[1] "ofn"        "-oTSARC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/22507207/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/22534095/transformed.cor.cli.txt"

nPatients in clinical file=261, in cluster file=257, common to both=257
[1]  82 257
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               59               198 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               59               198 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               51               206 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               51               206 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               22               235 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               22               235 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               22               235 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               22               235 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               38               219 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               38               219 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               35               222 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               35               222 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               69               188 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               69               188 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               48               209 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               48               209 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               98               159 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               98               159 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               72               185 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               72               185 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               52               205 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               52               205 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               49               208 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               49               208 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               82               175 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               82               175 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               67               190 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               67               190 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               205 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               205 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               66               191 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               66               191 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               53               204 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               53               204 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               186 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               186 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                235 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                235 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                246 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                246 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                234 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                234 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                21                236 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                21                236 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                41                216 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                41                216 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                31                226 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                31                226 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                242 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                242 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                56                201 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                56                201 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                62                195 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                62                195 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                40                217 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                40                217 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                238 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                238 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                61                196 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                61                196 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                56                201 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                56                201 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                52                205 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                52                205 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                37                220 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                37                220 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                88                169 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                88                169 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                64                193 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                64                193 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                62                195 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                62                195 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                83                174 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                83                174 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                59                198 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                59                198 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                58                199 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                58                199 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               74               183 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               74               183 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34               223 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34               223 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               225 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               225 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               40               217 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               40               217 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               92               165 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               92               165 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               75               182 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               75               182 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               56               201 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               56               201 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               51               206 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               51               206 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               41               216 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               41               216 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               50               207 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               50               207 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               23               234 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               23               234 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               34               223 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               34               223 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               60               197 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               60               197 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               52               205 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               52               205 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               32               225 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               32               225 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               36               221 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               36               221 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               62               195 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               62               195 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               45               212 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               45               212 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               82               175 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               82               175 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50               207 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50               207 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               121                136 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               121                136 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               131                126 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               131                126 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                96                161 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                96                161 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                93                164 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                93                164 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                67                190 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                67                190 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                59                198 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                59                198 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               132                125 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               132                125 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                62                195 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                62                195 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                46                211 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                46                211 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                75                182 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                75                182 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               124                133 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               124                133 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                57                200 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                57                200 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                49                208 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                49                208 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                61                196 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                61                196 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                69                188 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                69                188 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                24                233 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                24                233 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                41                216 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                41                216 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                55                202 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                55                202 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                25                232 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                25                232 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                50                207 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                50                207 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                67                190 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                67                190 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               63               194 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               63               194 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              102               155 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              102               155 
[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 257 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=95,	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=156,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=33,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 8:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'HISTOLOGICAL_TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 257 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 = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    28  31
  1P GAIN WILD-TYPE 131  67
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               59               198 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               31                67 
$`1P GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB2P TCGA-DX-AB2W TCGA-HB-A43Z 
       34.36        15.22        17.95        12.07       106.45        37.02 
TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-SG-A849 
       52.11        52.27        11.70        17.75         6.35        17.52 
TCGA-VT-A80J TCGA-3B-A9HL TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A2J0 TCGA-DX-A3LT 
       26.17        19.69        18.64        26.56         9.70        49.05 
TCGA-DX-A3U9 TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YV 
       14.99        45.99        24.26        26.47        15.95        50.50 
TCGA-DX-A6YX TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BS 
       16.87         9.34        61.97        45.14        40.77        27.95 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2T TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A8OO 
       36.69         6.58        77.88        49.15        20.32         8.05 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A6BZ 
       67.63         4.57         9.80        80.48        19.53        19.89 
TCGA-IF-A4AJ TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU 
       25.22         1.05        62.17        23.38        63.81        35.28 
TCGA-MB-A8JK TCGA-N1-A6IA TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-SI-A71O 
       21.73         7.36        13.08        48.59         3.88        22.82 
TCGA-SI-AA8B TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A7W8 TCGA-X6-A8C4 
        8.61        84.79        38.27        26.43        20.65 

$`1P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB30 
       14.43        14.07        15.85        40.60        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
      101.98        30.51        60.00        84.66        32.15        16.60 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-MB-A5Y9 
       12.62        26.93        28.21       159.29        22.62         8.28 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
       18.08        20.94       188.15        41.49        35.08        50.01 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       53.49        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX 
       14.37        42.84        10.32        38.47        36.03         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04        32.71        68.61        12.85        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       95.38        79.17         9.04        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       44.68        31.86        35.77        51.02         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       35.28        52.77        46.03       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A6Z0 
       26.99         3.06        41.00        78.28        86.30        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
      101.23        21.30        34.49        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR 
       29.49        48.20        20.05        47.87        38.17       150.35 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       40.44        60.66        19.43         1.15        17.79        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V 
       15.72        65.98        86.10        66.74         9.21       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       50.40        50.89        71.31        31.13        21.70        19.89 
TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-IE-A4EK 
       15.48        34.88        33.30         0.72         3.22         1.38 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       37.12       171.09        13.58        85.97         5.92        16.41 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
        3.91       101.26        53.33       123.78        17.36         5.19 
TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       16.41        30.31        25.41         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        22.39        11.57        10.45       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        81.01        17.65         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90        37.12       130.32       111.98        64.77        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
        0.72        16.77        18.94        25.35        32.75        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-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46        22.62         8.58        63.35        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
       45.34        30.84        35.18        19.17        50.86        29.46 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        36.43         4.37        13.38        15.95        15.98 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.05              0.49 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           106.45            188.15 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            23.38             33.37 
[1] "1.1 - 106.5 (23.4)" "0.5 - 188.2 (33.4)"
[1] "hr=" "2"  
D1V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  1P GAIN MUTATED                0                  2                   1
  1P GAIN WILD-TYPE              1                  5                   1
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  1P GAIN MUTATED                     0                             0
  1P GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  1P GAIN MUTATED                       0                      8
  1P GAIN WILD-TYPE                     1                     20
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  1P GAIN MUTATED                      1                    0
  1P GAIN WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  1P GAIN MUTATED                                       0
  1P GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  1P GAIN MUTATED                                  0
  1P GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  1P GAIN MUTATED                                                1
  1P GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  1P GAIN MUTATED                                 1
  1P GAIN WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  1P GAIN MUTATED                                         0
  1P GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  1P GAIN MUTATED                              0                       1
  1P GAIN WILD-TYPE                            4                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  1P GAIN MUTATED                                  7
  1P GAIN WILD-TYPE                               10
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  1P GAIN MUTATED                                         2
  1P GAIN WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  1P GAIN MUTATED                             17
  1P GAIN WILD-TYPE                           27
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  1P GAIN MUTATED                                         0
  1P GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  1P GAIN MUTATED                                           1
  1P GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  1P GAIN MUTATED                                                  0
  1P GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  1P GAIN MUTATED                                          2
  1P GAIN WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  1P GAIN MUTATED                                                         1
  1P GAIN WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  1P GAIN MUTATED                                            1
  1P GAIN WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  1P GAIN MUTATED                                                   6
  1P GAIN WILD-TYPE                                                67
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  1P GAIN MUTATED                                                    0
  1P GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  1P GAIN MUTATED                                    1                        0
  1P GAIN WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  1P GAIN MUTATED                             2                         0
  1P GAIN WILD-TYPE                           2                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  1P GAIN MUTATED                                   2
  1P GAIN WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  1P GAIN MUTATED                                   2
  1P GAIN WILD-TYPE                                 3
D1V3, multiclass
                                                         clus
vv                                                        1P GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    2
  CHEST - LUNG/PLEURA                                                   1
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                8
  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                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                         17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     6
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           2
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        1P GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     1
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 20
  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                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 1
  LOWER EXTREMITY - LOWER LEG/CALF                                       10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           27
  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                 1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      67
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  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"
D1V4, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    34  25
  1P GAIN WILD-TYPE 105  93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     34   25
  1P GAIN WILD-TYPE  105   93
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              34               105
  MALE                25                93
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    36  23
  1P GAIN WILD-TYPE 143  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     36   23
  1P GAIN WILD-TYPE  143   49
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               36               143
  YES              23                49
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  1P GAIN MUTATED                              5             0
  1P GAIN WILD-TYPE                           54             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  1P GAIN MUTATED                                                                          0
  1P GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  1P GAIN MUTATED                     25
  1P GAIN WILD-TYPE                   78
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  1P GAIN MUTATED                                                  1
  1P GAIN WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  1P GAIN MUTATED                  7
  1P GAIN WILD-TYPE               17
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  1P GAIN MUTATED                                                         12
  1P GAIN WILD-TYPE                                                       16
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  1P GAIN MUTATED                                          1
  1P GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  1P GAIN MUTATED                             0                             0
  1P GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  1P GAIN MUTATED                                            8
  1P GAIN WILD-TYPE                                         13
D1V6, multiclass
                                                                          clus
vv                                                                         1P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           5
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  25
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             8
                                                                          clus
vv                                                                         1P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            54
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    78
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  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
  1P GAIN MUTATED    32  16   2   9
  1P GAIN WILD-TYPE 120  53   7  17
D1V7, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              32               120
  R1              16                53
  R2               2                 7
  RX               9                17
[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
  1P GAIN MUTATED       0                         8    48
  1P GAIN WILD-TYPE     6                        10   176
D1V8, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               8                10
  WHITE                                  48               176
[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
  1P GAIN MUTATED     0  52
  1P GAIN WILD-TYPE   5 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   52
  1P GAIN WILD-TYPE    5  168
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              52               168
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    29  22
  1Q GAIN WILD-TYPE 130  76
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               51               206 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               22                76 
$`1Q GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB2W TCGA-HB-A43Z TCGA-HS-A5N9 
       34.36        15.22        17.95       106.45        37.02        52.11 
TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-KF-A41W TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HX 
       52.27        22.62        11.70        19.69        53.49        42.84 
TCGA-3B-A9I3 TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K 
       26.56        49.05        14.99        50.43        85.45        45.99 
TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BS 
       52.77        26.47         9.34        45.14        40.77        27.95 
TCGA-DX-AB2T TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N8 
       77.88        20.32         8.05        67.63        34.88         0.72 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-K1-A42W 
        9.80        80.48        19.53        19.89        25.22        62.17 
TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QQ-A5VB 
       23.38        63.81        35.28        38.63        13.08        48.59 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A7W8 TCGA-X6-A7WB 
        3.88        22.82        84.79        38.27        26.43        18.08 
TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X9-A971 
       45.34        20.65        27.32 

$`1Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X 
       14.43        14.07        15.85        40.60        12.07        13.28 
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-FX-A3NK TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-LI-A9QH 
       16.60        12.62        26.93        28.21       159.29        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 
        8.28         6.35        18.08        20.94       188.15        17.52 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HQ TCGA-3B-A9HR 
       26.17        41.49        35.08        50.01        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ 
       44.91        54.74        25.25        14.37        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       36.03        18.64         0.56        14.04        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        45.11        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       66.94        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77        51.02         4.54        10.68        73.87        68.55 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48U 
       34.88         9.73        24.26        35.28        46.03       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       78.28        50.50        16.87        86.30        64.21       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       21.30        34.49        62.20        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR 
       48.20        20.05        61.97        47.87        38.17       150.35 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       40.44        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3YV TCGA-HS-A5N7 
       31.13        21.70        19.89        15.48         4.57        33.30 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        3.22         1.38        37.12       171.09        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        16.41         1.05         3.91       101.26        53.33 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 
      123.78        17.36         5.19        16.41        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO 
       11.57        10.45         7.36       122.96        37.55        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       17.65         1.84        46.82        18.08        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       18.94        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-A8XY 
       13.41        10.72        12.46        11.93         4.80        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 
       22.62         8.58        63.35        35.90        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       19.17        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.72              0.49 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           106.45            188.15 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           34.360            30.985 
[1] "0.7 - 106.5 (34.4)" "0.5 - 188.2 (31.0)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  1Q GAIN MUTATED                0                  2                   1
  1Q GAIN WILD-TYPE              1                  5                   1
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  1Q GAIN MUTATED                     0                             0
  1Q GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  1Q GAIN MUTATED                       0                     10
  1Q GAIN WILD-TYPE                     1                     18
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  1Q GAIN MUTATED                      1                    0
  1Q GAIN WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  1Q GAIN MUTATED                                       0
  1Q GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  1Q GAIN MUTATED                                  0
  1Q GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  1Q GAIN MUTATED                                                1
  1Q GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  1Q GAIN MUTATED                                 0
  1Q GAIN WILD-TYPE                              10
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  1Q GAIN MUTATED                                         0
  1Q GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  1Q GAIN MUTATED                              0                       1
  1Q GAIN WILD-TYPE                            4                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  1Q GAIN MUTATED                                  4
  1Q GAIN WILD-TYPE                               13
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  1Q GAIN MUTATED                                         1
  1Q GAIN WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  1Q GAIN MUTATED                             11
  1Q GAIN WILD-TYPE                           33
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  1Q GAIN MUTATED                                         1
  1Q GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  1Q GAIN MUTATED                                           1
  1Q GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  1Q GAIN MUTATED                                                  0
  1Q GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  1Q GAIN MUTATED                                          2
  1Q GAIN WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  1Q GAIN MUTATED                                                         0
  1Q GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  1Q GAIN MUTATED                                            1
  1Q GAIN WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  1Q GAIN MUTATED                                                   9
  1Q GAIN WILD-TYPE                                                64
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  1Q GAIN MUTATED                                                    0
  1Q GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  1Q GAIN MUTATED                                    1                        0
  1Q GAIN WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  1Q GAIN MUTATED                             1                         0
  1Q GAIN WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  1Q GAIN MUTATED                                   2
  1Q GAIN WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  1Q GAIN MUTATED                                   1
  1Q GAIN WILD-TYPE                                 4
D2V3, multiclass
                                                         clus
vv                                                        1Q GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    2
  CHEST - LUNG/PLEURA                                                   1
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                               10
  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                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  LOWER EXTREMITY - THIGH/KNEE                                         11
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  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                                    1
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        1Q GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     1
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 18
  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                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 1
  LOWER EXTREMITY - LOWER LEG/CALF                                       13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           33
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  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                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      64
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    33  18
  1Q GAIN WILD-TYPE 106 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     33   18
  1Q GAIN WILD-TYPE  106  100
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              33               106
  MALE                18               100
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    37  14
  1Q GAIN WILD-TYPE 142  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     37   14
  1Q GAIN WILD-TYPE  142   58
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               37               142
  YES              14                58
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  1Q GAIN MUTATED                              3             0
  1Q GAIN WILD-TYPE                           56             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  1Q GAIN MUTATED                                                                          0
  1Q GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  1Q GAIN MUTATED                     30
  1Q GAIN WILD-TYPE                   73
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  1Q GAIN MUTATED                                                  1
  1Q GAIN WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  1Q GAIN MUTATED                  5
  1Q GAIN WILD-TYPE               19
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  1Q GAIN MUTATED                                                          7
  1Q GAIN WILD-TYPE                                                       21
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  1Q GAIN MUTATED                                          1
  1Q GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  1Q GAIN MUTATED                             0                             0
  1Q GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  1Q GAIN MUTATED                                            4
  1Q GAIN WILD-TYPE                                         17
D2V6, multiclass
                                                                          clus
vv                                                                         1Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           3
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  30
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             4
                                                                          clus
vv                                                                         1Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            56
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    73
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              17
[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
  1Q GAIN MUTATED    30  14   1   6
  1Q GAIN WILD-TYPE 122  55   8  20
D2V7, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              30               122
  R1              14                55
  R2               1                 8
  RX               6                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
  1Q GAIN MUTATED       1                         4    43
  1Q GAIN WILD-TYPE     5                        14   181
D2V8, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  43               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
  1Q GAIN MUTATED     0  46
  1Q GAIN WILD-TYPE   5 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   46
  1Q GAIN WILD-TYPE    5  174
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              46               174
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    13   9
  2P GAIN WILD-TYPE 146  89
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               22               235 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                9                89 
$`2P GAIN MUTATED`
TCGA-DX-AB2X TCGA-KF-A41W TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A23R TCGA-DX-A3LT 
       13.28        11.70        14.04        32.71        74.66        49.05 
TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q 
       86.30        21.30        34.49        17.79        86.10        66.74 
TCGA-FX-A2QS TCGA-IW-A3M5 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-RN-AAAQ 
       49.15         5.92        10.45        37.55        13.08        16.77 
TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-Z4-AAPF 
        3.88        25.35        32.75        15.95 

