150  87
  COL18A1 MUTATED COL18A1 WILD-TYPE 
                7               237 
  COL18A1 MUTATED COL18A1 WILD-TYPE 
                2                87 
$`COL18A1 MUTATED`
TCGA-3B-A9HI TCGA-DX-A3U7 TCGA-DX-A6BK TCGA-DX-AB2E TCGA-QC-AA9N TCGA-RN-AAAQ 
       50.01        51.02        16.18        17.79        17.65        16.77 
TCGA-SG-A849 
       17.52 

$`COL18A1 WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       36.30        19.69        31.53        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        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        43.76        86.83       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        34.68        31.86        35.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        61.91        55.07        50.43        34.88        81.90 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        31.27        24.26        24.69        40.80        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       102.41        47.57        25.15        15.95        24.59 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        34.55        23.54        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       88.31        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU 
      135.48        29.49        48.20        20.05        15.22        12.20 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        61.97        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS 
       38.17        35.77        14.07        51.91       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.54        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
       12.00        15.72        15.85        40.60        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       66.74         9.21        77.88       106.55       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       50.40        22.85       101.98        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK 
       32.15        50.89        71.31        31.63        31.13        16.60 
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        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        33.30         0.72 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        26.93        19.53         3.22         1.38        19.89 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        52.27        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
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-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       36.36        16.41        35.28        11.70        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       25.41         8.28         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       120.20        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 
       38.63        81.01        20.52        20.94        13.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
       46.82        18.08        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       64.77        10.52         0.72        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-A8XT 
       10.72        12.46        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       38.27        65.46        56.61        22.62         9.04        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       26.43        36.82        18.35        25.71        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       38.96        35.08        17.72        15.58        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  COL18A1 MUTATED COL18A1 WILD-TYPE 
            16.18              0.49 
  COL18A1 MUTATED COL18A1 WILD-TYPE 
            51.02            143.41 
  COL18A1 MUTATED COL18A1 WILD-TYPE 
            17.65             26.43 
[1] "16.2 - 51.0 (17.6)" "0.5 - 143.4 (26.4)"
[1] "hr=" "1"  
D18V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  COL18A1 MUTATED                0                  0                   0
  COL18A1 WILD-TYPE              1                  7                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  COL18A1 MUTATED                     0                             0
  COL18A1 WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  COL18A1 MUTATED                       0                      0
  COL18A1 WILD-TYPE                     1                     25
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  COL18A1 MUTATED                      0                    0
  COL18A1 WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  COL18A1 MUTATED                                       0
  COL18A1 WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  COL18A1 MUTATED                                  0
  COL18A1 WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  COL18A1 MUTATED                                                0
  COL18A1 WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  COL18A1 MUTATED                                 0
  COL18A1 WILD-TYPE                              11
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  COL18A1 MUTATED                                         0
  COL18A1 WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  COL18A1 MUTATED                              0                       0
  COL18A1 WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  COL18A1 MUTATED                                  0
  COL18A1 WILD-TYPE                               15
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  COL18A1 MUTATED                                         0
  COL18A1 WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  COL18A1 MUTATED                              1
  COL18A1 WILD-TYPE                           41
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  COL18A1 MUTATED                                         0
  COL18A1 WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  COL18A1 MUTATED                                           0
  COL18A1 WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  COL18A1 MUTATED                                                  0
  COL18A1 WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  COL18A1 MUTATED                                          0
  COL18A1 WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  COL18A1 MUTATED                                                         0
  COL18A1 WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  COL18A1 MUTATED                                            0
  COL18A1 WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  COL18A1 MUTATED                                                   1
  COL18A1 WILD-TYPE                                                70
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  COL18A1 MUTATED                                                    0
  COL18A1 WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  COL18A1 MUTATED                                    0                        0
  COL18A1 WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  COL18A1 MUTATED                             1                         0
  COL18A1 WILD-TYPE                           2                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  COL18A1 MUTATED                                   2
  COL18A1 WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  COL18A1 MUTATED                                   2
  COL18A1 WILD-TYPE                                 3
D18V3, multiclass
                                                         clus
vv                                                        COL18A1 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                                      0
  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               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                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        COL18A1 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                                           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                      70
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             2
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       3
[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"
D18V4, binary
                   cls
clus                  0   1
  COL18A1 MUTATED     2   5
  COL18A1 WILD-TYPE 129 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL18A1 MUTATED      2    5
  COL18A1 WILD-TYPE  129  108
        clus
vv       COL18A1 MUTATED COL18A1 WILD-TYPE
  FEMALE               2               129
  MALE                 5               108
[1] 2 2
[1] FALSE
D18V5, binary
                   cls
clus                  0   1
  COL18A1 MUTATED     4   3
  COL18A1 WILD-TYPE 166  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL18A1 MUTATED      4    3
  COL18A1 WILD-TYPE  166   64
     clus
vv    COL18A1 MUTATED COL18A1 WILD-TYPE
  NO                4               166
  YES               3                64
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  COL18A1 MUTATED                              2             0
  COL18A1 WILD-TYPE                           54             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  COL18A1 MUTATED                                                                          0
  COL18A1 WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  COL18A1 MUTATED                      1
  COL18A1 WILD-TYPE                   96
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  COL18A1 MUTATED                                                  1
  COL18A1 WILD-TYPE                                                7
                   vv
clus                MYXOFIBROSARCOMA
  COL18A1 MUTATED                  1
  COL18A1 WILD-TYPE               20
                   vv
clus                PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  COL18A1 MUTATED                                                         0
  COL18A1 WILD-TYPE                                                      29
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  COL18A1 MUTATED                                          0
  COL18A1 WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  COL18A1 MUTATED                             0                             0
  COL18A1 WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  COL18A1 MUTATED                                            2
  COL18A1 WILD-TYPE                                         18
D18V6, multiclass
                                                                          clus