$`2P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       75.32        15.22        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       40.60        12.07       106.45        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       52.11        26.93        52.27        28.21       159.29        22.62 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       17.75         8.28         6.35        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       17.52        26.17        41.49        35.08        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       53.49        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       14.37        42.84        10.32        38.47        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       26.56         0.56        68.61        12.85        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       54.21        85.02        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       95.38        79.17         9.04        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       82.68        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 
        3.06        41.00        78.28        50.50        16.87        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
      101.23        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       20.05         9.34        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       40.77       150.35        27.95        40.44        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       19.43         6.58         1.15        12.00        15.72        65.98 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
        9.21        77.88       106.55        50.40        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       67.63        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF 
       25.22       171.09        13.58        85.97        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
       23.38         5.19        63.81        16.41        35.28        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57         7.36       122.96        38.63        81.01 
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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       18.94        22.82         8.61        19.63        13.22        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX 
       10.72        12.46        11.93         4.80        84.79        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       65.46        22.62         8.58        63.35        26.43        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       18.08        45.34        30.84        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPG 
       15.98 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             3.88              0.49 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            86.30            188.15 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           23.325            31.530 
[1] "3.9 - 86.3 (23.3)"  "0.5 - 188.2 (31.5)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  2P GAIN MUTATED                0                  1                   0
  2P GAIN WILD-TYPE              1                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  2P GAIN MUTATED                     0                             0
  2P GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  2P GAIN MUTATED                       0                      2
  2P GAIN WILD-TYPE                     1                     26
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  2P GAIN MUTATED                      1                    0
  2P GAIN WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  2P GAIN MUTATED                                       0
  2P GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  2P GAIN MUTATED                                  0
  2P GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  2P GAIN MUTATED                                                0
  2P GAIN WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  2P GAIN MUTATED                                 0
  2P GAIN WILD-TYPE                              10
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  2P GAIN MUTATED                                         0
  2P GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  2P GAIN MUTATED                              0                       0
  2P GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  2P GAIN MUTATED                                  3
  2P GAIN WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  2P GAIN MUTATED                                         0
  2P GAIN WILD-TYPE                                       5
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  2P GAIN MUTATED                              2
  2P GAIN WILD-TYPE                           42
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  2P GAIN MUTATED                                         0
  2P GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  2P GAIN MUTATED                                           0
  2P GAIN WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  2P GAIN MUTATED                                                  1
  2P GAIN WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  2P GAIN MUTATED                                          1
  2P GAIN WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  2P GAIN MUTATED                                                         1
  2P GAIN WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  2P GAIN MUTATED                                            0
  2P GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  2P GAIN MUTATED                                                   5
  2P GAIN WILD-TYPE                                                68
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  2P GAIN MUTATED                                                    0
  2P GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  2P GAIN MUTATED                                    0                        0
  2P GAIN WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  2P GAIN MUTATED                             0                         0
  2P GAIN WILD-TYPE                           4                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  2P GAIN MUTATED                                   2
  2P GAIN WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  2P GAIN MUTATED                                   2
  2P GAIN WILD-TYPE                                 3
D3V3, multiclass
                                                         clus
vv                                                        2P GAIN 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                                                2
  HEAD AND NECK - HEAD                                                  1
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                       0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      3
  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                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     5
  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                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        2P GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      6
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 26
  HEAD AND NECK - HEAD                                                    1
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 5
  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                 1
  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                                             4
  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"
D3V4, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    13   9
  2P GAIN WILD-TYPE 126 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     13    9
  2P GAIN WILD-TYPE  126  109
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              13               126
  MALE                 9               109
[1] 2 2
[1] FALSE
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    15   7
  2P GAIN WILD-TYPE 164  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15    7
  2P GAIN WILD-TYPE  164   65
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               15               164
  YES               7                65
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  2P GAIN MUTATED                              7             0
  2P GAIN WILD-TYPE                           52             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  2P GAIN MUTATED                                                                          0
  2P GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  2P GAIN MUTATED                      4
  2P GAIN WILD-TYPE                   99
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  2P GAIN MUTATED                                                  3
  2P GAIN WILD-TYPE                                                6
                   vv
clus                MYXOFIBROSARCOMA
  2P GAIN MUTATED                  2
  2P GAIN WILD-TYPE               22
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  2P GAIN MUTATED                                                          5
  2P GAIN WILD-TYPE                                                       23
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  2P GAIN MUTATED                                          1
  2P GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  2P GAIN MUTATED                             0                             0
  2P GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  2P GAIN MUTATED                                            0
  2P GAIN WILD-TYPE                                         21
D3V6, multiclass
                                                                          clus
vv                                                                         2P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           7
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                   4
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       3
  MYXOFIBROSARCOMA                                                                       2
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             0
                                                                          clus
vv                                                                         2P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            52
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    99
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         6
  MYXOFIBROSARCOMA                                                                        22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                23
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    12   3   1   5
  2P GAIN WILD-TYPE 140  66   8  21
D3V7, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              12               140
  R1               3                66
  R2               1                 8
  RX               5                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
  2P GAIN MUTATED       1                         1    20
  2P GAIN WILD-TYPE     5                        17   204
D3V8, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               1                17
  WHITE                                  20               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"
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1  19
  2P GAIN WILD-TYPE   4 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   19
  2P GAIN WILD-TYPE    4  201
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              19               201
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    15   7
  2Q GAIN WILD-TYPE 144  91
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               22               235 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                91 
$`2Q GAIN MUTATED`
TCGA-DX-AB2X TCGA-DX-AB37 TCGA-KF-A41W TCGA-QQ-A8VB TCGA-DX-A1KU TCGA-DX-A1KW 
       13.28        84.66        11.70       188.15        14.04        32.71 
TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A6BA TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI 
       74.66        49.05        82.68        86.30        21.30        34.49 
TCGA-DX-A8BO TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-MO-A47R 
       40.77        17.79        12.00        66.74        77.88        10.45 
TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q TCGA-Z4-AAPF 
       16.77        25.35        32.75        15.95 

$`2Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       75.32        15.22        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       40.60        12.07       106.45        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       60.00        32.15        16.60        37.02        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH 
       26.93        52.27        28.21       159.29        22.62        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
        8.28         6.35        18.08        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       41.49        35.08        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       88.57        44.91        54.74        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       10.32        38.47        36.03        18.64        26.56         0.56 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        66.94         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       35.77        51.02         4.54        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       68.55        50.43        34.88        85.45         9.73        45.99 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       59.84        37.58        15.95        37.41        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       31.96        36.85        26.99         3.06        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN 
       50.50        16.87        64.21       101.23        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       45.14        47.87        38.17       150.35        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2G 
       36.69        60.66        19.43         6.58         1.15        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       65.98        86.10         9.21       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       15.48         8.05        67.63        34.88         4.57        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.72         9.80        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
       19.89        37.12        25.22       171.09        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        16.41         1.05         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS 
       62.17       123.78        17.36        23.38         5.19        63.81 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       16.41        35.28        30.31        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        22.39        11.57         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
      122.96        37.55        38.63        81.01        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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 
      130.32       111.98        64.77        10.52         0.72        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        3.88        22.82         8.61        19.63        13.22        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX 
       10.72        12.46        11.93         4.80        84.79        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       65.46        22.62         8.58        63.35        26.43        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       18.08        45.34        30.84        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPG 
       15.98 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            10.45              0.49 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           188.15            171.09 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            32.73             30.84 
[1] "10.4 - 188.2 (32.7)" "0.5 - 171.1 (30.8)" 
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  2Q GAIN MUTATED                0                  1                   0
  2Q GAIN WILD-TYPE              1                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  2Q GAIN MUTATED                     0                             0
  2Q GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  2Q GAIN MUTATED                       0                      1
  2Q GAIN WILD-TYPE                     1                     27
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  2Q GAIN MUTATED                      0                    0
  2Q GAIN WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  2Q GAIN MUTATED                                       0
  2Q GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  2Q GAIN MUTATED                                  0
  2Q GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  2Q GAIN MUTATED                                                0
  2Q GAIN WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  2Q GAIN MUTATED                                 1
  2Q GAIN WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  2Q GAIN MUTATED                                         0
  2Q GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  2Q GAIN MUTATED                              0                       0
  2Q GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  2Q GAIN MUTATED                                  3
  2Q GAIN WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  2Q GAIN MUTATED                                         0
  2Q GAIN WILD-TYPE                                       5
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  2Q GAIN MUTATED                              4
  2Q GAIN WILD-TYPE                           40
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  2Q GAIN MUTATED                                         0
  2Q GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  2Q GAIN MUTATED                                           0
  2Q GAIN WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  2Q GAIN MUTATED                                                  1
  2Q GAIN WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  2Q GAIN MUTATED                                          0
  2Q GAIN WILD-TYPE                                        8
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  2Q GAIN MUTATED                                                         0
  2Q GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  2Q GAIN MUTATED                                            0
  2Q GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  2Q GAIN MUTATED                                                   5
  2Q GAIN WILD-TYPE                                                68
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  2Q GAIN MUTATED                                                    0
  2Q GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  2Q GAIN MUTATED                                    0                        0
  2Q GAIN WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  2Q GAIN MUTATED                             1                         0
  2Q GAIN WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  2Q GAIN MUTATED                                   2
  2Q GAIN WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  2Q GAIN MUTATED                                   2
  2Q GAIN WILD-TYPE                                 3
D4V3, multiclass
                                                         clus
vv                                                        2Q GAIN 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                                                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                                      3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               0
  LOWER EXTREMITY - THIGH/KNEE                                          4
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     5
  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                                                        2Q GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      6
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 27
  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                                 5
  LOWER EXTREMITY - THIGH/KNEE                                           40
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                8
  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                                       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"
D4V4, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    15   7
  2Q GAIN WILD-TYPE 124 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     15    7
  2Q GAIN WILD-TYPE  124  111
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              15               124
  MALE                 7               111
[1] 2 2
[1] FALSE
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    15   7
  2Q GAIN WILD-TYPE 164  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     15    7
  2Q GAIN WILD-TYPE  164   65
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               15               164
  YES               7                65
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  2Q GAIN MUTATED                              7             0
  2Q GAIN WILD-TYPE                           52             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  2Q GAIN MUTATED                                                                          0
  2Q GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  2Q GAIN MUTATED                      3
  2Q GAIN WILD-TYPE                  100
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  2Q GAIN MUTATED                                                  4
  2Q GAIN WILD-TYPE                                                5
                   vv
clus                MYXOFIBROSARCOMA
  2Q GAIN MUTATED                  3
  2Q GAIN WILD-TYPE               21
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  2Q GAIN MUTATED                                                          4
  2Q GAIN WILD-TYPE                                                       24
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  2Q GAIN MUTATED                                          1
  2Q GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  2Q GAIN MUTATED                             0                             0
  2Q GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  2Q GAIN MUTATED                                            0
  2Q GAIN WILD-TYPE                                         21
D4V6, multiclass
                                                                          clus
vv                                                                         2Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           7
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                   3
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       4
  MYXOFIBROSARCOMA                                                                       3
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             0
                                                                          clus
vv                                                                         2Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            52
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                   100
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         5
  MYXOFIBROSARCOMA                                                                        21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                24
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    13   4   1   3
  2Q GAIN WILD-TYPE 139  65   8  23
D4V7, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              13               139
  R1               4                65
  R2               1                 8
  RX               3                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
  2Q GAIN MUTATED       1                         2    19
  2Q GAIN WILD-TYPE     5                        16   205
D4V8, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  19               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
  2Q GAIN MUTATED     1  19
  2Q GAIN WILD-TYPE   4 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   19
  2Q GAIN WILD-TYPE    4  201
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              19               201
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    21  17
  3P GAIN WILD-TYPE 138  81
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               38               219 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17                81 
$`3P GAIN MUTATED`
TCGA-DX-A7ET TCGA-DX-A8BP TCGA-DX-AB2W TCGA-KF-A41W TCGA-PC-A5DP TCGA-SG-A849 
       15.22        14.07       106.45        11.70        18.08        17.52 
TCGA-VT-A80J TCGA-3B-A9HR TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A3U7 
       26.17        88.57        42.84        18.64         0.56        51.02 
TCGA-DX-A3U8 TCGA-DX-A3UF TCGA-DX-A6YX TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BO 
        4.54        85.45        16.87        61.97        38.17        40.77 
TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-HB-A2OT 
       27.95        36.69        17.79       106.55        50.40        67.63 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MJ-A68H 
       80.48        19.53        25.22        63.81        35.28        14.99 
TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8XS 
       13.08        48.59        18.94         8.61        13.41        84.79 
TCGA-WK-A8Y0 TCGA-X6-A7WC 
       22.62        45.34 

$`3P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       75.32        17.95        14.43        15.85        40.60        12.07 
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-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       32.15        16.60        37.02        12.62        52.11        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 
       52.27        28.21       159.29        22.62        17.75         8.28 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
        6.35        20.94       188.15        41.49        35.08        50.01 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       19.69        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU 
       14.37        10.32        38.47        36.03        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        68.61        12.85        45.11        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       85.02        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A3UA 
       33.44        44.68        31.86        35.77        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       73.87        68.55        50.43        34.88         9.73        45.99 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       78.28        50.50        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BR TCGA-DX-A8BT 
       20.05         9.34        45.14        47.87       150.35        40.44 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G 
       60.66        19.43         6.58         1.15        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B 
       65.98        86.10        66.74         9.21        77.88        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
       15.48         8.05        34.88         4.57        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 
        9.80         3.22         1.38        19.89        37.12       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        85.97         5.92        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
      101.26        53.33        62.17       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
        5.19        16.41        30.31        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       19.73        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 
      122.96        37.55        38.63        81.01        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       46.82        18.08        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O 
       64.77        10.52         0.72        16.77         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-AB3D 
       25.35        32.75        19.63        13.22        10.72        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
       11.93         4.80        38.27        65.46         8.58        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       26.43        35.90        18.08        30.84        35.18        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       20.65        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.56              0.49 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           106.55            188.15 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            27.06             31.53 
[1] "0.6 - 106.5 (27.1)" "0.5 - 188.2 (31.5)"
[1] "hr=" "1.2"
D5V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  3P GAIN MUTATED                0                  1                   0
  3P GAIN WILD-TYPE              1                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  3P GAIN MUTATED                     0                             0
  3P GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  3P GAIN MUTATED                       0                      4
  3P GAIN WILD-TYPE                     1                     24
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  3P GAIN MUTATED                      1                    0
  3P GAIN WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  3P GAIN MUTATED                                       0
  3P GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  3P GAIN MUTATED                                  0
  3P GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  3P GAIN MUTATED                                                1
  3P GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  3P GAIN MUTATED                                 0
  3P GAIN WILD-TYPE                              10
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  3P GAIN MUTATED                                         1
  3P GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  3P GAIN MUTATED                              0                       1
  3P GAIN WILD-TYPE                            4                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  3P GAIN MUTATED                                  3
  3P GAIN WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  3P GAIN MUTATED                                         0
  3P GAIN WILD-TYPE                                       5
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  3P GAIN MUTATED                             16
  3P GAIN WILD-TYPE                           28
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  3P GAIN MUTATED                                         1
  3P GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  3P GAIN MUTATED                                           1
  3P GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  3P GAIN MUTATED                                                  0
  3P GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  3P GAIN MUTATED                                          0
  3P GAIN WILD-TYPE                                        8
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  3P GAIN MUTATED                                                         0
  3P GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  3P GAIN MUTATED                                            0
  3P GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  3P GAIN MUTATED                                                   3
  3P GAIN WILD-TYPE                                                70
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  3P GAIN MUTATED                                                    0
  3P GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  3P GAIN MUTATED                                    1                        1
  3P GAIN WILD-TYPE                                  1                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  3P GAIN MUTATED                             0                         0
  3P GAIN WILD-TYPE                           4                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  3P GAIN MUTATED                                   2
  3P GAIN WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  3P GAIN MUTATED                                   1
  3P GAIN WILD-TYPE                                 4
D5V3, multiclass
                                                         clus
vv                                                        3P GAIN 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                                                4
  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                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               1
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               0
  LOWER EXTREMITY - THIGH/KNEE                                         16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  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                     3
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           0
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        3P GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      6
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 24
  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                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 1
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 1
  LOWER EXTREMITY - LOWER LEG/CALF                                       14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 5
  LOWER EXTREMITY - THIGH/KNEE                                           28
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                8
  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                                      1
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             4
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    24  14
  3P GAIN WILD-TYPE 115 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     24   14
  3P GAIN WILD-TYPE  115  104
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              24               115
  MALE                14               104
[1] 2 2
[1] FALSE
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    25  13
  3P GAIN WILD-TYPE 154  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     25   13
  3P GAIN WILD-TYPE  154   59
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               25               154
  YES              13                59
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  3P GAIN MUTATED                              1             0
  3P GAIN WILD-TYPE                           58             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  3P GAIN MUTATED                                                                          0
  3P GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  3P GAIN MUTATED                     17
  3P GAIN WILD-TYPE                   86
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  3P GAIN MUTATED                                                  0
  3P GAIN WILD-TYPE                                                9
                   vv
clus                MYXOFIBROSARCOMA
  3P GAIN MUTATED                  3
  3P GAIN WILD-TYPE               21
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  3P GAIN MUTATED                                                         11
  3P GAIN WILD-TYPE                                                       17
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  3P GAIN MUTATED                                          0
  3P GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  3P GAIN MUTATED                             0                             0
  3P GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  3P GAIN MUTATED                                            6
  3P GAIN WILD-TYPE                                         15
D5V6, multiclass
                                                                          clus
vv                                                                         3P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           1
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  17
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       0
  MYXOFIBROSARCOMA                                                                       3
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             6
                                                                          clus
vv                                                                         3P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            58
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    86
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         9
  MYXOFIBROSARCOMA                                                                        21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              15
[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
  3P GAIN MUTATED    23  10   1   4
  3P GAIN WILD-TYPE 129  59   8  22
D5V7, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              23               129
  R1              10                59
  R2               1                 8
  RX               4                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
  3P GAIN MUTATED       1                         6    28
  3P GAIN WILD-TYPE     5                        12   196
D5V8, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  28               196
[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
  3P GAIN MUTATED     0  33
  3P GAIN WILD-TYPE   5 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   33
  3P GAIN WILD-TYPE    5  187
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              33               187
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    19  16
  3Q GAIN WILD-TYPE 140  82
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               35               222 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16                82 
$`3Q GAIN MUTATED`
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-KF-A41W TCGA-PC-A5DP TCGA-SG-A849 
       15.22        17.95        14.07        11.70        18.08        17.52 
TCGA-VT-A80J TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A3U7 TCGA-DX-A3U8 
       26.17        88.57        18.64         0.56        51.02         4.54 
TCGA-DX-A3UF TCGA-DX-A6YX TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS 
       85.45        16.87        61.97        38.17        40.77        27.95 
TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-HB-A2OT TCGA-HS-A5N8 
       36.69        17.79       106.55        50.40        67.63         0.72 
TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-KD-A5QS TCGA-KD-A5QU TCGA-QC-A7B5 TCGA-QQ-A5VB 
       19.53        25.22        63.81        35.28        13.08        48.59 
TCGA-SG-A6Z4 TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A7WC 
       18.94        13.41        84.79        22.62        45.34 

$`3Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W 
       75.32        14.43        15.85        40.60        12.07       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-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       32.15        16.60        37.02        12.62        52.11        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 
       52.27        28.21       159.29        22.62        17.75         8.28 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
        6.35        20.94       188.15        41.49        35.08        50.01 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       19.69        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 
       14.37        42.84        10.32        38.47        36.03        26.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04        32.71        68.61        12.85        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 
      136.44        33.44        44.68        31.86        35.77        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        73.87        68.55        50.43        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       41.00        78.28        50.50        86.30        64.21       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       21.30        34.49        62.20        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BR 
       48.20        20.05         9.34        45.14        47.87       150.35 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F 
       40.44        60.66        19.43         6.58         1.15        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       15.72        65.98        86.10        66.74         9.21        77.88 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       19.89        15.48         8.05        34.88         4.57        33.30 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
        9.80        80.48         3.22         1.38        19.89        37.12 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
      171.09        13.58        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       23.38         5.19        16.41        30.31        25.41         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
       21.73        19.73        14.99        17.98        22.39        11.57 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       10.45         7.36       122.96        37.55        38.63        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       17.65         1.84        46.82        18.08        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
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-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX 
       13.22        10.72        12.46        11.93         4.80        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46         8.58        63.35        26.43        35.90        18.08 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       30.84        35.18        19.17        20.65        50.86        29.46 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        36.43         4.37        13.38        15.95        15.98 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.56              0.49 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           106.55            188.15 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            25.22             31.91 
[1] "0.6 - 106.5 (25.2)" "0.5 - 188.2 (31.9)"
[1] "hr=" "1.3"
D6V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  3Q GAIN MUTATED                0                  1                   0
  3Q GAIN WILD-TYPE              1                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  3Q GAIN MUTATED                     0                             0
  3Q GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  3Q GAIN MUTATED                       0                      5
  3Q GAIN WILD-TYPE                     1                     23
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  3Q GAIN MUTATED                      1                    0
  3Q GAIN WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  3Q GAIN MUTATED                                       0
  3Q GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  3Q GAIN MUTATED                                  0
  3Q GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  3Q GAIN MUTATED                                                0
  3Q GAIN WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  3Q GAIN MUTATED                                 0
  3Q GAIN WILD-TYPE                              10
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  3Q GAIN MUTATED                                         1
  3Q GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  3Q GAIN MUTATED                              0                       1
  3Q GAIN WILD-TYPE                            4                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  3Q GAIN MUTATED                                  3
  3Q GAIN WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  3Q GAIN MUTATED                                         0
  3Q GAIN WILD-TYPE                                       5
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  3Q GAIN MUTATED                             14
  3Q GAIN WILD-TYPE                           30
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  3Q GAIN MUTATED                                         0
  3Q GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  3Q GAIN MUTATED                                           1
  3Q GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  3Q GAIN MUTATED                                                  0
  3Q GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  3Q GAIN MUTATED                                          0
  3Q GAIN WILD-TYPE                                        8
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  3Q GAIN MUTATED                                                         0
  3Q GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  3Q GAIN MUTATED                                            0
  3Q GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  3Q GAIN MUTATED                                                   3
  3Q GAIN WILD-TYPE                                                70
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  3Q GAIN MUTATED                                                    0
  3Q GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  3Q GAIN MUTATED                                    1                        1
  3Q GAIN WILD-TYPE                                  1                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  3Q GAIN MUTATED                             0                         0
  3Q GAIN WILD-TYPE                           4                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  3Q GAIN MUTATED                                   2
  3Q GAIN WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  3Q GAIN MUTATED                                   1
  3Q GAIN WILD-TYPE                                 4
D6V3, multiclass
                                                         clus
vv                                                        3Q GAIN 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                                                  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                               1
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               0
  LOWER EXTREMITY - THIGH/KNEE                                         14
  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                     3
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           0
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        3Q GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      6
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 23
  HEAD AND NECK - HEAD                                                    1
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 1
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 1
  LOWER EXTREMITY - LOWER LEG/CALF                                       14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 5
  LOWER EXTREMITY - THIGH/KNEE                                           30
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                8
  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                                      1
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             4
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    22  13
  3Q GAIN WILD-TYPE 117 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     22   13
  3Q GAIN WILD-TYPE  117  105
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              22               117
  MALE                13               105
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    22  13
  3Q GAIN WILD-TYPE 157  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     22   13
  3Q GAIN WILD-TYPE  157   59
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               22               157
  YES              13                59
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  3Q GAIN MUTATED                              1             0
  3Q GAIN WILD-TYPE                           58             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  3Q GAIN MUTATED                                                                          0
  3Q GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  3Q GAIN MUTATED                     15
  3Q GAIN WILD-TYPE                   88
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  3Q GAIN MUTATED                                                  0
  3Q GAIN WILD-TYPE                                                9
                   vv
clus                MYXOFIBROSARCOMA
  3Q GAIN MUTATED                  4
  3Q GAIN WILD-TYPE               20
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  3Q GAIN MUTATED                                                         10
  3Q GAIN WILD-TYPE                                                       18
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  3Q GAIN MUTATED                                          0
  3Q GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  3Q GAIN MUTATED                             0                             0
  3Q GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  3Q GAIN MUTATED                                            5
  3Q GAIN WILD-TYPE                                         16
D6V6, multiclass
                                                                          clus
vv                                                                         3Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           1
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  15
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       0
  MYXOFIBROSARCOMA                                                                       4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             5
                                                                          clus
vv                                                                         3Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            58
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    88
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         9
  MYXOFIBROSARCOMA                                                                        20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              16
[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
  3Q GAIN MUTATED    20   9   2   4
  3Q GAIN WILD-TYPE 132  60   7  22
D6V7, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              20               132
  R1               9                60
  R2               2                 7
  RX               4                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
  3Q GAIN MUTATED       1                         5    25
  3Q GAIN WILD-TYPE     5                        13   199
D6V8, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  25               199
[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
  3Q GAIN MUTATED     0  29
  3Q GAIN WILD-TYPE   5 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   29
  3Q GAIN WILD-TYPE    5  191
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              29               191
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    39  30
  4P GAIN WILD-TYPE 120  68
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               69               188 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               30                68 
$`4P GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-AB2P TCGA-DX-AB2X 
       34.68        34.36        75.32        14.43        12.07        13.28 
TCGA-HS-A5N9 TCGA-KF-A41W TCGA-QQ-A8VB TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HS 
       52.11        11.70       188.15        26.17        35.08        44.91 
TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 
       42.84        18.64         0.56        68.61        18.54        54.21 
TCGA-DX-A23R TCGA-DX-A48K TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YZ 
       74.66        45.99        82.68         3.06        41.00        86.30 
TCGA-DX-A6Z0 TCGA-DX-A8BL TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2Q 
       64.21        45.14        36.69         1.15        12.00        66.74 
TCGA-HB-A3YV TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-K1-A6RU 
        4.57        19.89        25.22       171.09        16.41        23.38 
TCGA-K1-A6RV TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A8JK TCGA-MJ-A68H TCGA-N1-A6IA 
        5.19        35.28        30.31        21.73        14.99         7.36 
TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5VA TCGA-QQ-A5VB 
       37.55        81.01        13.08        17.65        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       35.90        10.52        16.77        18.94         3.88        22.82 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS 
        8.61        13.22        13.41        10.72        12.46        84.79 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 
       22.62         8.58        26.43        45.34        35.18        20.65 
TCGA-X9-A971 TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        15.95        15.98 

$`4P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BG 
       36.30        31.53        16.18        67.20        15.22        17.95 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 
       14.07        15.85        40.60       106.45        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
       30.51        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        26.93        52.27        28.21       159.29        22.62 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 
       17.75         8.28         6.35        18.08        20.94        17.52 
TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        50.01        19.69        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-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 
       26.56        14.04        32.71        12.85        45.11        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        66.94         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       59.84        37.58        15.95        37.41        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX 
       31.96        36.85        26.99        78.28        50.50        16.87 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
      101.23        21.30        34.49        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM 
       29.49        48.20        20.05         9.34        61.97        47.87 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV 
       38.17        40.77       150.35        27.95        40.44        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
       19.43         6.58        17.79        15.72        65.98        86.10 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
        9.21        77.88       106.55        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       49.15        31.13        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        8.05        67.63        34.88        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3KA 
       80.48        19.53         3.22         1.38        37.12        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       85.97         5.92         1.05         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 
       62.17       123.78        17.36        63.81        16.41        25.41 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        0.49        19.73        17.98        22.39        11.57        10.45 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-QQ-A8VD 
      122.96        38.63         1.84        46.82        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
      111.98        64.77         0.72        25.35        32.75        19.63 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA 
       11.93         4.80        38.27        65.46        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       18.08        30.84        19.17        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC 
        4.37        13.38 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.56              0.49 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           188.15            159.29 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           22.820            33.025 
[1] "0.6 - 188.2 (22.8)" "0.5 - 159.3 (33.0)"
[1] "hr=" "1.5"
D7V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  4P GAIN MUTATED                0                  3                   0
  4P GAIN WILD-TYPE              1                  4                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  4P GAIN MUTATED                     0                             1
  4P GAIN WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  4P GAIN MUTATED                       0                      7
  4P GAIN WILD-TYPE                     1                     21
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  4P GAIN MUTATED                      2                    0
  4P GAIN WILD-TYPE                    0                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  4P GAIN MUTATED                                       0
  4P GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  4P GAIN MUTATED                                  0
  4P GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  4P GAIN MUTATED                                                1
  4P GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  4P GAIN MUTATED                                 3
  4P GAIN WILD-TYPE                               7
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  4P GAIN MUTATED                                         0
  4P GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  4P GAIN MUTATED                              0                       1
  4P GAIN WILD-TYPE                            4                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  4P GAIN MUTATED                                  7
  4P GAIN WILD-TYPE                               10
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  4P GAIN MUTATED                                         3
  4P GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  4P GAIN MUTATED                             14
  4P GAIN WILD-TYPE                           30
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  4P GAIN MUTATED                                         1
  4P GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  4P GAIN MUTATED                                           1
  4P GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  4P GAIN MUTATED                                                  0
  4P GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  4P GAIN MUTATED                                          2
  4P GAIN WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  4P GAIN MUTATED                                                         1
  4P GAIN WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  4P GAIN MUTATED                                            0
  4P GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  4P GAIN MUTATED                                                  12
  4P GAIN WILD-TYPE                                                61
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  4P GAIN MUTATED                                                    0
  4P GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  4P GAIN MUTATED                                    1                        0
  4P GAIN WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  4P GAIN MUTATED                             3                         0
  4P GAIN WILD-TYPE                           1                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  4P GAIN MUTATED                                   4
  4P GAIN WILD-TYPE                                 3
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  4P GAIN MUTATED                                   2
  4P GAIN WILD-TYPE                                 3
D7V3, multiclass
                                                         clus
vv                                                        4P GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    3
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                7
  HEAD AND NECK - HEAD                                                  2
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         14
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        4P GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      4
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           1
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 21
  HEAD AND NECK - HEAD                                                    0
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 1
  LOWER EXTREMITY - LOWER LEG/CALF                                       10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 2
  LOWER EXTREMITY - THIGH/KNEE                                           30
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      61
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             1
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       3
  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"
D7V4, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   41 28
  4P GAIN WILD-TYPE 98 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     41   28
  4P GAIN WILD-TYPE   98   90
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              41                98
  MALE                28                90
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    45  24
  4P GAIN WILD-TYPE 134  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     45   24
  4P GAIN WILD-TYPE  134   48
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               45               134
  YES              24                48
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  4P GAIN MUTATED                              9             0
  4P GAIN WILD-TYPE                           50             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  4P GAIN MUTATED                                                                          0
  4P GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  4P GAIN MUTATED                     23
  4P GAIN WILD-TYPE                   80
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  4P GAIN MUTATED                                                  4
  4P GAIN WILD-TYPE                                                5
                   vv
clus                MYXOFIBROSARCOMA
  4P GAIN MUTATED                  9
  4P GAIN WILD-TYPE               15
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  4P GAIN MUTATED                                                         10
  4P GAIN WILD-TYPE                                                       18
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  4P GAIN MUTATED                                          1
  4P GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  4P GAIN MUTATED                             0                             0
  4P GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  4P GAIN MUTATED                                           13
  4P GAIN WILD-TYPE                                          8
D7V6, multiclass
                                                                          clus
vv                                                                         4P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           9
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  23
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       4
  MYXOFIBROSARCOMA                                                                       9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            13
                                                                          clus
vv                                                                         4P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            50
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    80
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         5
  MYXOFIBROSARCOMA                                                                        15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               8
[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
  4P GAIN MUTATED    36  17   1  14
  4P GAIN WILD-TYPE 116  52   8  12
D7V7, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              36               116
  R1              17                52
  R2               1                 8
  RX              14                12
[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
  4P GAIN MUTATED       2                         5    59
  4P GAIN WILD-TYPE     4                        13   165
D7V8, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  59               165
[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
  4P GAIN MUTATED     1  61
  4P GAIN WILD-TYPE   4 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   61
  4P GAIN WILD-TYPE    4  159
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              61               159
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    27  21
  4Q GAIN WILD-TYPE 132  77
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               48               209 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21                77 
$`4Q GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A7EL TCGA-DX-AB2P TCGA-HS-A5N9 TCGA-VT-A80J TCGA-3B-A9HS 
       34.68        75.32        12.07        52.11        26.17        44.91 
TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A3LY 
       42.84        18.64        68.61        18.54        54.21        33.44 
TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A8BL TCGA-DX-A8BU 
       45.99        15.95        50.50       101.23        45.14        36.69 
TCGA-DX-AATS TCGA-DX-AB2Q TCGA-HB-A3YV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ 
        1.15        66.74         4.57         3.22        19.89        25.22 
TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-K1-A6RU TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A8JK 
      171.09        16.41        23.38        35.28        30.31        21.73 
TCGA-MJ-A68H TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       14.99        37.55        81.01        13.08        18.08        48.59 
TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-VT-A80G 
       10.52        16.77        18.94         8.61        13.22        10.72 
TCGA-VT-AB3D TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-Z4-AAPF TCGA-Z4-AAPG 
       12.46        22.62        26.43        35.18        15.95        15.98 