vv                                                                         COL18A1 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           2
  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                                0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             2
                                                                          clus
vv                                                                         COL18A1 WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            54
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    96
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         7
  MYXOFIBROSARCOMA                                                                        20
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 29
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              18
[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
  COL18A1 MUTATED     2   3   0   1
  COL18A1 WILD-TYPE 145  61   9  22
D18V7, multiclass
    clus
vv   COL18A1 MUTATED COL18A1 WILD-TYPE
  R0               2               145
  R1               3                61
  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
  COL18A1 MUTATED       0                         1     6
  COL18A1 WILD-TYPE     5                        17   208
D18V8, multiclass
                           clus
vv                          COL18A1 MUTATED COL18A1 WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                17
  WHITE                                   6               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"
D18V9, binary
                   cls
clus                  0   1
  COL18A1 MUTATED     0   6
  COL18A1 WILD-TYPE   5 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL18A1 MUTATED      0    6
  COL18A1 WILD-TYPE    5  205
                        clus
vv                       COL18A1 MUTATED COL18A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6               205
[1] 2 2
[1] FALSE

Clustering(19) Variable = LHCGR MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  LHCGR MUTATED     3   3
  LHCGR WILD-TYPE 152  86
  LHCGR MUTATED LHCGR WILD-TYPE 
              6             238 
  LHCGR MUTATED LHCGR WILD-TYPE 
              3              86 
$`LHCGR MUTATED`
TCGA-DX-A8BU TCGA-DX-AB2E TCGA-QC-A6FX TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-WK-A8XT 
       36.69        17.79        20.94        35.90        10.52        41.49 

$`LHCGR WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        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 
       83.38        54.77         9.04        43.76        86.83       124.73 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       33.44        44.68        34.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        61.91        55.07        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        81.90         9.73        31.27        24.26        24.69 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       40.80        46.03        26.47       102.41        47.57        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        24.59        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU 
       17.79        21.63        16.18         3.06        34.55        23.54 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        74.10        64.21        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ 
       20.05        15.22        12.20        17.95        14.43         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP 
       61.97        33.07        44.68        38.17        35.77        14.07 
TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX 
       51.91       124.37        27.95        35.54        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        6.58         1.15        12.00        15.72        15.85        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       86.10        12.07        66.74         9.21        77.88       106.55 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31        31.63 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       31.13        16.60        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        8.05        48.30        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       33.30         0.72        80.48        26.93        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        19.89        25.22        52.27        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-KF-A41W 
       23.38         5.19        36.36        16.41        35.28        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
       22.03        13.35        25.41         8.28         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 
      120.20        37.55        38.63        81.01        20.52        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
       17.65         1.84        46.82        18.08        48.59        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
      130.32        64.77         0.72        16.77        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
       17.52        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 
       72.72        38.27        65.46        56.61        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       63.35        26.43        36.82        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  LHCGR MUTATED LHCGR WILD-TYPE 
          10.52            0.49 
  LHCGR MUTATED LHCGR WILD-TYPE 
          41.49          143.41 
  LHCGR MUTATED LHCGR WILD-TYPE 
          28.42           25.56 
[1] "10.5 - 41.5 (28.4)" "0.5 - 143.4 (25.6)"
[1] "hr=" "1.7"
D19V2, continuous
                 vv
clus              CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  LHCGR MUTATED                0                  0                   0
  LHCGR WILD-TYPE              1                  7                   2
                 vv
clus              CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  LHCGR MUTATED                     0                             1
  LHCGR WILD-TYPE                   1                             0
                 vv
clus              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  LHCGR MUTATED                       0                      0
  LHCGR WILD-TYPE                     1                     25
                 vv
clus              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  LHCGR MUTATED                      0                    0
  LHCGR WILD-TYPE                    2                    1
                 vv
clus              HEAD AND NECK - OTHER (PLEASE SPECIFY
  LHCGR MUTATED                                       0
  LHCGR WILD-TYPE                                     2
                 vv
clus              LOWER ABDOMINAL/PELVIC - BLADDER
  LHCGR MUTATED                                  0
  LHCGR WILD-TYPE                                1
                 vv
clus              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  LHCGR MUTATED                                                0
  LHCGR WILD-TYPE                                              2
                 vv
clus              LOWER ABDOMINAL/PELVIC - PELVIC
  LHCGR MUTATED                                 0
  LHCGR WILD-TYPE                              11
                 vv
clus              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  LHCGR MUTATED                                         0
  LHCGR WILD-TYPE                                       2
                 vv
clus              LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  LHCGR MUTATED                              0                       0
  LHCGR WILD-TYPE                            4                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  LHCGR MUTATED                                  0
  LHCGR WILD-TYPE                               15
                 vv
clus              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  LHCGR MUTATED                                         0
  LHCGR WILD-TYPE                                       3
                 vv
clus              LOWER EXTREMITY - THIGH/KNEE
  LHCGR MUTATED                              2
  LHCGR WILD-TYPE                           40
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  LHCGR MUTATED                                         0
  LHCGR WILD-TYPE                                       4
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  LHCGR MUTATED                                           0
  LHCGR WILD-TYPE                                         2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  LHCGR MUTATED                                                  0
  LHCGR WILD-TYPE                                                5
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  LHCGR MUTATED                                          1
  LHCGR WILD-TYPE                                        6
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  LHCGR MUTATED                                                         0
  LHCGR WILD-TYPE                                                       2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  LHCGR MUTATED                                            0
  LHCGR WILD-TYPE                                          1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  LHCGR MUTATED                                                   0
  LHCGR WILD-TYPE                                                71
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  LHCGR MUTATED                                                    0
  LHCGR WILD-TYPE                                                  3
                 vv
clus              SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  LHCGR MUTATED                                    0                        1
  LHCGR WILD-TYPE                                  2                        4
                 vv
clus              SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  LHCGR MUTATED                             0                         0
  LHCGR WILD-TYPE                           3                         1
                 vv
clus              UPPER EXTREMITY - SHOULDER/AXILLA
  LHCGR MUTATED                                   1
  LHCGR WILD-TYPE                                 6
                 vv
clus              UPPER EXTREMITY - UPPER ARM/ELBOW
  LHCGR MUTATED                                   0