$`4Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        34.36        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W 
       17.95        14.43        14.07        15.85        40.60       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-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK 
       32.15        16.60        37.02        12.62        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       28.21       159.29        22.62        11.70        17.75         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-WK-A8XT 
        6.35        18.08        20.94       188.15        17.52        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       35.08        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-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-A1KY TCGA-DX-A1KZ 
       26.56         0.56        14.04        32.71        12.85        45.11 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       85.02        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
      108.82        59.84        37.58        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI 
       78.28        16.87        86.30        64.21        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
        9.34        61.97        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E 
       27.95        40.44        60.66        19.43         6.58        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T 
       12.00        15.72        65.98        86.10         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      106.55        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       34.88        33.30         0.72         9.80        80.48        19.53 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF 
        1.38        37.12        13.58        85.97         5.92         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL 
        5.19        63.81        16.41        25.41         0.49        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DN TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD 
       38.63        17.65         1.84        46.82        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71O 
      130.32       111.98        64.77         0.72         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
       25.35        32.75        19.63        13.41        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       84.79        38.27        65.46         8.58        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08        45.34        30.84        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       29.46        27.32        36.43         4.37        13.38 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.15              0.49 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           171.09            188.15 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            24.30             32.15 
[1] "1.1 - 171.1 (24.3)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1.4"
D8V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  4Q GAIN MUTATED                0                  1                   0
  4Q GAIN WILD-TYPE              1                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  4Q GAIN MUTATED                     0                             1
  4Q GAIN WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  4Q GAIN MUTATED                       0                      4
  4Q GAIN WILD-TYPE                     1                     24
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  4Q GAIN MUTATED                      2                    0
  4Q GAIN WILD-TYPE                    0                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  4Q GAIN MUTATED                                       0
  4Q GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  4Q GAIN MUTATED                                  0
  4Q GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  4Q GAIN MUTATED                                                1
  4Q GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  4Q GAIN MUTATED                                 2
  4Q GAIN WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  4Q GAIN MUTATED                                         0
  4Q GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  4Q GAIN MUTATED                              0                       1
  4Q GAIN WILD-TYPE                            4                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  4Q GAIN MUTATED                                  5
  4Q GAIN WILD-TYPE                               12
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  4Q GAIN MUTATED                                         1
  4Q GAIN WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  4Q GAIN MUTATED                             10
  4Q GAIN WILD-TYPE                           34
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  4Q GAIN MUTATED                                         1
  4Q GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  4Q GAIN MUTATED                                           0
  4Q GAIN WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  4Q GAIN MUTATED                                                  0
  4Q GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  4Q GAIN MUTATED                                          1
  4Q GAIN WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  4Q GAIN MUTATED                                                         1
  4Q GAIN WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  4Q GAIN MUTATED                                            0
  4Q GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  4Q GAIN MUTATED                                                  11
  4Q GAIN WILD-TYPE                                                62
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  4Q GAIN MUTATED                                                    0
  4Q GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  4Q GAIN MUTATED                                    0                        0
  4Q GAIN WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  4Q GAIN MUTATED                             1                         0
  4Q GAIN WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  4Q GAIN MUTATED                                   3
  4Q GAIN WILD-TYPE                                 4
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  4Q GAIN MUTATED                                   2
  4Q GAIN WILD-TYPE                                 3
D8V3, multiclass
                                                         clus
vv                                                        4Q GAIN 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                                                4
  HEAD AND NECK - HEAD                                                  2
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  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               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    11
  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                                     3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        4Q GAIN 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                                                 24
  HEAD AND NECK - HEAD                                                    0
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 1
  LOWER EXTREMITY - LOWER LEG/CALF                                       12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           34
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  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                      62
  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                                       4
  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"
D8V4, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    25  23
  4Q GAIN WILD-TYPE 114  95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     25   23
  4Q GAIN WILD-TYPE  114   95
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              25               114
  MALE                23                95
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    30  17
  4Q GAIN WILD-TYPE 149  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     30   17
  4Q GAIN WILD-TYPE  149   55
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               30               149
  YES              17                55
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  4Q GAIN MUTATED                              6             0
  4Q GAIN WILD-TYPE                           53             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  4Q GAIN MUTATED                                                                          0
  4Q GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  4Q GAIN MUTATED                     16
  4Q GAIN WILD-TYPE                   87
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  4Q GAIN MUTATED                                                  2
  4Q GAIN WILD-TYPE                                                7
                   vv
clus                MYXOFIBROSARCOMA
  4Q GAIN MUTATED                  4
  4Q GAIN WILD-TYPE               20
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  4Q GAIN MUTATED                                                          8
  4Q GAIN WILD-TYPE                                                       20
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  4Q GAIN MUTATED                                          1
  4Q GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  4Q GAIN MUTATED                             0                             0
  4Q GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  4Q GAIN MUTATED                                           11
  4Q GAIN WILD-TYPE                                         10
D8V6, multiclass
                                                                          clus
vv                                                                         4Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           6
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  16
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       2
  MYXOFIBROSARCOMA                                                                       4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            11
                                                                          clus
vv                                                                         4Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            53
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    87
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         7
  MYXOFIBROSARCOMA                                                                        20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                20
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              10
[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
  4Q GAIN MUTATED    27  13   0   7
  4Q GAIN WILD-TYPE 125  56   9  19
D8V7, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              27               125
  R1              13                56
  R2               0                 9
  RX               7                19
[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
  4Q GAIN MUTATED       1                         3    43
  4Q GAIN WILD-TYPE     5                        15   181
D8V8, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  43               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"
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  42
  4Q GAIN WILD-TYPE   4 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   42
  4Q GAIN WILD-TYPE    4  178
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              42               178
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    58  40
  5P GAIN WILD-TYPE 101  58
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               98               159 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               40                58 
$`5P GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2W 
       34.68        34.36        75.32        14.07        12.07       106.45 
TCGA-DX-AB35 TCGA-DX-AB3A TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-KF-A41W TCGA-LI-A9QH 
       30.51        32.15        12.62        52.27        11.70        17.75 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-3B-A9HI TCGA-3B-A9HQ 
        6.35        18.08        20.94       188.15        50.01        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KX 
       88.57        44.91        54.74        18.64        26.56        68.61 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3U8 
       54.21        33.53         6.28        33.44        51.02         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R 
       14.99        50.43        85.45        24.26        46.03        26.47 
TCGA-DX-A6B8 TCGA-DX-A6BG TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ 
       15.95        36.85        41.00        78.28        16.87        86.30 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN 
       21.30        34.49        30.35        61.97        45.14        38.17 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       27.95        40.44        36.69        60.66        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2Z 
       17.79        12.00        15.72        66.74       106.55        50.40 
TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ 
       20.32        67.63         4.57         0.72        19.53         3.22 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RV TCGA-KD-A5QS 
       19.89        25.22       101.26        62.17         5.19        63.81 
TCGA-LI-A67I TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-QC-A7B5 TCGA-QQ-A5V9 
       30.31        14.99        10.45         7.36        13.08        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       18.08        35.90       111.98        16.77        18.94         3.88 
TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS 
       22.82         8.61        13.22        13.41        10.72        84.79 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 
       38.27         8.58        63.35        26.43        45.34        35.18 
TCGA-X9-A971 TCGA-Z4-AAPG 
       27.32        15.98 

$`5P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BG 
       36.30        31.53        16.18        67.20        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       14.43        15.85        40.60        13.28        22.85       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EH 
       60.00        84.66        16.60        37.02        52.11        26.93 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-SG-A849 TCGA-VT-A80J 
       28.21       159.29        22.62         8.28        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HU TCGA-3B-A9HV 
       41.49        35.08        19.69        53.49        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU 
       42.84        10.32        38.47        36.03         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L4 
       32.71        12.85        45.11        18.54        85.02        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3UA 
       86.83       136.44        44.68        31.86        35.77        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       73.87        68.55        34.88         9.73        45.99        35.28 
TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       52.77       108.82        59.84        37.58        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YV 
       36.33        28.96        31.96        26.99         3.06        50.50 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       64.21       101.23        62.20       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BZ 
       20.05         9.34        47.87        40.77       150.35         6.58 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        86.10         9.21        77.88        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        21.70        19.89        15.48         8.05 
TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IF-A3RQ 
       34.88        33.30         9.80        80.48         1.38        37.12 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
      171.09        13.58        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT 
        3.91        53.33       123.78        17.36        23.38        16.41 
TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
       35.28        25.41         0.49        21.73        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57       122.96        37.55        38.63        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
       17.65         1.84        48.59        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-VT-AB3D 
       10.52         0.72        25.35        32.75        19.63        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A7WB 
       11.93         4.80        65.46        22.62        35.90        18.08 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       30.84        19.17        20.65        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.72              0.49 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           188.15            171.09 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            29.13             31.96 
[1] "0.7 - 188.2 (29.1)" "0.5 - 171.1 (32.0)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  5P GAIN MUTATED                0                  2                   0
  5P GAIN WILD-TYPE              1                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  5P GAIN MUTATED                     0                             0
  5P GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  5P GAIN MUTATED                       0                      8
  5P GAIN WILD-TYPE                     1                     20
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  5P GAIN MUTATED                      2                    0
  5P GAIN WILD-TYPE                    0                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  5P GAIN MUTATED                                       1
  5P GAIN WILD-TYPE                                     1
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  5P GAIN MUTATED                                  0
  5P GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  5P GAIN MUTATED                                                2
  5P GAIN WILD-TYPE                                              0
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  5P GAIN MUTATED                                 1
  5P GAIN WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  5P GAIN MUTATED                                         1
  5P GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  5P GAIN MUTATED                              0                       0
  5P GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  5P GAIN MUTATED                                  6
  5P GAIN WILD-TYPE                               11
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  5P GAIN MUTATED                                         4
  5P GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  5P GAIN MUTATED                             24
  5P GAIN WILD-TYPE                           20
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  5P GAIN MUTATED                                         0
  5P GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  5P GAIN MUTATED                                           1
  5P GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  5P GAIN MUTATED                                                  1
  5P GAIN WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  5P GAIN MUTATED                                          4
  5P GAIN WILD-TYPE                                        4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  5P GAIN MUTATED                                                         1
  5P GAIN WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  5P GAIN MUTATED                                            1
  5P GAIN WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  5P GAIN MUTATED                                                  27
  5P GAIN WILD-TYPE                                                46
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  5P GAIN MUTATED                                                    0
  5P GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  5P GAIN MUTATED                                    0                        2
  5P GAIN WILD-TYPE                                  2                        3
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  5P GAIN MUTATED                             2                         0
  5P GAIN WILD-TYPE                           2                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  5P GAIN MUTATED                                   7
  5P GAIN WILD-TYPE                                 0
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  5P GAIN MUTATED                                   1
  5P GAIN WILD-TYPE                                 4
D9V3, multiclass
                                                         clus
vv                                                        5P GAIN 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                                                8
  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                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                       1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               1
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               4
  LOWER EXTREMITY - THIGH/KNEE                                         24
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    27
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              2
  SUPERFICIAL TRUNK - BUTTOCK                                           2
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     7
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        5P GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 20
  HEAD AND NECK - HEAD                                                    0
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   1
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          0
  LOWER ABDOMINAL/PELVIC - PELVIC                                         9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 1
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 1
  LOWER EXTREMITY - THIGH/KNEE                                           20
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      46
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                3
  SUPERFICIAL TRUNK - BUTTOCK                                             2
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       0
  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"
D9V4, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   51 47
  5P GAIN WILD-TYPE 88 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     51   47
  5P GAIN WILD-TYPE   88   71
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              51                88
  MALE                47                71
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    61  36
  5P GAIN WILD-TYPE 118  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     61   36
  5P GAIN WILD-TYPE  118   36
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               61               118
  YES              36                36
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  5P GAIN MUTATED                             15             0
  5P GAIN WILD-TYPE                           44             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  5P GAIN MUTATED                                                                          0
  5P GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  5P GAIN MUTATED                     40
  5P GAIN WILD-TYPE                   63
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  5P GAIN MUTATED                                                  3
  5P GAIN WILD-TYPE                                                6
                   vv
clus                MYXOFIBROSARCOMA
  5P GAIN MUTATED                 10
  5P GAIN WILD-TYPE               14
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  5P GAIN MUTATED                                                         18
  5P GAIN WILD-TYPE                                                       10
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  5P GAIN MUTATED                                          0
  5P GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  5P GAIN MUTATED                             0                             0
  5P GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  5P GAIN MUTATED                                           12
  5P GAIN WILD-TYPE                                          9
D9V6, multiclass
                                                                          clus
vv                                                                         5P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          15
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  40
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       3
  MYXOFIBROSARCOMA                                                                      10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            12
                                                                          clus
vv                                                                         5P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            44
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    63
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         6
  MYXOFIBROSARCOMA                                                                        14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               9
[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
  5P GAIN MUTATED   59 24  2 12
  5P GAIN WILD-TYPE 93 45  7 14
D9V7, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              59                93
  R1              24                45
  R2               2                 7
  RX              12                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
  5P GAIN MUTATED       3                         6    86
  5P GAIN WILD-TYPE     3                        12   138
D9V8, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 3
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  86               138
[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
  5P GAIN MUTATED     2  86
  5P GAIN WILD-TYPE   3 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   86
  5P GAIN WILD-TYPE    3  134
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              86               134
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    39  33
  5Q GAIN WILD-TYPE 120  65
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               72               185 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               33                65 
$`5Q GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-AB2P TCGA-DX-AB35 
       34.68        16.18        34.36        75.32        12.07        30.51 
TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-KF-A41W TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-3B-A9HI 
       12.62        52.27        11.70         6.35       188.15        50.01 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KX 
       68.55        88.57        54.74        18.64        26.56        68.61 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD 
       54.21        33.53         6.28         4.54        14.99        50.43 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YQ 
       85.45        24.26        46.03        26.47        15.95         3.06 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EI TCGA-DX-A8BK TCGA-DX-A8BL 
       78.28        16.87        86.30        34.49        61.97        45.14 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
       38.17        27.95        40.44        36.69        60.66        19.43 
TCGA-DX-AB2V TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A3OV 
      106.55        20.32        67.63         4.57         0.72        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-K1-A42W TCGA-K1-A6RV 
       19.53         3.22       171.09        13.58        62.17         5.19 
TCGA-KD-A5QS TCGA-LI-A67I TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-QC-A7B5 
       63.81        30.31        14.99        10.45         7.36        13.08 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O 
       18.08        35.90       111.98        16.77         3.88        22.82 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XS TCGA-X6-A7W8 TCGA-X9-A971 
        8.61        13.22        13.41        84.79        26.43        27.32 

$`5Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       36.30        31.53        67.20        15.22        17.95        14.43 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       14.07        15.85        40.60       106.45        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
      101.98        60.00        84.66        32.15        16.60        37.02 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH 
       52.11        26.93        28.21       159.29        22.62        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
        8.28        18.08        20.94        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV 
       35.08        19.69        53.49        44.91        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU 
       42.84        10.32        38.47        36.03         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L4 
       32.71        12.85        45.11        18.54        85.02        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
       51.02        10.68        73.87        68.55        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       45.99        35.28        52.77       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       26.99        41.00        50.50        64.21       101.23        21.30 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BZ TCGA-DX-AATS 
        9.34        47.87        40.77       150.35         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21        77.88        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       31.13        21.70        19.89        15.48         8.05        34.88 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       33.30         9.80         1.38        19.89        37.12        25.22 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT TCGA-KD-A5QU 
       53.33       123.78        17.36        23.38        16.41        35.28 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
       25.41         0.49        21.73        19.73        17.98        22.39 
TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N 
       11.57       122.96        37.55        38.63        81.01        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
        1.84        46.82        48.59        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
       10.52         0.72        18.94        25.35        32.75        19.63 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY 
       10.72        12.46        11.93         4.80        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62         8.58        63.35        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       30.84        35.18        19.17        20.65        50.86        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.72              0.49 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           188.15            159.29 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           27.635            31.960 
[1] "0.7 - 188.2 (27.6)" "0.5 - 159.3 (32.0)"
[1] "hr=" "1.3"
D10V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  5Q GAIN MUTATED                0                  1                   0
  5Q GAIN WILD-TYPE              1                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  5Q GAIN MUTATED                     0                             0
  5Q GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  5Q GAIN MUTATED                       0                      7
  5Q GAIN WILD-TYPE                     1                     21
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  5Q GAIN MUTATED                      2                    0
  5Q GAIN WILD-TYPE                    0                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  5Q GAIN MUTATED                                       1
  5Q GAIN WILD-TYPE                                     1
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  5Q GAIN MUTATED                                  0
  5Q GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  5Q GAIN MUTATED                                                2
  5Q GAIN WILD-TYPE                                              0
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  5Q GAIN MUTATED                                 1
  5Q GAIN WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  5Q GAIN MUTATED                                         1
  5Q GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  5Q GAIN MUTATED                              0                       0
  5Q GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  5Q GAIN MUTATED                                  2
  5Q GAIN WILD-TYPE                               15
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  5Q GAIN MUTATED                                         4
  5Q GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  5Q GAIN MUTATED                             18
  5Q GAIN WILD-TYPE                           26
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  5Q GAIN MUTATED                                         0
  5Q GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  5Q GAIN MUTATED                                           1
  5Q GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  5Q GAIN MUTATED                                                  1
  5Q GAIN WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  5Q GAIN MUTATED                                          4
  5Q GAIN WILD-TYPE                                        4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  5Q GAIN MUTATED                                                         1
  5Q GAIN WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  5Q GAIN MUTATED                                            1
  5Q GAIN WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  5Q GAIN MUTATED                                                  16
  5Q GAIN WILD-TYPE                                                57
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  5Q GAIN MUTATED                                                    0
  5Q GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  5Q GAIN MUTATED                                    0                        1
  5Q GAIN WILD-TYPE                                  2                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  5Q GAIN MUTATED                             1                         0
  5Q GAIN WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  5Q GAIN MUTATED                                   6
  5Q GAIN WILD-TYPE                                 1
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  5Q GAIN MUTATED                                   1
  5Q GAIN WILD-TYPE                                 4
D10V3, multiclass
                                                         clus
vv                                                        5Q GAIN 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                                                7
  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                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                       1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               1
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               4
  LOWER EXTREMITY - THIGH/KNEE                                         18
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        5Q GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      6
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 21
  HEAD AND NECK - HEAD                                                    0
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   1
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          0
  LOWER ABDOMINAL/PELVIC - PELVIC                                         9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 1
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 1
  LOWER EXTREMITY - THIGH/KNEE                                           26
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      57
  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                                       1
  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"
D10V4, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   42 30
  5Q GAIN WILD-TYPE 97 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     42   30
  5Q GAIN WILD-TYPE   97   88
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              42                97
  MALE                30                88
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    47  24
  5Q GAIN WILD-TYPE 132  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     47   24
  5Q GAIN WILD-TYPE  132   48
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               47               132
  YES              24                48
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  5Q GAIN MUTATED                             11             0
  5Q GAIN WILD-TYPE                           48             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  5Q GAIN MUTATED                                                                          0
  5Q GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  5Q GAIN MUTATED                     33
  5Q GAIN WILD-TYPE                   70
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  5Q GAIN MUTATED                                                  3
  5Q GAIN WILD-TYPE                                                6
                   vv
clus                MYXOFIBROSARCOMA
  5Q GAIN MUTATED                  9
  5Q GAIN WILD-TYPE               15
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  5Q GAIN MUTATED                                                          9
  5Q GAIN WILD-TYPE                                                       19
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  5Q GAIN MUTATED                                          0
  5Q GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  5Q GAIN MUTATED                             0                             0
  5Q GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  5Q GAIN MUTATED                                            7
  5Q GAIN WILD-TYPE                                         14
D10V6, multiclass
                                                                          clus
vv                                                                         5Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          11
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  33
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       3
  MYXOFIBROSARCOMA                                                                       9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             7
                                                                          clus
vv                                                                         5Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            48
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    70
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         6
  MYXOFIBROSARCOMA                                                                        15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              14
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    39  20   1  11
  5Q GAIN WILD-TYPE 113  49   8  15
D10V7, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              39               113
  R1              20                49
  R2               1                 8
  RX              11                15
[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
  5Q GAIN MUTATED       3                         6    59
  5Q GAIN WILD-TYPE     3                        12   165
D10V8, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   3                 3
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  59               165
[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
  5Q GAIN MUTATED     1  60
  5Q GAIN WILD-TYPE   4 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   60
  5Q GAIN WILD-TYPE    4  160
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              60               160
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    22  30
  6P GAIN WILD-TYPE 137  68
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               52               205 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               30                68 
$`6P GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-AB35 TCGA-HS-A5N9 TCGA-MB-A5Y9 
       34.68        34.36        15.22        30.51        52.11         8.28 
TCGA-PC-A5DM TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS 
        6.35        35.08        50.01        19.69        88.57        44.91 
TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3U9 
        0.56        32.71        68.61        85.02         6.28        14.99 
TCGA-DX-A6B8 TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
       15.95        41.00        50.50        86.30        64.21        21.30 
TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-HB-A2OT 
       27.95        36.69        60.66        19.43         1.15        67.63 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 
        4.57         0.72         3.22        19.89        37.12       171.09 
TCGA-IW-A3M5 TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A8JK 
        5.92        17.36        23.38        35.28        30.31        21.73 
TCGA-N1-A6IA TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-UE-A6QU 
        7.36        46.82        35.90         3.88         8.61        13.41 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A8C2 TCGA-X9-A971 
       22.62         8.58        35.18        27.32 