  LHCGR WILD-TYPE                                 5
D19V3, multiclass
                                                         clus
vv                                                        LHCGR 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                               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                            1
  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                                   1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                   0
                                                         clus
vv                                                        LHCGR 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                                      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                              6
  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                                     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"
D19V4, binary
                 cls
clus                0   1
  LHCGR MUTATED     3   3
  LHCGR WILD-TYPE 128 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED      3    3
  LHCGR WILD-TYPE  128  110
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  FEMALE             3             128
  MALE               3             110
[1] 2 2
[1] FALSE
D19V5, binary
                 cls
clus                0   1
  LHCGR MUTATED     3   3
  LHCGR WILD-TYPE 167  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED      3    3
  LHCGR WILD-TYPE  167   64
     clus
vv    LHCGR MUTATED LHCGR WILD-TYPE
  NO              3             167
  YES             3              64
[1] 2 2
[1] FALSE
                 vv
clus              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  LHCGR MUTATED                              0             0
  LHCGR WILD-TYPE                           56             2
                 vv
clus              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  LHCGR MUTATED                                                                          0
  LHCGR WILD-TYPE                                                                        1
                 vv
clus              LEIOMYOSARCOMA (LMS)
  LHCGR MUTATED                      1
  LHCGR WILD-TYPE                   96
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  LHCGR MUTATED                                                  1
  LHCGR WILD-TYPE                                                7
                 vv
clus              MYXOFIBROSARCOMA
  LHCGR MUTATED                  1
  LHCGR WILD-TYPE               20
                 vv
clus              PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  LHCGR MUTATED                                                         2
  LHCGR WILD-TYPE                                                      27
                 vv
clus              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  LHCGR MUTATED                                          0
  LHCGR WILD-TYPE                                        2
                 vv
clus              SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  LHCGR MUTATED                             0                             1
  LHCGR WILD-TYPE                           2                             5
                 vv
clus              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  LHCGR MUTATED                                            0
  LHCGR WILD-TYPE                                         20
D19V6, multiclass
                                                                          clus
vv                                                                         LHCGR 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)                                     1
  MYXOFIBROSARCOMA                                                                     1
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                             0
  SYNOVIAL SARCOMA - BIPHASIC                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                        1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           0
                                                                          clus
vv                                                                         LHCGR 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)                                       7
  MYXOFIBROSARCOMA                                                                      20
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               27
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                          5
  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
  LHCGR MUTATED     4   1   0   1
  LHCGR WILD-TYPE 143  63   9  22
D19V7, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  R0             4             143
  R1             1              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
  LHCGR MUTATED       0                         0     6
  LHCGR WILD-TYPE     5                        18   208
D19V8, multiclass
                           clus
vv                          LHCGR MUTATED LHCGR WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 6             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"
D19V9, binary
                 cls
clus                0   1
  LHCGR MUTATED     0   5
  LHCGR WILD-TYPE   5 206
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED      0    5
  LHCGR WILD-TYPE    5  206
                        clus
vv                       LHCGR MUTATED LHCGR WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             206
[1] 2 2
[1] FALSE

Clustering(20) Variable = NF1 MUTATION ANALYSIS
D20V1, survival
               sevent
clus2             0   1
  NF1 MUTATED     6   4
  NF1 WILD-TYPE 149  85
  NF1 MUTATED NF1 WILD-TYPE 
           10           234 
  NF1 MUTATED NF1 WILD-TYPE 
            4            85 
$`NF1 MUTATED`
TCGA-3B-A9HT TCGA-DX-A6BG TCGA-DX-A6YU TCGA-DX-A8BP TCGA-DX-AB2X TCGA-DX-AB30 
       54.74        17.79        23.54        14.07        13.28        22.85 
TCGA-QQ-A5VC TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-SI-A71P 
       35.90        64.77        10.52        25.35 

$`NF1 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       88.57        44.91        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        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        43.76        86.83       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       44.68        34.68        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        61.91        55.07        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       81.90         9.73        31.27        24.26        24.69        40.80 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       102.41        47.57        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BH 
       24.59        66.05        23.44        28.96         9.11        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       16.18         3.06        34.55        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       88.31        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A7EU 
      135.48        29.49        48.20        20.05        15.22        12.20 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        61.97        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BQ TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        35.77        51.91       124.37        27.95        35.54 
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-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
       12.00        15.72        15.85        40.60        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z 
       66.74         9.21        77.88       106.55       106.45        50.40 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
      101.98        30.51        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO 
       71.31        31.63        31.13        16.60        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        48.30        34.88         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH 
       15.91        12.62        33.30         0.72        80.48        26.93 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       19.53         3.22         1.38        19.89        25.22        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W 
       22.62        16.41         1.05         3.91        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        36.36        16.41 
TCGA-KD-A5QU TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       35.28        11.70        22.03        13.35        25.41         8.28 
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       120.20        37.55        38.63        81.01 
TCGA-PT-A8TR TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       20.52        20.94        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-RN-A68Q TCGA-RN-AAAQ 
       18.08        48.59        37.12       130.32         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        17.52        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-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8XZ 
        4.80        72.72        41.49        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         9.04        63.35        26.43        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       25.71        15.95        16.83        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.58        36.43         4.37        13.38        15.95        15.98 

  NF1 MUTATED NF1 WILD-TYPE 
        10.52          0.49 
  NF1 MUTATED NF1 WILD-TYPE 
        64.77        143.41 
  NF1 MUTATED NF1 WILD-TYPE 
       23.195        26.450 
[1] "10.5 - 64.8 (23.2)" "0.5 - 143.4 (26.4)"
[1] "hr=" "1.3"
D20V2, continuous
               vv
clus            CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  NF1 MUTATED                0                  1                   0
  NF1 WILD-TYPE              1                  6                   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                     25
               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                               14
               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                           39
               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
D20V3, multiclass
                                                         clus
vv                                                        NF1 MUTATED
  CHEST - BREAST                                                    0
  CHEST - CHEST WALL                                                1
  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                                                  6
  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                               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                                   14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                             3
  LOWER EXTREMITY - THIGH/KNEE                                       39
  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"
D20V4, binary
               cls
clus              0   1
  NF1 MUTATED     5   5
  NF1 WILD-TYPE 126 108
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      5    5
  NF1 WILD-TYPE  126  108
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE           5           126
  MALE             5           108
[1] 2 2
[1] FALSE
D20V5, binary
               cls
clus              0   1
  NF1 MUTATED     6   4
  NF1 WILD-TYPE 164  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      6    4
  NF1 WILD-TYPE  164   63
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO            6           164
  YES           4            63
[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                   95
               vv
clus            MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  NF1 MUTATED                                                  3
  NF1 WILD-TYPE                                                5
               vv
clus            MYXOFIBROSARCOMA
  NF1 MUTATED                  2
  NF1 WILD-TYPE               19
               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                                         20
D20V6, 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                                                                   2
  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)                                                                95
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     5
  MYXOFIBROSARCOMA                                                                    19
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                             27
  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
  NF1 MUTATED     6   1   0   3
  NF1 WILD-TYPE 141  63   9  20
D20V7, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0           6           141
  R1           1            63
  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    10
  NF1 WILD-TYPE     5                        18   204
D20V8, multiclass
                           clus
vv                          NF1 MUTATED NF1 WILD-TYPE
  ASIAN                               0             5
  BLACK OR AFRICAN AMERICAN           0            18
  WHITE                              10           204
[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"
D20V9, binary
               cls
clus              0   1
  NF1 MUTATED     0  10
  NF1 WILD-TYPE   5 201
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      0   10
  NF1 WILD-TYPE    5  201
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO          10           201
[1] 2 2
[1] FALSE

Clustering(21) Variable = FOXD2 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  FOXD2 MUTATED     1   2
  FOXD2 WILD-TYPE 154  87
  FOXD2 MUTATED FOXD2 WILD-TYPE 
              3             241 
  FOXD2 MUTATED FOXD2 WILD-TYPE 
              2              87 
$`FOXD2 MUTATED`
TCGA-3B-A9I3 TCGA-DX-A6YX TCGA-WK-A8XT 
       26.56        16.87        41.49 

$`FOXD2 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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-3R-A8YX TCGA-DX-A1KU 
       10.32        38.47        36.03        18.64         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        60.30         8.58         9.70        83.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        43.76        86.83       124.73        33.44 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       44.68        34.68        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        61.91        55.07        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       81.90         9.73        31.27        24.26        24.69        40.80 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       102.41        47.57        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       24.59        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YZ 
       21.63        16.18         3.06        34.55        23.54        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        20.05        15.22 
TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       12.20        17.95        14.43         9.34        61.97        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ TCGA-DX-A8BR 
       44.68        38.17        35.77        14.07        51.91       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        35.54        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        17.79        12.00        15.72        15.85        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       86.10        12.07        66.74         9.21        77.88       106.55 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31        31.63 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       31.13        16.60        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        8.05        48.30        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       33.30         0.72        80.48        26.93        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        19.89        25.22        52.27        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-KF-A41W 
       23.38         5.19        36.36        16.41        35.28        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
       22.03        13.35        25.41         8.28         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-A6FX 
      120.20        37.55        38.63        81.01        20.52        20.94 
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-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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       16.77        18.94         3.88        17.52        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        72.72        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         9.04        63.35        26.43        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.35        25.71        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       17.72        15.58        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  FOXD2 MUTATED FOXD2 WILD-TYPE 
          16.87            0.49 
  FOXD2 MUTATED FOXD2 WILD-TYPE 
          41.49          143.41 
  FOXD2 MUTATED FOXD2 WILD-TYPE 
          26.56           25.41 
[1] "16.9 - 41.5 (26.6)" "0.5 - 143.4 (25.4)"
[1] "hr=" "2.2"
D21V2, continuous
                 vv
clus              CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  FOXD2 MUTATED                0                  0                   0
  FOXD2 WILD-TYPE              1                  7                   2
                 vv
clus              CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  FOXD2 MUTATED                     0                             0
  FOXD2 WILD-TYPE                   1                             1
                 vv
clus              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  FOXD2 MUTATED                       0                      0
  FOXD2 WILD-TYPE                     1                     25
                 vv
clus              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  FOXD2 MUTATED                      0                    0
  FOXD2 WILD-TYPE                    2                    1
                 vv
clus              HEAD AND NECK - OTHER (PLEASE SPECIFY
  FOXD2 MUTATED                                       0
  FOXD2 WILD-TYPE                                     2
                 vv
clus              LOWER ABDOMINAL/PELVIC - BLADDER
  FOXD2 MUTATED                                  0
  FOXD2 WILD-TYPE                                1
                 vv
clus              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  FOXD2 MUTATED                                                0
  FOXD2 WILD-TYPE                                              2
                 vv
clus              LOWER ABDOMINAL/PELVIC - PELVIC
  FOXD2 MUTATED                                 0
  FOXD2 WILD-TYPE                              11
                 vv
clus              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  FOXD2 MUTATED                                         0
  FOXD2 WILD-TYPE                                       2
                 vv
clus              LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  FOXD2 MUTATED                              0                       0
  FOXD2 WILD-TYPE                            4                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  FOXD2 MUTATED                                  0
  FOXD2 WILD-TYPE                               15
                 vv
clus              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  FOXD2 MUTATED                                         0
  FOXD2 WILD-TYPE                                       3
                 vv
clus              LOWER EXTREMITY - THIGH/KNEE
  FOXD2 MUTATED                              1
  FOXD2 WILD-TYPE                           41
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  FOXD2 MUTATED                                         0
  FOXD2 WILD-TYPE                                       4
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  FOXD2 MUTATED                                           0
  FOXD2 WILD-TYPE                                         2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  FOXD2 MUTATED                                                  0
  FOXD2 WILD-TYPE                                                5
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  FOXD2 MUTATED                                          1
  FOXD2 WILD-TYPE                                        6
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  FOXD2 MUTATED                                                         0
  FOXD2 WILD-TYPE                                                       2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  FOXD2 MUTATED                                            0