$`6P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        31.53        16.18        67.20        75.32        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W 
       14.43        14.07        15.85        40.60        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       13.28        22.85       101.98        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       16.60        37.02        12.62        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DP TCGA-QC-A6FX 
      159.29        22.62        11.70        17.75        18.08        20.94 
TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ 
      188.15        17.52        26.17        41.49        53.49        68.55 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ 
       36.03        18.64        26.56        14.04        12.85        45.11 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       18.54        54.21        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47       108.82        59.84        37.58        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN 
       78.28        16.87       101.23        34.49        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT 
       45.14        47.87        38.17        40.77       150.35        40.44 
TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        6.58        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       66.74         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV 
       15.48         8.05        34.88        33.30         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE 
       19.53         1.38        25.22        13.58        85.97        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        1.05         3.91       101.26        53.33        62.17       123.78 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL 
        5.19        63.81        16.41        25.41         0.49        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK 
       14.99        17.98        22.39        11.57        10.45       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        81.01        13.08        17.65         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       18.08        48.59        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P 
       10.52         0.72        16.77        18.94        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       32.75        19.63        13.22        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7W8 
        4.80        84.79        38.27        65.46        63.35        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       35.90        18.08        45.34        30.84        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       50.86        29.46        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.56              0.49 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           171.09            188.15 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           27.635            31.960 
[1] "0.6 - 171.1 (27.6)" "0.5 - 188.2 (32.0)"
[1] "hr=" "2.1"
D11V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  6P GAIN MUTATED                0                  3                   0
  6P GAIN WILD-TYPE              1                  4                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  6P GAIN MUTATED                     0                             0
  6P GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  6P GAIN MUTATED                       0                      7
  6P GAIN WILD-TYPE                     1                     21
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  6P GAIN MUTATED                      0                    0
  6P GAIN WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  6P GAIN MUTATED                                       0
  6P GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  6P GAIN MUTATED                                  0
  6P GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  6P GAIN MUTATED                                                1
  6P GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  6P GAIN MUTATED                                 1
  6P GAIN WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  6P GAIN MUTATED                                         0
  6P GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  6P GAIN MUTATED                              0                       0
  6P GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  6P GAIN MUTATED                                  2
  6P GAIN WILD-TYPE                               15
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  6P GAIN MUTATED                                         1
  6P GAIN WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  6P GAIN MUTATED                             16
  6P GAIN WILD-TYPE                           28
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  6P GAIN MUTATED                                         0
  6P GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  6P GAIN MUTATED                                           0
  6P GAIN WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  6P GAIN MUTATED                                                  0
  6P GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  6P GAIN MUTATED                                          2
  6P GAIN WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  6P GAIN MUTATED                                                         0
  6P GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  6P GAIN MUTATED                                            0
  6P GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  6P GAIN MUTATED                                                  13
  6P GAIN WILD-TYPE                                                60
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  6P GAIN MUTATED                                                    0
  6P GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  6P GAIN MUTATED                                    1                        0
  6P GAIN WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  6P GAIN MUTATED                             1                         0
  6P GAIN WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  6P GAIN MUTATED                                   3
  6P GAIN WILD-TYPE                                 4
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  6P GAIN MUTATED                                   1
  6P GAIN WILD-TYPE                                 4
D11V3, multiclass
                                                         clus
vv                                                        6P GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    3
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                7
  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                        1
  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                                      2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  LOWER EXTREMITY - THIGH/KNEE                                         16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    13
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        6P GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      4
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 21
  HEAD AND NECK - HEAD                                                    2
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           28
  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                      60
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  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"
D11V4, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    25  27
  6P GAIN WILD-TYPE 114  91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     25   27
  6P GAIN WILD-TYPE  114   91
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              25               114
  MALE                27                91
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    31  20
  6P GAIN WILD-TYPE 148  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     31   20
  6P GAIN WILD-TYPE  148   52
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               31               148
  YES              20                52
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  6P GAIN MUTATED                             11             0
  6P GAIN WILD-TYPE                           48             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  6P GAIN MUTATED                                                                          0
  6P GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  6P GAIN MUTATED                     15
  6P GAIN WILD-TYPE                   88
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  6P GAIN MUTATED                                                  0
  6P GAIN WILD-TYPE                                                9
                   vv
clus                MYXOFIBROSARCOMA
  6P GAIN MUTATED                  9
  6P GAIN WILD-TYPE               15
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  6P GAIN MUTATED                                                          7
  6P GAIN WILD-TYPE                                                       21
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  6P GAIN MUTATED                                          0
  6P GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  6P GAIN MUTATED                             0                             0
  6P GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  6P GAIN MUTATED                                           10
  6P GAIN WILD-TYPE                                         11
D11V6, multiclass
                                                                          clus
vv                                                                         6P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          11
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  15
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       0
  MYXOFIBROSARCOMA                                                                       9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            10
                                                                          clus
vv                                                                         6P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            48
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    88
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         9
  MYXOFIBROSARCOMA                                                                        15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              11
[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
  6P GAIN MUTATED    28  17   2   5
  6P GAIN WILD-TYPE 124  52   7  21
D11V7, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              28               124
  R1              17                52
  R2               2                 7
  RX               5                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
  6P GAIN MUTATED       1                         5    43
  6P GAIN WILD-TYPE     5                        13   181
D11V8, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  43               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"
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1  43
  6P GAIN WILD-TYPE   4 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   43
  6P GAIN WILD-TYPE    4  177
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              43               177
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    25  24
  6Q GAIN WILD-TYPE 134  74
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               49               208 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               24                74 
$`6Q GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-AB35 TCGA-FX-A3NK TCGA-HS-A5N9 
       34.68        34.36        15.22        30.51        16.60        52.11 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HS 
       17.75         8.28        35.08        50.01        19.69        44.91 
TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A3LT TCGA-DX-A3LY 
        0.56        32.71        68.61        18.54        49.05        33.44 
TCGA-DX-A3U9 TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6Z0 TCGA-DX-A8BK TCGA-DX-A8BS 
       14.99        41.00        50.50        64.21        61.97        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-HB-A2OT TCGA-HB-A3YV 
       36.69        60.66        19.43         1.15        67.63         4.57 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-K1-A6RT 
        3.22        19.89        37.12       171.09         5.92        17.36 
TCGA-K1-A6RU TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DL 
       23.38        35.28        30.31        21.73         7.36        37.55 
TCGA-QQ-A5VC TCGA-SI-A71Q TCGA-UE-A6QU TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A8C2 
       35.90        32.75        13.41        38.27         8.58        35.18 
TCGA-X9-A971 
       27.32 

$`6Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        31.53        16.18        67.20        75.32        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W 
       14.43        14.07        15.85        40.60        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       13.28        22.85       101.98        60.00        84.66        32.15 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       37.02        12.62        26.93        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       22.62        11.70         6.35        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       17.52        26.17        41.49        53.49        68.55        88.57 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ 
       36.03        18.64        26.56        14.04        12.85        45.11 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        95.38        79.17         9.04        86.83       136.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       44.68        31.86        35.77        51.02         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       78.28        16.87        86.30       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
        9.34        45.14        47.87        38.17        40.77       150.35 
TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       40.44         6.58        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        66.74         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 
       19.89        15.48         8.05        34.88        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3KA 
        9.80        80.48        19.53         1.38        25.22        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       85.97        16.41         1.05         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MB-A5Y8 
       62.17       123.78         5.19        63.81        16.41        25.41 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        19.73        14.99        17.98        22.39        11.57 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
       10.45       122.96        38.63        81.01        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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      111.98        64.77        10.52         0.72        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
        3.88        22.82        25.35         8.61        19.63        13.22 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XY 
       10.72        12.46        11.93         4.80        84.79        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62        63.35        26.43        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       30.84        19.17        20.65        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.56              0.49 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           171.09            188.15 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           32.710            30.985 
[1] "0.6 - 171.1 (32.7)" "0.5 - 188.2 (31.0)"
[1] "hr=" "1.7"
D12V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  6Q GAIN MUTATED                0                  3                   0
  6Q GAIN WILD-TYPE              1                  4                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  6Q GAIN MUTATED                     0                             0
  6Q GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  6Q GAIN MUTATED                       0                      6
  6Q GAIN WILD-TYPE                     1                     22
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  6Q GAIN MUTATED                      0                    0
  6Q GAIN WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  6Q GAIN MUTATED                                       0
  6Q GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  6Q GAIN MUTATED                                  0
  6Q GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  6Q GAIN MUTATED                                                1
  6Q GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  6Q GAIN MUTATED                                 1
  6Q GAIN WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  6Q GAIN MUTATED                                         0
  6Q GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  6Q GAIN MUTATED                              0                       0
  6Q GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  6Q GAIN MUTATED                                  3
  6Q GAIN WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  6Q GAIN MUTATED                                         0
  6Q GAIN WILD-TYPE                                       5
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  6Q GAIN MUTATED                             13
  6Q GAIN WILD-TYPE                           31
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  6Q GAIN MUTATED                                         0
  6Q GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  6Q GAIN MUTATED                                           1
  6Q GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  6Q GAIN MUTATED                                                  0
  6Q GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  6Q GAIN MUTATED                                          1
  6Q GAIN WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  6Q GAIN MUTATED                                                         0
  6Q GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  6Q GAIN MUTATED                                            0
  6Q GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  6Q GAIN MUTATED                                                  14
  6Q GAIN WILD-TYPE                                                59
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  6Q GAIN MUTATED                                                    0
  6Q GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  6Q GAIN MUTATED                                    1                        0
  6Q GAIN WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  6Q GAIN MUTATED                             1                         0
  6Q GAIN WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  6Q GAIN MUTATED                                   2
  6Q GAIN WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  6Q GAIN MUTATED                                   2
  6Q GAIN WILD-TYPE                                 3
D12V3, multiclass
                                                         clus
vv                                                        6Q GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    3
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                6
  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                        1
  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                                      3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               0
  LOWER EXTREMITY - THIGH/KNEE                                         13
  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                    14
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  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                                                        6Q GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      4
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 22
  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                          1
  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                                 5
  LOWER EXTREMITY - THIGH/KNEE                                           31
  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                      59
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  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"
D12V4, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    22  27
  6Q GAIN WILD-TYPE 117  91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     22   27
  6Q GAIN WILD-TYPE  117   91
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              22               117
  MALE                27                91
[1] 2 2
[1] FALSE
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    30  18
  6Q GAIN WILD-TYPE 149  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     30   18
  6Q GAIN WILD-TYPE  149   54
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               30               149
  YES              18                54
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  6Q GAIN MUTATED                             12             0
  6Q GAIN WILD-TYPE                           47             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  6Q GAIN MUTATED                                                                          0
  6Q GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  6Q GAIN MUTATED                     13
  6Q GAIN WILD-TYPE                   90
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  6Q GAIN MUTATED                                                  1
  6Q GAIN WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  6Q GAIN MUTATED                  8
  6Q GAIN WILD-TYPE               16
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  6Q GAIN MUTATED                                                          8
  6Q GAIN WILD-TYPE                                                       20
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  6Q GAIN MUTATED                                          0
  6Q GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  6Q GAIN MUTATED                             0                             0
  6Q GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  6Q GAIN MUTATED                                            7
  6Q GAIN WILD-TYPE                                         14
D12V6, multiclass
                                                                          clus
vv                                                                         6Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          12
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  13
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       8
  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                                                                         6Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            47
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    90
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                20
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              14
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    27  15   2   5
  6Q GAIN WILD-TYPE 125  54   7  21
D12V7, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              27               125
  R1              15                54
  R2               2                 7
  RX               5                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
  6Q GAIN MUTATED       1                         5    41
  6Q GAIN WILD-TYPE     5                        13   183
D12V8, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  41               183
[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
  6Q GAIN MUTATED     1  42
  6Q GAIN WILD-TYPE   4 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   42
  6Q GAIN WILD-TYPE    4  178
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              42               178
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    47  35
  7P GAIN WILD-TYPE 112  63
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               82               175 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               35                63 
$`7P GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2W 
       34.68        34.36        15.22        17.95        14.43       106.45 
TCGA-DX-AB2X TCGA-DX-AB35 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-LI-A9QH TCGA-MB-A5Y9 
       13.28        30.51        52.11        52.27        17.75         8.28 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-3B-A9HI TCGA-3B-A9HX 
       18.08        20.94        17.52        26.17        50.01        42.84 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A3LT 
       68.61        12.85        45.11        85.02        74.66        49.05 
TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6YR 
       14.99        85.45        24.26        15.95        36.33        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI 
       78.28        50.50        16.87        86.30        64.21        34.49 
TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT 
       62.20         9.34        47.87        40.77        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2Q 
       36.69        19.43         6.58         1.15        17.79        66.74 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IE-A4EI 
       77.88       106.55        21.70        67.63         4.57        19.53 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF 
        3.22        19.89       171.09        13.58         5.92         1.05 
TCGA-K1-A42X TCGA-KD-A5QU TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A5V9 
      123.78        35.28        10.45        37.55        13.08        46.82 
TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q 
      111.98        10.52        16.77         3.88        22.82        32.75 
TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A8C2 
        8.61        13.41        22.62         8.58        26.43        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A973 TCGA-Z4-AAPG 
       19.17        20.65        36.43        15.98 