  FOXD2 WILD-TYPE                                          1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  FOXD2 MUTATED                                                   1
  FOXD2 WILD-TYPE                                                70
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  FOXD2 MUTATED                                                    0
  FOXD2 WILD-TYPE                                                  3
                 vv
clus              SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  FOXD2 MUTATED                                    0                        0
  FOXD2 WILD-TYPE                                  2                        5
                 vv
clus              SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  FOXD2 MUTATED                             0                         0
  FOXD2 WILD-TYPE                           3                         1
                 vv
clus              UPPER EXTREMITY - SHOULDER/AXILLA
  FOXD2 MUTATED                                   0
  FOXD2 WILD-TYPE                                 7
                 vv
clus              UPPER EXTREMITY - UPPER ARM/ELBOW
  FOXD2 MUTATED                                   0
  FOXD2 WILD-TYPE                                 5
D21V3, multiclass
                                                         clus
vv                                                        FOXD2 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                                    0
  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                            1
  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                                                        FOXD2 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                                         41
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               4
  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                            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"
D21V4, binary
                 cls
clus                0   1
  FOXD2 MUTATED     2   1
  FOXD2 WILD-TYPE 129 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXD2 MUTATED      2    1
  FOXD2 WILD-TYPE  129  112
        clus
vv       FOXD2 MUTATED FOXD2 WILD-TYPE
  FEMALE             2             129
  MALE               1             112
[1] 2 2
[1] FALSE
D21V5, binary
                 cls
clus                0   1
  FOXD2 MUTATED     2   1
  FOXD2 WILD-TYPE 168  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXD2 MUTATED      2    1
  FOXD2 WILD-TYPE  168   66
     clus
vv    FOXD2 MUTATED FOXD2 WILD-TYPE
  NO              2             168
  YES             1              66
[1] 2 2
[1] FALSE
                 vv
clus              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  FOXD2 MUTATED                              0             0
  FOXD2 WILD-TYPE                           56             2
                 vv
clus              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  FOXD2 MUTATED                                                                          0
  FOXD2 WILD-TYPE                                                                        1
                 vv
clus              LEIOMYOSARCOMA (LMS)
  FOXD2 MUTATED                      1
  FOXD2 WILD-TYPE                   96
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  FOXD2 MUTATED                                                  0
  FOXD2 WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  FOXD2 MUTATED                  1
  FOXD2 WILD-TYPE               20
                 vv
clus              PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  FOXD2 MUTATED                                                         0
  FOXD2 WILD-TYPE                                                      29
                 vv
clus              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  FOXD2 MUTATED                                          0
  FOXD2 WILD-TYPE                                        2
                 vv
clus              SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  FOXD2 MUTATED                             0                             1
  FOXD2 WILD-TYPE                           2                             5
                 vv
clus              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  FOXD2 MUTATED                                            0
  FOXD2 WILD-TYPE                                         20
D21V6, multiclass
                                                                          clus
vv                                                                         FOXD2 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                              0
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                             0
  SYNOVIAL SARCOMA - BIPHASIC                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                        1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           0
                                                                          clus
vv                                                                         FOXD2 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                                                                      20
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               29
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               2
  SYNOVIAL SARCOMA - BIPHASIC                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                          5
  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
  FOXD2 MUTATED     2   1   0   0
  FOXD2 WILD-TYPE 145  63   9  23
D21V7, multiclass
    clus
vv   FOXD2 MUTATED FOXD2 WILD-TYPE
  R0             2             145
  R1             1              63
  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
  FOXD2 MUTATED       0                         0     2
  FOXD2 WILD-TYPE     5                        18   212
D21V8, multiclass
[1] "Remove cluster labels:" "FOXD2 MUTATED"         
clus
  FOXD2 MUTATED FOXD2 WILD-TYPE 
              2             235 
     TCGA-3B-A9HI      TCGA-3B-A9HJ      TCGA-3B-A9HL      TCGA-3B-A9HO 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-3B-A9HP      TCGA-3B-A9HQ      TCGA-3B-A9HR      TCGA-3B-A9HS 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-3B-A9HT      TCGA-3B-A9HU      TCGA-3B-A9HV      TCGA-3B-A9HX 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-3B-A9HY      TCGA-3B-A9HZ      TCGA-3B-A9I0      TCGA-3B-A9I1 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A1KU      TCGA-DX-A1KW      TCGA-DX-A1KX      TCGA-DX-A1KY 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A1KZ      TCGA-DX-A1L0      TCGA-DX-A1L1      TCGA-DX-A1L2 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A1L3      TCGA-DX-A1L4      TCGA-DX-A23R      TCGA-DX-A23T 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A23U      TCGA-DX-A23V      TCGA-DX-A23Y      TCGA-DX-A240 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A2IZ      TCGA-DX-A2J0      TCGA-DX-A2J1      TCGA-DX-A2J4 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3LS      TCGA-DX-A3LT      TCGA-DX-A3LU      TCGA-DX-A3LW 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3LY      TCGA-DX-A3M1      TCGA-DX-A3M2      TCGA-DX-A3U5 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3U6      TCGA-DX-A3U7      TCGA-DX-A3U9      TCGA-DX-A3UA 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3UB      TCGA-DX-A3UC      TCGA-DX-A3UD      TCGA-DX-A3UE 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A3UF      TCGA-DX-A48J      TCGA-DX-A48K      TCGA-DX-A48L 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A48N      TCGA-DX-A48O      TCGA-DX-A48P      TCGA-DX-A48R 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A48U      TCGA-DX-A48V      TCGA-DX-A6B7      TCGA-DX-A6B8 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6B9      TCGA-DX-A6BA      TCGA-DX-A6BB      TCGA-DX-A6BE 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6BF      TCGA-DX-A6BG      TCGA-DX-A6BH      TCGA-DX-A6BK 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6YR      TCGA-DX-A6YU      TCGA-DX-A6YZ      TCGA-DX-A6Z0 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A6Z2      TCGA-DX-A7EF      TCGA-DX-A7EI      TCGA-DX-A7EL 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A7EM      TCGA-DX-A7EN      TCGA-DX-A7EO      TCGA-DX-A7EQ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A7ER      TCGA-DX-A7ES      TCGA-DX-A7ET      TCGA-DX-A7EU 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BG      TCGA-DX-A8BH      TCGA-DX-A8BJ      TCGA-DX-A8BK 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BL      TCGA-DX-A8BM      TCGA-DX-A8BN      TCGA-DX-A8BO 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BP      TCGA-DX-A8BQ      TCGA-DX-A8BR      TCGA-DX-A8BS 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BT      TCGA-DX-A8BU      TCGA-DX-A8BV      TCGA-DX-A8BX 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-A8BZ      TCGA-DX-AATS      TCGA-DX-AB2E      TCGA-DX-AB2F 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2G      TCGA-DX-AB2H      TCGA-DX-AB2J      TCGA-DX-AB2O 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2P      TCGA-DX-AB2Q      TCGA-DX-AB2S      TCGA-DX-AB2T 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB2V      TCGA-DX-AB2W      TCGA-DX-AB2X      TCGA-DX-AB2Z 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB30      TCGA-DX-AB32      TCGA-DX-AB35      TCGA-DX-AB36 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-DX-AB37      TCGA-DX-AB3A      TCGA-DX-AB3B      TCGA-DX-AB3C 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-FX-A2QS      TCGA-FX-A3NJ      TCGA-FX-A3NK      TCGA-FX-A3RE 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-FX-A3TO      TCGA-FX-A48G      TCGA-FX-A76Y      TCGA-FX-A8OO 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-HB-A2OT      TCGA-HB-A3L4      TCGA-HB-A3YV      TCGA-HB-A43Z 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-HB-A5W3      TCGA-IE-A3OV      TCGA-IE-A4EH      TCGA-IE-A4EI 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IE-A4EJ      TCGA-IE-A4EK      TCGA-IE-A6BZ      TCGA-IF-A4AJ 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IF-A4AK      TCGA-IS-A3K6      TCGA-IS-A3K7      TCGA-IS-A3K8 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-IS-A3KA      