$`7P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BP 
       36.30        31.53        16.18        67.20        75.32        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       15.85        40.60        12.07        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       84.66        32.15        16.60        37.02        12.62        26.93 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DM TCGA-QQ-A8VB 
       28.21       159.29        22.62        11.70         6.35       188.15 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        35.08        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ 
       44.91        54.74        25.25        14.37        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       18.54        54.21        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       95.38        79.17         9.04        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       44.68        31.86        35.77        51.02         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       73.87        68.55        50.43        34.88         9.73        45.99 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       35.28        52.77        46.03        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.58        37.41        82.68        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A7EO 
       26.99         3.06       101.23        21.30        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN 
       29.49        48.20        20.05        61.97        45.14        38.17 
TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
      150.35        60.66        12.00        15.72        65.98        86.10 
TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
        9.21        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 
       20.32        19.89        15.48         8.05        34.88        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
        0.72         9.80        80.48         1.38        37.12        25.22 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       85.97        16.41         3.91       101.26        53.33        62.17 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I 
       17.36        23.38         5.19        63.81        16.41        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57         7.36       122.96        38.63        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
       17.65         1.84        18.08        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-AA8C 
      130.32        64.77         0.72        18.94        25.35        19.63 
TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.22        10.72        12.46        11.93         4.80        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       38.27        65.46        63.35        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       30.84        50.86        29.46        27.32         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.05              0.49 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           171.09            188.15 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            26.30             31.96 
[1] "1.1 - 171.1 (26.3)" "0.5 - 188.2 (32.0)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  7P GAIN MUTATED                0                  5                   0
  7P GAIN WILD-TYPE              1                  2                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  7P GAIN MUTATED                     0                             1
  7P GAIN WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  7P GAIN MUTATED                       1                      7
  7P GAIN WILD-TYPE                     0                     21
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  7P GAIN MUTATED                      1                    0
  7P GAIN WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  7P GAIN MUTATED                                       0
  7P GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  7P GAIN MUTATED                                  0
  7P GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  7P GAIN MUTATED                                                1
  7P GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  7P GAIN MUTATED                                 4
  7P GAIN WILD-TYPE                               6
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  7P GAIN MUTATED                                         0
  7P GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  7P GAIN MUTATED                              0                       0
  7P GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  7P GAIN MUTATED                                 11
  7P GAIN WILD-TYPE                                6
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  7P GAIN MUTATED                                         2
  7P GAIN WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  7P GAIN MUTATED                             16
  7P GAIN WILD-TYPE                           28
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  7P GAIN MUTATED                                         1
  7P GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  7P GAIN MUTATED                                           0
  7P GAIN WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  7P GAIN MUTATED                                                  1
  7P GAIN WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  7P GAIN MUTATED                                          2
  7P GAIN WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  7P GAIN MUTATED                                                         0
  7P GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  7P GAIN MUTATED                                            0
  7P GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  7P GAIN MUTATED                                                  15
  7P GAIN WILD-TYPE                                                58
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  7P GAIN MUTATED                                                    0
  7P GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  7P GAIN MUTATED                                    2                        2
  7P GAIN WILD-TYPE                                  0                        3
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  7P GAIN MUTATED                             2                         0
  7P GAIN WILD-TYPE                           2                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  7P GAIN MUTATED                                   5
  7P GAIN WILD-TYPE                                 2
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  7P GAIN MUTATED                                   3
  7P GAIN WILD-TYPE                                 2
D13V3, multiclass
                                                         clus
vv                                                        7P GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    5
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                                7
  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                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                     11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                         16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    15
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              2
  SUPERFICIAL TRUNK - BUTTOCK                                           2
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     3
                                                         clus
vv                                                        7P GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      2
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           1
  GYNECOLOGICAL - OVARY                                                   0
  GYNECOLOGICAL - UTERUS                                                 21
  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                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                        6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           28
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      58
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      0
  SUPERFICIAL TRUNK - BACK                                                3
  SUPERFICIAL TRUNK - BUTTOCK                                             2
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       2
[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
  7P GAIN MUTATED   45 37
  7P GAIN WILD-TYPE 94 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     45   37
  7P GAIN WILD-TYPE   94   81
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              45                94
  MALE                37                81
[1] 2 2
[1] FALSE
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    49  32
  7P GAIN WILD-TYPE 130  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     49   32
  7P GAIN WILD-TYPE  130   40
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               49               130
  YES              32                40
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  7P GAIN MUTATED                             11             0
  7P GAIN WILD-TYPE                           48             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  7P GAIN MUTATED                                                                          0
  7P GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  7P GAIN MUTATED                     23
  7P GAIN WILD-TYPE                   80
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  7P GAIN MUTATED                                                  4
  7P GAIN WILD-TYPE                                                5
                   vv
clus                MYXOFIBROSARCOMA
  7P GAIN MUTATED                 13
  7P GAIN WILD-TYPE               11
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  7P GAIN MUTATED                                                         16
  7P GAIN WILD-TYPE                                                       12
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  7P GAIN MUTATED                                          0
  7P GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  7P GAIN MUTATED                             0                             0
  7P GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  7P GAIN MUTATED                                           15
  7P GAIN WILD-TYPE                                          6
D13V6, multiclass
                                                                          clus
vv                                                                         7P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          11
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  23
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       4
  MYXOFIBROSARCOMA                                                                      13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            15
                                                                          clus
vv                                                                         7P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            48
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    80
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         5
  MYXOFIBROSARCOMA                                                                        11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               6
[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
  7P GAIN MUTATED    47  24   2   8
  7P GAIN WILD-TYPE 105  45   7  18
D13V7, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              47               105
  R1              24                45
  R2               2                 7
  RX               8                18
[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
  7P GAIN MUTATED       3                         7    70
  7P GAIN WILD-TYPE     3                        11   154
D13V8, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   3                 3
  BLACK OR AFRICAN AMERICAN               7                11
  WHITE                                  70               154
[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
  7P GAIN MUTATED     2  70
  7P GAIN WILD-TYPE   3 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   70
  7P GAIN WILD-TYPE    3  150
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              70               150
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    38  29
  7Q GAIN WILD-TYPE 121  69
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               67               190 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               29                69 
$`7Q GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A8BH TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-IF-A4AK 
       34.68        14.43       106.45        13.28        30.51        52.27 
TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 
        8.28        20.94       188.15        17.52        26.17        35.08 
TCGA-3B-A9HI TCGA-3B-A9HS TCGA-3B-A9HX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       50.01        44.91        42.84        68.61        12.85        45.11 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L 
       85.02         6.28        49.05        14.99        85.45        24.26 
TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       15.95        36.33        41.00        50.50        16.87        86.30 
TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO 
       64.21        34.49        62.20         9.34        47.87        40.77 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       27.95        40.44        36.69        19.43         6.58         1.15 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV 
       66.74         9.21       106.55        21.70        67.63         4.57 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-JV-A5VF 
       19.53         3.22        19.89       171.09        13.58         1.05 
TCGA-K1-A6RU TCGA-KD-A5QU TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A8VF 
       23.38        35.28        10.45        37.55        13.08       111.98 
TCGA-RN-AAAQ TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C2 
       16.77        13.41        11.93        22.62        45.34        35.18 
TCGA-X9-A973 
       36.43 

$`7Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        16.18        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        17.95        14.07        15.85        40.60        12.07 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
       22.85       101.98        60.00        84.66        32.15        16.60 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 
       37.02        12.62        52.11        26.93        28.21       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP TCGA-WK-A8XT 
       22.62        11.70        17.75         6.35        18.08        41.49 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU 
       19.69        53.49        68.55        88.57        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       14.37        10.32        38.47        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
        0.56        14.04        32.71        18.54        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       66.94        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       51.02         4.54        10.68        73.87        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        45.99        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47       108.82        59.84        37.58        37.41        82.68 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YS 
       28.96        31.96        36.85        26.99         3.06        78.28 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
      101.23        21.30        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BV 
       20.05        61.97        45.14        38.17       150.35        60.66 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2T 
       17.79        12.00        15.72        65.98        86.10        77.88 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO 
       50.40        50.89        71.31        49.15        31.13        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 
       19.89        15.48         8.05        34.88        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IW-A3M4 
        9.80        80.48         1.38        37.12        25.22        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        5.92        16.41         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I 
      123.78        17.36         5.19        63.81        16.41        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57         7.36       122.96        38.63        81.01 
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-SG-A6Z4 
       37.12       130.32        64.77        10.52         0.72        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-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX 
       13.22        10.72        12.46         4.80        84.79        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46         8.58        63.35        26.43        35.90        18.08 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       30.84        19.17        20.65        50.86        29.46        27.32 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.05              0.49 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           188.15            159.29 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           34.490            30.985 
[1] "1.1 - 188.2 (34.5)" "0.5 - 159.3 (31.0)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  7Q GAIN MUTATED                0                  3                   0
  7Q GAIN WILD-TYPE              1                  4                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  7Q GAIN MUTATED                     0                             0
  7Q GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  7Q GAIN MUTATED                       1                      3
  7Q GAIN WILD-TYPE                     0                     25
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  7Q GAIN MUTATED                      1                    0
  7Q GAIN WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  7Q GAIN MUTATED                                       0
  7Q GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  7Q GAIN MUTATED                                  0
  7Q GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  7Q GAIN MUTATED                                                1
  7Q GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  7Q GAIN MUTATED                                 4
  7Q GAIN WILD-TYPE                               6
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  7Q GAIN MUTATED                                         0
  7Q GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  7Q GAIN MUTATED                              0                       0
  7Q GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  7Q GAIN MUTATED                                  8
  7Q GAIN WILD-TYPE                                9
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  7Q GAIN MUTATED                                         0
  7Q GAIN WILD-TYPE                                       5
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  7Q GAIN MUTATED                             15
  7Q GAIN WILD-TYPE                           29
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  7Q GAIN MUTATED                                         1
  7Q GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  7Q GAIN MUTATED                                           0
  7Q GAIN WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  7Q GAIN MUTATED                                                  1
  7Q GAIN WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  7Q GAIN MUTATED                                          1
  7Q GAIN WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  7Q GAIN MUTATED                                                         0
  7Q GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  7Q GAIN MUTATED                                            0
  7Q GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  7Q GAIN MUTATED                                                  14
  7Q GAIN WILD-TYPE                                                59
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  7Q GAIN MUTATED                                                    0
  7Q GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  7Q GAIN MUTATED                                    1                        3
  7Q GAIN WILD-TYPE                                  1                        2
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  7Q GAIN MUTATED                             3                         0
  7Q GAIN WILD-TYPE                           1                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  7Q GAIN MUTATED                                   4
  7Q GAIN WILD-TYPE                                 3
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  7Q GAIN MUTATED                                   3
  7Q GAIN WILD-TYPE                                 2
D14V3, multiclass
                                                         clus
vv                                                        7Q GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    3
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                                3
  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                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               0
  LOWER EXTREMITY - THIGH/KNEE                                         15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    14
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              3
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     3
                                                         clus
vv                                                        7Q GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      4
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   0
  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                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                        9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 5
  LOWER EXTREMITY - THIGH/KNEE                                           29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  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                      59
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                2
  SUPERFICIAL TRUNK - BUTTOCK                                             1
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       2
[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
  7Q GAIN MUTATED    32  35
  7Q GAIN WILD-TYPE 107  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     32   35
  7Q GAIN WILD-TYPE  107   83
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              32               107
  MALE                35                83
[1] 2 2
[1] FALSE
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    38  28
  7Q GAIN WILD-TYPE 141  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     38   28
  7Q GAIN WILD-TYPE  141   44
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               38               141
  YES              28                44
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  7Q GAIN MUTATED                             11             0
  7Q GAIN WILD-TYPE                           48             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  7Q GAIN MUTATED                                                                          0
  7Q GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  7Q GAIN MUTATED                     20
  7Q GAIN WILD-TYPE                   83
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  7Q GAIN MUTATED                                                  2
  7Q GAIN WILD-TYPE                                                7
                   vv
clus                MYXOFIBROSARCOMA
  7Q GAIN MUTATED                  9
  7Q GAIN WILD-TYPE               15
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  7Q GAIN MUTATED                                                         14
  7Q GAIN WILD-TYPE                                                       14
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  7Q GAIN MUTATED                                          0
  7Q GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  7Q GAIN MUTATED                             0                             0
  7Q GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  7Q GAIN MUTATED                                           11
  7Q GAIN WILD-TYPE                                         10
D14V6, multiclass
                                                                          clus
vv                                                                         7Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          11
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  20
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       2
  MYXOFIBROSARCOMA                                                                       9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            11
                                                                          clus
vv                                                                         7Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            48
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    83
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         7
  MYXOFIBROSARCOMA                                                                        15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              10
[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
  7Q GAIN MUTATED    39  21   1   5
  7Q GAIN WILD-TYPE 113  48   8  21
D14V7, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              39               113
  R1              21                48
  R2               1                 8
  RX               5                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
  7Q GAIN MUTATED       2                         4    60
  7Q GAIN WILD-TYPE     4                        14   164
D14V8, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  60               164
[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
  7Q GAIN MUTATED     3  57
  7Q GAIN WILD-TYPE   2 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3   57
  7Q GAIN WILD-TYPE    2  163
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              57               163
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    27  25
  8P GAIN WILD-TYPE 132  73
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               205 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               25                73 
$`8P GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 
       34.68        34.36        14.07        12.07       106.45        22.85 
TCGA-IF-A4AK TCGA-PC-A5DM TCGA-SG-A849 TCGA-VT-A80J TCGA-3B-A9HT TCGA-3B-A9I3 
       52.27         6.35        17.52        26.17        54.74        26.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UF 
       14.04        12.85        74.66         4.54        14.99        85.45 
TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6Z2 TCGA-DX-A7EM 
       82.68         3.06        41.00        78.28       101.23        62.20 
TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BU TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ 
        9.34        38.17        36.69        19.43        49.15        31.13 
TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3KA TCGA-IW-A3M5 
        4.57        80.48        19.53         3.22        13.58         5.92 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RU TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        1.05         3.91        23.38        14.99        17.98        10.45 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-UE-A6QT 
        7.36        37.55        16.77        18.94         8.61        13.22 
TCGA-UE-A6QU TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C3 
       13.41        22.62        26.43        19.17 

$`8P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB32 
       17.95        14.43        15.85        40.60        13.28       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
       30.51        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        52.11        26.93        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       11.70        17.75         8.28        18.08        20.94       188.15 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       41.49        35.08        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-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-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX 
       38.47        36.03        18.64         0.56        32.71        68.61 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       45.11        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       51.02        10.68        73.87        68.55        50.43        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV 
       36.33        28.96        31.96        36.85        26.99        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN 
       16.87        86.30        64.21        21.30        34.49        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL 
      152.12        29.49        48.20        20.05        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV 
       47.87        40.77       150.35        27.95        40.44        60.66 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
        6.58         1.15        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        66.74         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       50.89        71.31        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        8.05        67.63        34.88        33.30         0.72         9.80 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 
        1.38        19.89        37.12        25.22       171.09        85.97 
TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
       16.41       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
        5.19        63.81        16.41        35.28        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK 
        0.49        21.73        19.73        22.39        11.57       122.96 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        81.01        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-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
       64.77        10.52         0.72         3.88        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       32.75        19.63        10.72        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       84.79        38.27        65.46         8.58        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08        45.34        30.84        35.18        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.05              0.49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           106.45            188.15 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            19.30             33.53 
[1] "1.1 - 106.5 (19.3)" "0.5 - 188.2 (33.5)"
[1] "hr=" "1.8"
D15V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  8P GAIN MUTATED                0                  4                   0
  8P GAIN WILD-TYPE              1                  3                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  8P GAIN MUTATED                     0                             0
  8P GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  8P GAIN MUTATED                       0                      4
  8P GAIN WILD-TYPE                     1                     24
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  8P GAIN MUTATED                      1                    0
  8P GAIN WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  8P GAIN MUTATED                                       1
  8P GAIN WILD-TYPE                                     1
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  8P GAIN MUTATED                                  0
  8P GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  8P GAIN MUTATED                                                2
  8P GAIN WILD-TYPE                                              0
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  8P GAIN MUTATED                                 2
  8P GAIN WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  8P GAIN MUTATED                                         1
  8P GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  8P GAIN MUTATED                              0                       0
  8P GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  8P GAIN MUTATED                                  3
  8P GAIN WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  8P GAIN MUTATED                                         3
  8P GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  8P GAIN MUTATED                             14
  8P GAIN WILD-TYPE                           30
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  8P GAIN MUTATED                                         0
  8P GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  8P GAIN MUTATED                                           0
  8P GAIN WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  8P GAIN MUTATED                                                  1
  8P GAIN WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  8P GAIN MUTATED                                          2
  8P GAIN WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  8P GAIN MUTATED                                                         1
  8P GAIN WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  8P GAIN MUTATED                                            0
  8P GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  8P GAIN MUTATED                                                  10
  8P GAIN WILD-TYPE                                                63
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  8P GAIN MUTATED                                                    0
  8P GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  8P GAIN MUTATED                                    0                        0
  8P GAIN WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  8P GAIN MUTATED                             0                         0
  8P GAIN WILD-TYPE                           4                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  8P GAIN MUTATED                                   2
  8P GAIN WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  8P GAIN MUTATED                                   1
  8P GAIN WILD-TYPE                                 4
D15V3, multiclass
                                                         clus
vv                                                        8P GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    4
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                4
  HEAD AND NECK - HEAD                                                  1
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 1
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                       2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               1
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         14
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    10
  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                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        8P GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      3
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 24
  HEAD AND NECK - HEAD                                                    1
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   1
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          0
  LOWER ABDOMINAL/PELVIC - PELVIC                                         8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 1
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 2
  LOWER EXTREMITY - THIGH/KNEE                                           30
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      63
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             4
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    28  24
  8P GAIN WILD-TYPE 111  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     28   24
  8P GAIN WILD-TYPE  111   94
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              28               111
  MALE                24                94
[1] 2 2
[1] FALSE
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    31  19
  8P GAIN WILD-TYPE 148  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     31   19
  8P GAIN WILD-TYPE  148   53
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               31               148
  YES              19                53
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  8P GAIN MUTATED                              5             0
  8P GAIN WILD-TYPE                           54             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  8P GAIN MUTATED                                                                          0
  8P GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  8P GAIN MUTATED                     21
  8P GAIN WILD-TYPE                   82
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  8P GAIN MUTATED                                                  1
  8P GAIN WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  8P GAIN MUTATED                  9
  8P GAIN WILD-TYPE               15
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  8P GAIN MUTATED                                                          8
  8P GAIN WILD-TYPE                                                       20
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  8P GAIN MUTATED                                          0
  8P GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  8P GAIN MUTATED                             0                             0
  8P GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  8P GAIN MUTATED                                            8
  8P GAIN WILD-TYPE                                         13
D15V6, multiclass
                                                                          clus
vv                                                                         8P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           5
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  21
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             8
                                                                          clus
vv                                                                         8P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            54
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    82
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                20
  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
  8P GAIN MUTATED    27  19   3   2
  8P GAIN WILD-TYPE 125  50   6  24
D15V7, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              27               125
  R1              19                50
  R2               3                 6
  RX               2                24
[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
  8P GAIN MUTATED       4                         4    42
  8P GAIN WILD-TYPE     2                        14   182
D15V8, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   4                 2
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  42               182
[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
  8P GAIN MUTATED     2  46
  8P GAIN WILD-TYPE   3 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   46
  8P GAIN WILD-TYPE    3  174
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              46               174
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    33  33
  8Q GAIN WILD-TYPE 126  65
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               66               191 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               33                65 
$`8Q GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X 
       34.36        14.43        14.07        12.07       106.45        13.28 
TCGA-DX-AB30 TCGA-DX-AB35 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-SG-A849 TCGA-VT-A80J 
       22.85        30.51        52.11        52.27        17.52        26.17 
TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY 
       54.74        42.84        26.56         0.56        14.04        12.85 
TCGA-DX-A23R TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UF 
       74.66        51.02         4.54        14.99        10.68        85.45 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YR TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A8BJ 
       15.95        82.68        41.00       101.23        62.20         9.34 
TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-FX-A2QS 
       40.77        19.43        17.79        86.10        66.74        49.15 
TCGA-FX-A3NJ TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IW-A3M5 
       31.13         4.57        80.48        19.53        25.22         5.92 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 
        1.05         3.91        23.38        63.81        35.28        25.41 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QQ-A5VB 
       14.99        17.98        10.45         7.36        37.55        48.59 
TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-UE-A6QT 
       10.52        16.77        18.94         3.88        32.75        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A8C3 
       13.41        10.72        22.62         8.58        26.43        19.17 