TCGA-IW-A3M4      TCGA-IW-A3M5      TCGA-IW-A3M6 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-JV-A5VE      TCGA-JV-A5VF      TCGA-JV-A75J      TCGA-K1-A3PO 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-K1-A42W      TCGA-K1-A42X      TCGA-K1-A6RT      TCGA-K1-A6RU 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-K1-A6RV      TCGA-KD-A5QS      TCGA-KD-A5QU      TCGA-KF-A41W 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-LI-A67I      TCGA-LI-A9QH      TCGA-MB-A5Y8      TCGA-MB-A5Y9 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-MB-A5YA      TCGA-MB-A8JK      TCGA-MB-A8JL      TCGA-MJ-A68H 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-MJ-A68J      TCGA-MJ-A850      TCGA-MO-A47R      TCGA-N1-A6IA 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-PC-A5DK      TCGA-PC-A5DL      TCGA-PC-A5DN      TCGA-PC-A5DO 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-PT-A8TR      TCGA-QC-A6FX      TCGA-QC-A7B5      TCGA-QC-AA9N 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-QQ-A5V2      TCGA-QQ-A5V9      TCGA-QQ-A5VA      TCGA-QQ-A5VB 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-QQ-A5VC      TCGA-QQ-A5VD      TCGA-QQ-A8VD      TCGA-QQ-A8VG 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-QQ-A8VH      TCGA-RN-A68Q      TCGA-RN-AAAQ      TCGA-SG-A6Z4 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-SG-A6Z7      TCGA-SG-A849      TCGA-SI-A71O      TCGA-SI-A71P 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-SI-A71Q      TCGA-SI-AA8B      TCGA-SI-AA8C      TCGA-UE-A6QT 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-UE-A6QU      TCGA-VT-A80G      TCGA-VT-AB3D      TCGA-WK-A8XO 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-WK-A8XQ      TCGA-WK-A8XS      TCGA-WK-A8XX      TCGA-WK-A8XY 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-WK-A8XZ      TCGA-WK-A8Y0      TCGA-WP-A9GB      TCGA-X2-A95T 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-X6-A7W8      TCGA-X6-A7WC      TCGA-X6-A7WD      TCGA-X6-A8C2 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-X6-A8C3      TCGA-X6-A8C4      TCGA-X6-A8C5      TCGA-X6-A8C6 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-X6-A8C7      TCGA-X9-A971      TCGA-X9-A973      TCGA-Z4-A8JB 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
     TCGA-Z4-A9VC      TCGA-Z4-AAPF      TCGA-Z4-AAPG 
"FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" "FOXD2 WILD-TYPE" 
D21V9, binary
                 cls
clus                0   1
  FOXD2 MUTATED     0   2
  FOXD2 WILD-TYPE   5 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXD2 MUTATED      0    2
  FOXD2 WILD-TYPE    5  209
                        clus
vv                       FOXD2 MUTATED FOXD2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             209
[1] 2 2
[1] FALSE

Clustering(22) Variable = MMP17 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  MMP17 MUTATED     1   2
  MMP17 WILD-TYPE 154  87
  MMP17 MUTATED MMP17 WILD-TYPE 
              3             241 
  MMP17 MUTATED MMP17 WILD-TYPE 
              2              87 
$`MMP17 MUTATED`
TCGA-DX-A7ER TCGA-DX-A8BX TCGA-Z4-AAPF 
       48.20        19.43        15.95 

$`MMP17 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        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 
       83.38        54.77         9.04        43.76        86.83       124.73 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       33.44        44.68        34.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        61.91        55.07        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        81.90         9.73        31.27        24.26        24.69 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       40.80        46.03        26.47       102.41        47.57        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        24.59        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU 
       17.79        21.63        16.18         3.06        34.55        23.54 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        74.10        64.21        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ES 
       75.32        48.36        15.62       135.48        29.49        20.05 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       15.22        12.20        17.95        14.43         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ 
       33.07        44.68        38.17        35.77        14.07        51.91 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ 
      124.37        27.95        35.54        36.69        60.66         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        17.79        12.00        15.72        15.85        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       86.10        12.07        66.74         9.21        77.88       106.55 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31        31.63 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       31.13        16.60        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        8.05        48.30        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       33.30         0.72        80.48        26.93        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        19.89        25.22        52.27        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-KF-A41W 
       23.38         5.19        36.36        16.41        35.28        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
       22.03        13.35        25.41         8.28         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-A6FX 
      120.20        37.55        38.63        81.01        20.52        20.94 
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-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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       16.77        18.94         3.88        17.52        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-A8XT TCGA-WK-A8XX 
       12.46        11.93         4.80        72.72        41.49        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         9.04        63.35        26.43 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       36.82        18.35        25.71        15.95        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       35.08        17.72        15.58        36.43         4.37        13.38 
TCGA-Z4-AAPG 
       15.98 

  MMP17 MUTATED MMP17 WILD-TYPE 
          15.95            0.49 
  MMP17 MUTATED MMP17 WILD-TYPE 
          48.20          143.41 
  MMP17 MUTATED MMP17 WILD-TYPE 
          19.43           25.71 
[1] "15.9 - 48.2 (19.4)" "0.5 - 143.4 (25.7)"
[1] "hr=" "2.3"
D22V2, continuous
                 vv
clus              CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  MMP17 MUTATED                0                  0                   1
  MMP17 WILD-TYPE              1                  7                   1
                 vv
clus              CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  MMP17 MUTATED                     0                             0
  MMP17 WILD-TYPE                   1                             1
                 vv
clus              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  MMP17 MUTATED                       0                      0
  MMP17 WILD-TYPE                     1                     25
                 vv
clus              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  MMP17 MUTATED                      0                    0
  MMP17 WILD-TYPE                    2                    1
                 vv
clus              HEAD AND NECK - OTHER (PLEASE SPECIFY
  MMP17 MUTATED                                       0
  MMP17 WILD-TYPE                                     2
                 vv
clus              LOWER ABDOMINAL/PELVIC - BLADDER
  MMP17 MUTATED                                  0
  MMP17 WILD-TYPE                                1
                 vv
clus              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  MMP17 MUTATED                                                0
  MMP17 WILD-TYPE                                              2
                 vv
clus              LOWER ABDOMINAL/PELVIC - PELVIC
  MMP17 MUTATED                                 0
  MMP17 WILD-TYPE                              11
                 vv
clus              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  MMP17 MUTATED                                         0
  MMP17 WILD-TYPE                                       2
                 vv
clus              LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  MMP17 MUTATED                              0                       0
  MMP17 WILD-TYPE                            4                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  MMP17 MUTATED                                  0
  MMP17 WILD-TYPE                               15
                 vv
clus              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  MMP17 MUTATED                                         0
  MMP17 WILD-TYPE                                       3
                 vv
clus              LOWER EXTREMITY - THIGH/KNEE
  MMP17 MUTATED                              0
  MMP17 WILD-TYPE                           42
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  MMP17 MUTATED                                         0
  MMP17 WILD-TYPE                                       4
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  MMP17 MUTATED                                           0
  MMP17 WILD-TYPE                                         2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  MMP17 MUTATED                                                  0
  MMP17 WILD-TYPE                                                5
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  MMP17 MUTATED                                          0
  MMP17 WILD-TYPE                                        7
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  MMP17 MUTATED                                                         0
  MMP17 WILD-TYPE                                                       2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  MMP17 MUTATED                                            0
  MMP17 WILD-TYPE                                          1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  MMP17 MUTATED                                                   1
  MMP17 WILD-TYPE                                                70
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  MMP17 MUTATED                                                    0
  MMP17 WILD-TYPE                                                  3
                 vv
clus              SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  MMP17 MUTATED                                    0                        0
  MMP17 WILD-TYPE                                  2                        5
                 vv
clus              SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  MMP17 MUTATED                             0                         0
  MMP17 WILD-TYPE                           3                         1
                 vv
clus              UPPER EXTREMITY - SHOULDER/AXILLA
  MMP17 MUTATED                                   0
  MMP17 WILD-TYPE                                 7
                 vv
clus              UPPER EXTREMITY - UPPER ARM/ELBOW
  MMP17 MUTATED                                   1
  MMP17 WILD-TYPE                                 4
D22V3, multiclass
                                                         clus
vv                                                        MMP17 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                                        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                                   1
                                                         clus
vv                                                        MMP17 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                                     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               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                                     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"
D22V4, binary
                 cls
clus                0   1
  MMP17 MUTATED     1   2
  MMP17 WILD-TYPE 130 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP17 MUTATED      1    2
  MMP17 WILD-TYPE  130  111
        clus
vv       MMP17 MUTATED MMP17 WILD-TYPE
  FEMALE             1             130
  MALE               2             111
[1] 2 2
[1] FALSE
D22V5, binary
                 cls
clus                0   1
  MMP17 MUTATED     3   0
  MMP17 WILD-TYPE 167  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP17 MUTATED      3    0
  MMP17 WILD-TYPE  167   67
     clus
vv    MMP17 MUTATED MMP17 WILD-TYPE
  NO              3             167
  YES             0              67
[1] 2 2
[1] FALSE
                 vv
clus              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  MMP17 MUTATED                              0             0
  MMP17 WILD-TYPE                           56             2
                 vv
clus              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  MMP17 MUTATED                                                                          0
  MMP17 WILD-TYPE                                                                        1
                 vv
clus              LEIOMYOSARCOMA (LMS)
  MMP17 MUTATED                      0
  MMP17 WILD-TYPE                   97
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  MMP17 MUTATED                                                  0
  MMP17 WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  MMP17 MUTATED                  0
  MMP17 WILD-TYPE               21
                 vv
clus              PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  MMP17 MUTATED                                                         1
  MMP17 WILD-TYPE                                                      28
                 vv
clus              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  MMP17 MUTATED                                          1
  MMP17 WILD-TYPE                                        1
                 vv
clus              SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  MMP17 MUTATED                             0                             1
  MMP17 WILD-TYPE                           2                             5
                 vv
clus              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  MMP17 MUTATED                                            0
  MMP17 WILD-TYPE                                         20
D22V6, multiclass
                                                                          clus
vv                                                                         MMP17 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                         0
  DESMOID TUMOR                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             0
  LEIOMYOSARCOMA (LMS)                                                                 0
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     0
  MYXOFIBROSARCOMA                                                                     0
  PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              1
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                             1
  SYNOVIAL SARCOMA - BIPHASIC                                                          0
  SYNOVIAL SARCOMA - MONOPHASIC                                                        1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                           0
                                                                          clus
vv                                                                         MMP17 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                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                          5
  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
  MMP17 MUTATED     3   0   0   0
  MMP17 WILD-TYPE 144  64   9  23
D22V7, multiclass
    clus
vv   MMP17 MUTATED MMP17 WILD-TYPE
  R0             3             144
  R1             0              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
  MMP17 MUTATED       0                         0     3
  MMP17 WILD-TYPE     5                        18   211
D22V8, multiclass
                           clus
vv                          MMP17 MUTATED MMP17 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             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"
D22V9, binary
                 cls
clus                0   1
  MMP17 MUTATED     1   1
  MMP17 WILD-TYPE   4 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP17 MUTATED      1    1
  MMP17 WILD-TYPE    4  210
                        clus
vv                       MMP17 MUTATED MMP17 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             1             210
[1] 2 2
[1] FALSE

Clustering(23) Variable = ASTE1 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  ASTE1 MUTATED     1   2
  ASTE1 WILD-TYPE 154  87
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              3             241 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              2              87 
$`ASTE1 MUTATED`
TCGA-DX-A6YR TCGA-DX-A8BX TCGA-X6-A8C6 
       34.55        19.43        35.08 

$`ASTE1 WILD-TYPE`
TCGA-3B-A9HI TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HO TCGA-3B-A9HP TCGA-3B-A9HQ 
       50.01        36.30        19.69        31.53        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        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 
       83.38        54.77         9.04        43.76        86.83       124.73 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       33.44        44.68        34.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        61.91        55.07        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        81.90         9.73        31.27        24.26        24.69 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       40.80        46.03        26.47       102.41        47.57        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        24.59        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A6YX 
       17.79        21.63        16.18         3.06        23.54        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       74.10        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        20.05 
TCGA-DX-A7ET TCGA-DX-A7EU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       15.22        12.20        17.95        14.43         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BQ 
       33.07        44.68        38.17        35.77        14.07        51.91 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ 
      124.37        27.95        35.54        36.69        60.66         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        17.79        12.00        15.72        15.85        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       86.10        12.07        66.74         9.21        77.88       106.55 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31        31.63 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       31.13        16.60        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        8.05        48.30        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       33.30         0.72        80.48        26.93        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        19.89        25.22        52.27        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-KF-A41W 
       23.38         5.19        36.36        16.41        35.28        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
       22.03        13.35        25.41         8.28         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-A6FX 
      120.20        37.55        38.63        81.01        20.52        20.94 
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-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-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       16.77        18.94         3.88        17.52        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-A8XT TCGA-WK-A8XX 
       12.46        11.93         4.80        72.72        41.49        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         9.04        63.35        26.43 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       36.82        18.35        25.71        15.95        16.83        38.96 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       17.72        15.58        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  ASTE1 MUTATED ASTE1 WILD-TYPE 
          19.43            0.49 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
          35.08          143.41 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