$`8Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB32 TCGA-DX-AB36 
       15.22        17.95        15.85        40.60       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       84.66        32.15        16.60        37.02        12.62        26.93 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       28.21       159.29        22.62        11.70        17.75         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-X6-A8C6 
        6.35        18.08        20.94       188.15        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       50.01        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        14.37        10.32        38.47        36.03        18.64 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       32.71        68.61        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        66.94         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       31.86        35.77        73.87        68.55        50.43        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB 
       26.47       108.82        59.84        37.58        37.41        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YS 
       28.96        31.96        36.85        26.99         3.06        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI 
       50.50        16.87        86.30        64.21        21.30        34.49 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       30.35       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       45.14        47.87        38.17       150.35        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G 
       36.69        60.66         6.58         1.15        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       65.98         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       71.31        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ 
       67.63        34.88        33.30         0.72         9.80         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        19.89        37.12       171.09        13.58        85.97 
TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
       16.41       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
        5.19        16.41        30.31         0.49        21.73        19.73 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
       22.39        11.57       122.96        38.63        81.01        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       17.65         1.84        46.82        18.08        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SI-A71O TCGA-SI-A71P 
      130.32       111.98        64.77         0.72        22.82        25.35 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
        8.61        19.63        12.46        11.93         4.80        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       38.27        65.46        63.35        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       30.84        35.18        20.65        50.86        29.46        27.32 
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 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.56              0.49 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           106.45            188.15 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           21.075            34.680 
[1] "0.6 - 106.5 (21.1)" "0.5 - 188.2 (34.7)"
[1] "hr=" "1.9"
D16V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  8Q GAIN MUTATED                0                  5                   0
  8Q GAIN WILD-TYPE              1                  2                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  8Q GAIN MUTATED                     0                             1
  8Q GAIN WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  8Q GAIN MUTATED                       0                      7
  8Q GAIN WILD-TYPE                     1                     21
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  8Q GAIN MUTATED                      1                    0
  8Q GAIN WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  8Q GAIN MUTATED                                       1
  8Q GAIN WILD-TYPE                                     1
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  8Q GAIN MUTATED                                  0
  8Q GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  8Q GAIN MUTATED                                                2
  8Q GAIN WILD-TYPE                                              0
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  8Q GAIN MUTATED                                 2
  8Q GAIN WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  8Q GAIN MUTATED                                         1
  8Q GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  8Q GAIN MUTATED                              1                       1
  8Q GAIN WILD-TYPE                            3                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  8Q GAIN MUTATED                                  9
  8Q GAIN WILD-TYPE                                8
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  8Q GAIN MUTATED                                         1
  8Q GAIN WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  8Q GAIN MUTATED                             11
  8Q GAIN WILD-TYPE                           33
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  8Q GAIN MUTATED                                         1
  8Q GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  8Q GAIN MUTATED                                           0
  8Q GAIN WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  8Q GAIN MUTATED                                                  1
  8Q GAIN WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  8Q GAIN MUTATED                                          3
  8Q GAIN WILD-TYPE                                        5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  8Q GAIN MUTATED                                                         1
  8Q GAIN WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  8Q GAIN MUTATED                                            0
  8Q GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  8Q GAIN MUTATED                                                  11
  8Q GAIN WILD-TYPE                                                62
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  8Q GAIN MUTATED                                                    0
  8Q GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  8Q GAIN MUTATED                                    1                        0
  8Q GAIN WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  8Q GAIN MUTATED                             0                         0
  8Q GAIN WILD-TYPE                           4                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  8Q GAIN MUTATED                                   4
  8Q GAIN WILD-TYPE                                 3
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  8Q GAIN MUTATED                                   1
  8Q GAIN WILD-TYPE                                 4
D16V3, multiclass
                                                         clus
vv                                                        8Q GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    5
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                7
  HEAD AND NECK - HEAD                                                  1
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 1
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        2
  LOWER ABDOMINAL/PELVIC - PELVIC                                       2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               1
  LOWER EXTREMITY - FOOT/ANKLE                                          1
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  LOWER EXTREMITY - THIGH/KNEE                                         11
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    11
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           0
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        8Q GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      2
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           1
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 21
  HEAD AND NECK - HEAD                                                    1
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   1
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          0
  LOWER ABDOMINAL/PELVIC - PELVIC                                         8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 1
  LOWER EXTREMITY - FOOT/ANKLE                                            3
  LOWER EXTREMITY - GROIN                                                 1
  LOWER EXTREMITY - LOWER LEG/CALF                                        8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           33
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      62
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             4
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       3
  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
  8Q GAIN MUTATED    38  28
  8Q GAIN WILD-TYPE 101  90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     38   28
  8Q GAIN WILD-TYPE  101   90
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              38               101
  MALE                28                90
[1] 2 2
[1] FALSE
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    44  21
  8Q GAIN WILD-TYPE 135  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     44   21
  8Q GAIN WILD-TYPE  135   51
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               44               135
  YES              21                51
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  8Q GAIN MUTATED                              7             0
  8Q GAIN WILD-TYPE                           52             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  8Q GAIN MUTATED                                                                          0
  8Q GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  8Q GAIN MUTATED                     29
  8Q GAIN WILD-TYPE                   74
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  8Q GAIN MUTATED                                                  3
  8Q GAIN WILD-TYPE                                                6
                   vv
clus                MYXOFIBROSARCOMA
  8Q GAIN MUTATED                  8
  8Q GAIN WILD-TYPE               16
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  8Q GAIN MUTATED                                                         11
  8Q GAIN WILD-TYPE                                                       17
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  8Q GAIN MUTATED                                          0
  8Q GAIN WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  8Q GAIN MUTATED                             0                             0
  8Q GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  8Q GAIN MUTATED                                            8
  8Q GAIN WILD-TYPE                                         13
D16V6, multiclass
                                                                          clus
vv                                                                         8Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           7
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  29
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       3
  MYXOFIBROSARCOMA                                                                       8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             8
                                                                          clus
vv                                                                         8Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            52
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    74
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         6
  MYXOFIBROSARCOMA                                                                        16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                17
  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
  8Q GAIN MUTATED    40  15   4   6
  8Q GAIN WILD-TYPE 112  54   5  20
D16V7, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              40               112
  R1              15                54
  R2               4                 5
  RX               6                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
  8Q GAIN MUTATED       4                         5    54
  8Q GAIN WILD-TYPE     2                        13   170
D16V8, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   4                 2
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  54               170
[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
  8Q GAIN MUTATED     3  57
  8Q GAIN WILD-TYPE   2 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3   57
  8Q GAIN WILD-TYPE    2  163
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              57               163
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    29  24
  9P GAIN WILD-TYPE 130  74
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               53               204 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               24                74 
$`9P GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2X TCGA-DX-AB35 
       34.36        15.22        17.95        14.43        13.28        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-IF-A4AK TCGA-KF-A41W TCGA-PC-A5DP TCGA-QC-A6FX 
       60.00        84.66        52.27        11.70        18.08        20.94 
TCGA-SG-A849 TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HX TCGA-DX-A1KW TCGA-DX-A1KX 
       17.52        35.08        19.69        42.84        32.71        68.61 
TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A3LU TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A48N 
       45.11        85.02        86.83        14.99        10.68        35.28 
TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6YV TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BS 
       15.95        36.33        50.50        61.97        45.14        27.95 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB2Z 
       36.69        19.43         1.15        86.10       106.55        50.40 
TCGA-FX-A3TO TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-JV-A5VF TCGA-K1-A6RV TCGA-LI-A67I 
       20.32        19.89        13.58         1.05         5.19        30.31 
TCGA-MB-A8JK TCGA-QQ-A5V9 TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-VT-AB3D 
       21.73        46.82        18.94         3.88        22.82        12.46 
TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-Z4-AAPF 
       11.93        84.79         8.58        26.43        15.95 

$`9P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 
       14.07        15.85        40.60        12.07       106.45        22.85 
TCGA-DX-AB32 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
      101.98        32.15        16.60        37.02        12.62        52.11 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 
       26.93        28.21       159.29        22.62        17.75         8.28 
TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HP 
        6.35       188.15        26.17        41.49        50.01        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       68.55        88.57        44.91        54.74        25.25        14.37 
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-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        18.54        54.21        33.53        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       51.02         4.54        73.87        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       85.45         9.73        45.99        24.26        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47       108.82        59.84        37.58        37.41        82.68 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       78.28        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       20.05         9.34        47.87        38.17        40.77       150.35 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       40.44        60.66         6.58        17.79        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        66.74         9.21        77.88        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        21.70        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       67.63        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        19.53         3.22         1.38        37.12        25.22 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN 
      171.09        85.97         5.92        16.41         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS 
       53.33        62.17       123.78        17.36        23.38        63.81 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       16.41        35.28        25.41         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        81.01        13.08        17.65         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q 
       64.77        10.52         0.72        16.77        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XQ 
        8.61        19.63        13.22        13.41        10.72         4.80 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46        22.62        63.35        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       45.34        30.84        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       29.46        27.32        36.43         4.37        13.38        15.98 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.05              0.49 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           106.55            188.15 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            22.82             32.45 
[1] "1.1 - 106.5 (22.8)" "0.5 - 188.2 (32.5)"
[1] "hr=" "1.4"
D17V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  9P GAIN MUTATED                0                  2                   0
  9P GAIN WILD-TYPE              1                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  9P GAIN MUTATED                     0                             0
  9P GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  9P GAIN MUTATED                       0                      3
  9P GAIN WILD-TYPE                     1                     25
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  9P GAIN MUTATED                      0                    0
  9P GAIN WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  9P GAIN MUTATED                                       0
  9P GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  9P GAIN MUTATED                                  0
  9P GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  9P GAIN MUTATED                                                1
  9P GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  9P GAIN MUTATED                                 3
  9P GAIN WILD-TYPE                               7
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  9P GAIN MUTATED                                         0
  9P GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  9P GAIN MUTATED                              1                       0
  9P GAIN WILD-TYPE                            3                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  9P GAIN MUTATED                                  2
  9P GAIN WILD-TYPE                               15
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  9P GAIN MUTATED                                         1
  9P GAIN WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  9P GAIN MUTATED                             14
  9P GAIN WILD-TYPE                           30
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  9P GAIN MUTATED                                         1
  9P GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  9P GAIN MUTATED                                           1
  9P GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  9P GAIN MUTATED                                                  0
  9P GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  9P GAIN MUTATED                                          1
  9P GAIN WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  9P GAIN MUTATED                                                         0
  9P GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  9P GAIN MUTATED                                            0
  9P GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  9P GAIN MUTATED                                                  13
  9P GAIN WILD-TYPE                                                60
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  9P GAIN MUTATED                                                    0
  9P GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  9P GAIN MUTATED                                    2                        2
  9P GAIN WILD-TYPE                                  0                        3
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  9P GAIN MUTATED                             1                         0
  9P GAIN WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  9P GAIN MUTATED                                   2
  9P GAIN WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  9P GAIN MUTATED                                   3
  9P GAIN WILD-TYPE                                 2
D17V3, multiclass
                                                         clus
vv                                                        9P GAIN 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                                                3
  HEAD AND NECK - HEAD                                                  0
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          1
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  LOWER EXTREMITY - THIGH/KNEE                                         14
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  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                    13
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              2
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     3
                                                         clus
vv                                                        9P GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  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                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         7
  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                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           30
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  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                      60
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      0
  SUPERFICIAL TRUNK - BACK                                                3
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       2
[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
  9P GAIN MUTATED    23  30
  9P GAIN WILD-TYPE 116  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     23   30
  9P GAIN WILD-TYPE  116   88
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              23               116
  MALE                30                88
[1] 2 2
[1] FALSE
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    36  17
  9P GAIN WILD-TYPE 143  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     36   17
  9P GAIN WILD-TYPE  143   55
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               36               143
  YES              17                55
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  9P GAIN MUTATED                             12             0
  9P GAIN WILD-TYPE                           47             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  9P GAIN MUTATED                                                                          0
  9P GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  9P GAIN MUTATED                     13
  9P GAIN WILD-TYPE                   90
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  9P GAIN MUTATED                                                  1
  9P GAIN WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  9P GAIN MUTATED                  7
  9P GAIN WILD-TYPE               17
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  9P GAIN MUTATED                                                         14
  9P GAIN WILD-TYPE                                                       14
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  9P GAIN MUTATED                                          1
  9P GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  9P GAIN MUTATED                             0                             0
  9P GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  9P GAIN MUTATED                                            5
  9P GAIN WILD-TYPE                                         16
D17V6, multiclass
                                                                          clus
vv                                                                         9P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          12
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  13
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             5
                                                                          clus
vv                                                                         9P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            47
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    90
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              16
[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
  9P GAIN MUTATED    29  17   1   6
  9P GAIN WILD-TYPE 123  52   8  20
D17V7, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              29               123
  R1              17                52
  R2               1                 8
  RX               6                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
  9P GAIN MUTATED       0                         3    50
  9P GAIN WILD-TYPE     6                        15   174
D17V8, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  50               174
[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
  9P GAIN MUTATED     1  50
  9P GAIN WILD-TYPE   4 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   50
  9P GAIN WILD-TYPE    4  170
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              50               170
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    45  26
  9Q GAIN WILD-TYPE 114  72
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               186 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26                72 
$`9Q GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2P 
       34.36        15.22        17.95        14.43        14.07        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-IF-A4AK 
      106.45        13.28        30.51        60.00        84.66        52.27 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 
       11.70        17.75         8.28        18.08        20.94        17.52 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HX TCGA-DX-A1KW TCGA-DX-A1KX 
       50.01        19.69        88.57        42.84        32.71        68.61 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A3LU TCGA-DX-A3M1 
       45.11        54.21        85.02        74.66        86.83        44.68 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6BA 
       51.02        14.99        10.68        35.28        15.95        82.68 
TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A8BK TCGA-DX-A8BL 
       36.33         3.06        41.00        50.50        61.97        45.14 
TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F 
       40.77        27.95        36.69        19.43         1.15        12.00 
TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A2QS TCGA-FX-A3TO TCGA-IE-A4EI 
       86.10       106.55        50.40        49.15        20.32        19.53 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-JV-A5VF TCGA-LI-A67I TCGA-MB-A8JK TCGA-QQ-A5V9 
        3.22        19.89         1.05        30.31        21.73        46.82 
TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XS 
       35.90        18.94        22.82        12.46        11.93        84.79 
TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X9-A971 TCGA-Z4-AAPF 
       26.43        35.18        19.17        27.32        15.95 