          34.55           25.41 
[1] "19.4 - 35.1 (34.5)" "0.5 - 143.4 (25.4)"
[1] "hr=" "2.2"
D23V2, continuous
                 vv
clus              CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  ASTE1 MUTATED                0                  1                   0
  ASTE1 WILD-TYPE              1                  6                   2
                 vv
clus              CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  ASTE1 MUTATED                     0                             0
  ASTE1 WILD-TYPE                   1                             1
                 vv
clus              GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  ASTE1 MUTATED                       0                      0
  ASTE1 WILD-TYPE                     1                     25
                 vv
clus              HEAD AND NECK - HEAD HEAD AND NECK - NECK
  ASTE1 MUTATED                      0                    0
  ASTE1 WILD-TYPE                    2                    1
                 vv
clus              HEAD AND NECK - OTHER (PLEASE SPECIFY
  ASTE1 MUTATED                                       0
  ASTE1 WILD-TYPE                                     2
                 vv
clus              LOWER ABDOMINAL/PELVIC - BLADDER
  ASTE1 MUTATED                                  0
  ASTE1 WILD-TYPE                                1
                 vv
clus              LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  ASTE1 MUTATED                                                0
  ASTE1 WILD-TYPE                                              2
                 vv
clus              LOWER ABDOMINAL/PELVIC - PELVIC
  ASTE1 MUTATED                                 0
  ASTE1 WILD-TYPE                              11
                 vv
clus              LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  ASTE1 MUTATED                                         0
  ASTE1 WILD-TYPE                                       2
                 vv
clus              LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  ASTE1 MUTATED                              0                       0
  ASTE1 WILD-TYPE                            4                       2
                 vv
clus              LOWER EXTREMITY - LOWER LEG/CALF
  ASTE1 MUTATED                                  0
  ASTE1 WILD-TYPE                               15
                 vv
clus              LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  ASTE1 MUTATED                                         0
  ASTE1 WILD-TYPE                                       3
                 vv
clus              LOWER EXTREMITY - THIGH/KNEE
  ASTE1 MUTATED                              1
  ASTE1 WILD-TYPE                           41
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - COLON
  ASTE1 MUTATED                                         0
  ASTE1 WILD-TYPE                                       4
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  ASTE1 MUTATED                                           0
  ASTE1 WILD-TYPE                                         2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  ASTE1 MUTATED                                                  0
  ASTE1 WILD-TYPE                                                5
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  ASTE1 MUTATED                                          0
  ASTE1 WILD-TYPE                                        7
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  ASTE1 MUTATED                                                         0
  ASTE1 WILD-TYPE                                                       2
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  ASTE1 MUTATED                                            0
  ASTE1 WILD-TYPE                                          1
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  ASTE1 MUTATED                                                   1
  ASTE1 WILD-TYPE                                                70
                 vv
clus              RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  ASTE1 MUTATED                                                    0
  ASTE1 WILD-TYPE                                                  3
                 vv
clus              SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  ASTE1 MUTATED                                    0                        0
  ASTE1 WILD-TYPE                                  2                        5
                 vv
clus              SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  ASTE1 MUTATED                             0                         0
  ASTE1 WILD-TYPE                           3                         1
                 vv
clus              UPPER EXTREMITY - SHOULDER/AXILLA
  ASTE1 MUTATED                                   0
  ASTE1 WILD-TYPE                                 7
                 vv
clus              UPPER EXTREMITY - UPPER ARM/ELBOW
  ASTE1 MUTATED                                   0
  ASTE1 WILD-TYPE                                 5
D23V3, multiclass
                                                         clus
vv                                                        ASTE1 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                                                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                                        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             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                                                        ASTE1 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                                               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                                         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                    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"
D23V4, binary
                 cls
clus                0   1
  ASTE1 MUTATED     0   3
  ASTE1 WILD-TYPE 131 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      0    3
  ASTE1 WILD-TYPE  131  110
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  FEMALE             0             131
  MALE               3             110
[1] 2 2
[1] FALSE
D23V5, binary
                 cls
clus                0   1
  ASTE1 MUTATED     2   1
  ASTE1 WILD-TYPE 168  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      2    1
  ASTE1 WILD-TYPE  168   66
     clus
vv    ASTE1 MUTATED ASTE1 WILD-TYPE
  NO              2             168
  YES             1              66
[1] 2 2
[1] FALSE
                 vv
clus              DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  ASTE1 MUTATED                              0             0
  ASTE1 WILD-TYPE                           56             2
                 vv
clus              GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  ASTE1 MUTATED                                                                          0
  ASTE1 WILD-TYPE                                                                        1
                 vv
clus              LEIOMYOSARCOMA (LMS)
  ASTE1 MUTATED                      0
  ASTE1 WILD-TYPE                   97
                 vv
clus              MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  ASTE1 MUTATED                                                  0
  ASTE1 WILD-TYPE                                                8
                 vv
clus              MYXOFIBROSARCOMA
  ASTE1 MUTATED                  2
  ASTE1 WILD-TYPE               19
                 vv
clus              PLEOMORPHIC 'MFH'/ UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  ASTE1 MUTATED                                                         1
  ASTE1 WILD-TYPE                                                      28
                 vv
clus              SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  ASTE1 MUTATED                                          0
  ASTE1 WILD-TYPE                                        2
                 vv
clus              SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  ASTE1 MUTATED                             0                             0
  ASTE1 WILD-TYPE                           2                             6
                 vv
clus              UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  ASTE1 MUTATED                                            0
  ASTE1 WILD-TYPE                                         20
D23V6, multiclass
                                                                          clus
vv                                                                         ASTE1 MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                         0
  DESMOID TUMOR                                                                        0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS             0
  LEIOMYOSARCOMA (LMS)                                                                 0
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                     0
  MYXOFIBROSARCOMA                                                                     2
  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                                                                         ASTE1 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                                                                      19
  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
  ASTE1 MUTATED     2   1   0   0
  ASTE1 WILD-TYPE 145  63   9  23
D23V7, multiclass
    clus
vv   ASTE1 MUTATED ASTE1 WILD-TYPE
  R0             2             145
  R1             1              63
  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
  ASTE1 MUTATED       0                         0     3
  ASTE1 WILD-TYPE     5                        18   211
D23V8, multiclass
                           clus
vv                          ASTE1 MUTATED ASTE1 WILD-TYPE
  ASIAN                                 0               5
  BLACK OR AFRICAN AMERICAN             0              18
  WHITE                                 3             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"
D23V9, binary
                 cls
clus                0   1
  ASTE1 MUTATED     1   2
  ASTE1 WILD-TYPE   4 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      1    2
  ASTE1 WILD-TYPE    4  209
                        clus
vv                       ASTE1 MUTATED ASTE1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             2             209
[1] 2 2
[1] FALSE