$`9Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB3A TCGA-FX-A3NK 
       15.85        40.60        22.85       101.98        32.15        16.60 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 
       37.02        12.62        52.11        26.93        28.21       159.29 
TCGA-IW-A3M6 TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       22.62         6.35       188.15        26.17        41.49        35.08 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       53.49        68.55        44.91        54.74        25.25        14.37 
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-A1KY TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       14.04        12.85        18.54        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW 
        9.70        95.38        79.17         9.04        49.05       136.44 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       33.44        31.86        35.77         4.54        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       50.43        34.88        85.45         9.73        45.99        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS 
       37.41        28.96        31.96        36.85        26.99        78.28 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        86.30        64.21       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV 
        9.34        47.87        38.17       150.35        40.44        60.66 
TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S 
        6.58        17.79        15.72        65.98        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       77.88        50.89        71.31        31.13        21.70        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       15.48         8.05        67.63        34.88         4.57        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
        0.72         9.80        80.48         1.38        37.12        25.22 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J 
      171.09        13.58        85.97         5.92        16.41         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
      101.26        53.33        62.17       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA 
        5.19        63.81        16.41        35.28        25.41         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
        7.36       122.96        37.55        38.63        81.01        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD 
       17.65         1.84        18.08        48.59        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 
      111.98        64.77        10.52         0.72        16.77         3.88 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       25.35        32.75         8.61        19.63        13.22        13.41 
TCGA-VT-A80G TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       10.72         4.80        38.27        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C4 
       63.35        35.90        18.08        45.34        30.84        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       50.86        29.46        36.43         4.37        13.38        15.98 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.05              0.49 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           106.55            188.15 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           30.310            31.695 
[1] "1.1 - 106.5 (30.3)" "0.5 - 188.2 (31.7)"
[1] "hr=" "1"  
D18V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  9Q GAIN MUTATED                0                  3                   0
  9Q GAIN WILD-TYPE              1                  4                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  9Q GAIN MUTATED                     0                             0
  9Q GAIN WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  9Q GAIN MUTATED                       0                      1
  9Q GAIN WILD-TYPE                     1                     27
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  9Q GAIN MUTATED                      0                    0
  9Q GAIN WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  9Q GAIN MUTATED                                       0
  9Q GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  9Q GAIN MUTATED                                  0
  9Q GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  9Q GAIN MUTATED                                                1
  9Q GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  9Q GAIN MUTATED                                 4
  9Q GAIN WILD-TYPE                               6
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  9Q GAIN MUTATED                                         0
  9Q GAIN WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  9Q GAIN MUTATED                              1                       0
  9Q GAIN WILD-TYPE                            3                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  9Q GAIN MUTATED                                  7
  9Q GAIN WILD-TYPE                               10
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  9Q GAIN MUTATED                                         2
  9Q GAIN WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  9Q GAIN MUTATED                             20
  9Q GAIN WILD-TYPE                           24
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  9Q GAIN MUTATED                                         1
  9Q GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  9Q GAIN MUTATED                                           1
  9Q GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  9Q GAIN MUTATED                                                  0
  9Q GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  9Q GAIN MUTATED                                          0
  9Q GAIN WILD-TYPE                                        8
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  9Q GAIN MUTATED                                                         1
  9Q GAIN WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  9Q GAIN MUTATED                                            0
  9Q GAIN WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  9Q GAIN MUTATED                                                  17
  9Q GAIN WILD-TYPE                                                56
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  9Q GAIN MUTATED                                                    0
  9Q GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  9Q GAIN MUTATED                                    2                        2
  9Q GAIN WILD-TYPE                                  0                        3
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  9Q GAIN MUTATED                             1                         0
  9Q GAIN WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  9Q GAIN MUTATED                                   3
  9Q GAIN WILD-TYPE                                 4
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  9Q GAIN MUTATED                                   4
  9Q GAIN WILD-TYPE                                 1
D18V3, multiclass
                                                         clus
vv                                                        9Q GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    3
  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                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          1
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                         20
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  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                    17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              2
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     4
                                                         clus
vv                                                        9Q GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      4
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 27
  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                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            3
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           24
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      56
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      0
  SUPERFICIAL TRUNK - BACK                                                3
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       1
[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
  9Q GAIN MUTATED    34  37
  9Q GAIN WILD-TYPE 105  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     34   37
  9Q GAIN WILD-TYPE  105   81
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              34               105
  MALE                37                81
[1] 2 2
[1] FALSE
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    47  23
  9Q GAIN WILD-TYPE 132  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     47   23
  9Q GAIN WILD-TYPE  132   49
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               47               132
  YES              23                49
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  9Q GAIN MUTATED                             17             0
  9Q GAIN WILD-TYPE                           42             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  9Q GAIN MUTATED                                                                          0
  9Q GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  9Q GAIN MUTATED                     16
  9Q GAIN WILD-TYPE                   87
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  9Q GAIN MUTATED                                                  1
  9Q GAIN WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  9Q GAIN MUTATED                  9
  9Q GAIN WILD-TYPE               15
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  9Q GAIN MUTATED                                                         19
  9Q GAIN WILD-TYPE                                                        9
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  9Q GAIN MUTATED                                          1
  9Q GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  9Q GAIN MUTATED                             0                             0
  9Q GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  9Q GAIN MUTATED                                            8
  9Q GAIN WILD-TYPE                                         13
D18V6, multiclass
                                                                          clus
vv                                                                         9Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          17
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  16
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             8
                                                                          clus
vv                                                                         9Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            42
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    87
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  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
  9Q GAIN MUTATED    41  23   3   4
  9Q GAIN WILD-TYPE 111  46   6  22
D18V7, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              41               111
  R1              23                46
  R2               3                 6
  RX               4                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
  9Q GAIN MUTATED       1                         4    65
  9Q GAIN WILD-TYPE     5                        14   159
D18V8, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  65               159
[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
  9Q GAIN MUTATED     1  68
  9Q GAIN WILD-TYPE   4 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   68
  9Q GAIN WILD-TYPE    4  152
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              68               152
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    12  10
  10P GAIN WILD-TYPE 147  88
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                235 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                 88 
$`10P GAIN MUTATED`
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-HS-A5N9 TCGA-PC-A5DP TCGA-X6-A8C6 TCGA-DX-A1KU 
      106.45        13.28        52.11        18.08        35.08        14.04 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A6YV TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-AB2E 
       51.02         4.54        50.50        61.97        45.14        17.79 
TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-LI-A67I TCGA-QQ-A5VA 
       77.88        50.40        19.89        13.58        30.31        18.08 
TCGA-SG-A6Z4 TCGA-WK-A8Y0 TCGA-X6-A8C2 TCGA-Z4-AAPF 
       18.94        22.62        35.18        15.95 

$`10P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       75.32        15.22        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       40.60        12.07        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       84.66        32.15        16.60        37.02        12.62        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH 
       52.27        28.21       159.29        22.62        11.70        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
        8.28         6.35        20.94       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW 
       38.47        36.03        18.64        26.56         0.56        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       79.17         9.04        49.05        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       44.68        31.86        35.77        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       68.55        50.43        34.88        85.45         9.73        45.99 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       78.28        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       20.05         9.34        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
        1.15        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
        9.21       106.55        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       34.88         4.57        33.30         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
       19.53         3.22         1.38        37.12        25.22       171.09 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       53.33        62.17       123.78        17.36        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       63.81        16.41        35.28        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
        7.36       122.96        37.55        38.63        81.01        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
       17.65         1.84        46.82        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        3.88        22.82        25.35        32.75         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22        13.41        10.72        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       84.79        38.27        65.46         8.58        63.35        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       35.90        18.08        45.34        30.84        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPG 
       15.98 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              4.54               0.49 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            106.45             188.15 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            26.465             31.530 
[1] "4.5 - 106.5 (26.5)" "0.5 - 188.2 (31.5)"
[1] "hr=" "1.3"
D19V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  10P GAIN MUTATED                0                  1                   0
  10P GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  10P GAIN MUTATED                     0                             0
  10P GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  10P GAIN MUTATED                       0                      2
  10P GAIN WILD-TYPE                     1                     26
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  10P GAIN MUTATED                      0                    0
  10P GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  10P GAIN MUTATED                                       0
  10P GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  10P GAIN MUTATED                                  0
  10P GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  10P GAIN MUTATED                                                0
  10P GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  10P GAIN MUTATED                                 0
  10P GAIN WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  10P GAIN MUTATED                                         1
  10P GAIN WILD-TYPE                                       1
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  10P GAIN MUTATED                              0                       0
  10P GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  10P GAIN MUTATED                                  2
  10P GAIN WILD-TYPE                               15
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  10P GAIN MUTATED                                         0
  10P GAIN WILD-TYPE                                       5
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  10P GAIN MUTATED                              9
  10P GAIN WILD-TYPE                           35
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  10P GAIN MUTATED                                         0
  10P GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  10P GAIN MUTATED                                           0
  10P GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  10P GAIN MUTATED                                                  0
  10P GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  10P GAIN MUTATED                                          0
  10P GAIN WILD-TYPE                                        8
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  10P GAIN MUTATED                                                         0
  10P GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  10P GAIN MUTATED                                            0
  10P GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  10P GAIN MUTATED                                                   3
  10P GAIN WILD-TYPE                                                70
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  10P GAIN MUTATED                                                    0
  10P GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  10P GAIN MUTATED                                    0
  10P GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  10P GAIN MUTATED                          0                           1
  10P GAIN WILD-TYPE                        5                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  10P GAIN MUTATED                           0
  10P GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  10P GAIN MUTATED                                   2
  10P GAIN WILD-TYPE                                 5
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  10P GAIN MUTATED                                   1
  10P GAIN WILD-TYPE                                 4
D19V3, multiclass
                                                         clus
vv                                                        10P GAIN 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                                                 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                                        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                1
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                0
  LOWER EXTREMITY - THIGH/KNEE                                           9
  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                                            1
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        10P GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  26
  HEAD AND NECK - HEAD                                                     2
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  1
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  5
  LOWER EXTREMITY - THIGH/KNEE                                            35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 8
  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                                        5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    13   9
  10P GAIN WILD-TYPE 126 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     13    9
  10P GAIN WILD-TYPE  126  109
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               13                126
  MALE                  9                109
[1] 2 2
[1] FALSE
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    15   7
  10P GAIN WILD-TYPE 164  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     15    7
  10P GAIN WILD-TYPE  164   65
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                15                164
  YES                7                 65
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  10P GAIN MUTATED                              2             0
  10P GAIN WILD-TYPE                           57             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  10P GAIN MUTATED                                                                          0
  10P GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  10P GAIN MUTATED                      5
  10P GAIN WILD-TYPE                   98
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  10P GAIN MUTATED                                                  0
  10P GAIN WILD-TYPE                                                9
                    vv
clus                 MYXOFIBROSARCOMA
  10P GAIN MUTATED                  5
  10P GAIN WILD-TYPE               19
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  10P GAIN MUTATED                                                          6
  10P GAIN WILD-TYPE                                                       22
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  10P GAIN MUTATED                                          1
  10P GAIN WILD-TYPE                                        1
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  10P GAIN MUTATED                             0                             0
  10P GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  10P GAIN MUTATED                                            3
  10P GAIN WILD-TYPE                                         18
D19V6, multiclass
                                                                          clus
vv                                                                         10P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            2
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    5
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        0
  MYXOFIBROSARCOMA                                                                        5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                1
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              3
                                                                          clus
vv                                                                         10P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             57
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     98
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          9
  MYXOFIBROSARCOMA                                                                         19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 22
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  1
  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
  10P GAIN MUTATED    15   4   1   2
  10P GAIN WILD-TYPE 137  65   8  24
D19V7, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               15                137
  R1                4                 65
  R2                1                  8
  RX                2                 24
[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
  10P GAIN MUTATED       0                         1    19
  10P GAIN WILD-TYPE     6                        17   205
D19V8, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                 17
  WHITE                                   19                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"
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  20
  10P GAIN WILD-TYPE   5 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   20
  10P GAIN WILD-TYPE    5  200
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               20                200
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     6   5
  10Q GAIN WILD-TYPE 153  93
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                246 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 5                 93 
$`10Q GAIN MUTATED`
TCGA-DX-AB2X TCGA-DX-AB35 TCGA-X6-A8C6 TCGA-DX-A1KU TCGA-DX-A3U8 TCGA-DX-A8BK 
       13.28        30.51        35.08        14.04         4.54        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-AB2Z TCGA-SG-A6Z7 TCGA-Z4-AAPF 
       45.14        47.87        50.40         3.88        15.95 

$`10Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       75.32        15.22        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       40.60        12.07       106.45        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       84.66        32.15        16.60        37.02        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       17.75         8.28         6.35        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP 
       17.52        26.17        41.49        50.01        19.69        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       68.55        88.57        44.91        54.74        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        38.47        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        32.71        68.61        12.85        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      136.44        33.44        44.68        31.86        35.77        51.02 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        73.87        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       85.45         9.73        45.99        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       108.82        59.84        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX 
       26.99         3.06        41.00        78.28        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM 
       86.30        64.21       101.23        21.30        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       38.17        40.77       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        17.79        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       15.72        65.98        86.10        66.74         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
      106.55        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32        19.89        15.48         8.05        67.63        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
        4.57        33.30         0.72         9.80        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
        3.22         1.38        19.89        37.12        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        85.97         5.92        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
      101.26        53.33        62.17       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
        5.19        63.81        16.41        35.28        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       81.01        13.08        17.65         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        35.90        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P 
       10.52         0.72        16.77        18.94        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       32.75         8.61        19.63        13.22        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       12.46        11.93         4.80        84.79        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       22.62         8.58        63.35        26.43        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       45.34        30.84        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       29.46        27.32        36.43         4.37        13.38        15.98 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              3.88               0.49 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             61.97             188.15 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             30.51              31.33 
[1] "3.9 - 62.0 (30.5)"  "0.5 - 188.2 (31.3)"
[1] "hr=" "1.6"
D20V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  10Q GAIN MUTATED                0                  0                   0
  10Q GAIN WILD-TYPE              1                  7                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  10Q GAIN MUTATED                     0                             0
  10Q GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  10Q GAIN MUTATED                       0                      0
  10Q GAIN WILD-TYPE                     1                     28
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  10Q GAIN MUTATED                      0                    0
  10Q GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  10Q GAIN MUTATED                                       0
  10Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  10Q GAIN MUTATED                                  0
  10Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  10Q GAIN MUTATED                                                0
  10Q GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  10Q GAIN MUTATED                                 0
  10Q GAIN WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  10Q GAIN MUTATED                                         1
  10Q GAIN WILD-TYPE                                       1
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  10Q GAIN MUTATED                              0                       0
  10Q GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  10Q GAIN MUTATED                                  1
  10Q GAIN WILD-TYPE                               16
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  10Q GAIN MUTATED                                         0
  10Q GAIN WILD-TYPE                                       5
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  10Q GAIN MUTATED                              4
  10Q GAIN WILD-TYPE                           40
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  10Q GAIN MUTATED                                         0
  10Q GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  10Q GAIN MUTATED                                           0
  10Q GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  10Q GAIN MUTATED                                                  0
  10Q GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  10Q GAIN MUTATED                                          1
  10Q GAIN WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  10Q GAIN MUTATED                                                         0
  10Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  10Q GAIN MUTATED                                            0
  10Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  10Q GAIN MUTATED                                                   2
  10Q GAIN WILD-TYPE                                                71
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  10Q GAIN MUTATED                                                    0
  10Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  10Q GAIN MUTATED                                    0
  10Q GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  10Q GAIN MUTATED                          0                           0
  10Q GAIN WILD-TYPE                        5                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  10Q GAIN MUTATED                           0
  10Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  10Q GAIN MUTATED                                   1
  10Q GAIN WILD-TYPE                                 6
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  10Q GAIN MUTATED                                   1
  10Q GAIN WILD-TYPE                                 4
D20V3, multiclass
                                                         clus
vv                                                        10Q GAIN 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                                1
  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                                           4
  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                                               0
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        10Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       7
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  28
  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                                  1
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  5
  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                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        6
  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"
D20V4, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5   6
  10Q GAIN WILD-TYPE 134 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    6
  10Q GAIN WILD-TYPE  134  112
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                5                134
  MALE                  6                112
[1] 2 2
[1] FALSE
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     8   3
  10Q GAIN WILD-TYPE 171  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      8    3
  10Q GAIN WILD-TYPE  171   69
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 8                171
  YES                3                 69
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  10Q GAIN MUTATED                              3             0
  10Q GAIN WILD-TYPE                           56             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  10Q GAIN MUTATED                                                                          0
  10Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  10Q GAIN MUTATED                      1
  10Q GAIN WILD-TYPE                  102
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  10Q GAIN MUTATED                                                  0
  10Q GAIN WILD-TYPE                                                9
                    vv
clus                 MYXOFIBROSARCOMA
  10Q GAIN MUTATED                  1
  10Q GAIN WILD-TYPE               23
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  10Q GAIN MUTATED                                                          5
  10Q GAIN WILD-TYPE                                                       23
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  10Q GAIN MUTATED                                          1
  10Q GAIN WILD-TYPE                                        1
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  10Q GAIN MUTATED                             0                             0
  10Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  10Q GAIN MUTATED                                            0
  10Q GAIN WILD-TYPE                                         21
D20V6, multiclass
                                                                          clus
vv                                                                         10Q GAIN 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)                                        0
  MYXOFIBROSARCOMA                                                                        1
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                1
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              0
                                                                          clus
vv                                                                         10Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             56
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                    102
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          9
  MYXOFIBROSARCOMA                                                                         23
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 23
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  1
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     8   1   1   1
  10Q GAIN WILD-TYPE 144  68   8  25
D20V7, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                8                144
  R1                1                 68
  R2                1                  8
  RX                1                 25
[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
  10Q GAIN MUTATED       0                         0    10
  10Q GAIN WILD-TYPE     6                        18   214
D20V8, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   10                214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0  10
  10Q GAIN WILD-TYPE   5 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   10
  10Q GAIN WILD-TYPE    5  210
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               10                210
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     9  14
  11P GAIN WILD-TYPE 150  84
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                23                234 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                14                 84 
$`11P GAIN MUTATED`
TCGA-DX-A6BK TCGA-DX-A8BH TCGA-DX-AB2W TCGA-KF-A41W TCGA-PC-A5DP TCGA-3B-A9HI 
       16.18        14.43       106.45        11.70        18.08        50.01 
TCGA-DX-A1KU TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BJ 
       14.04        41.00        50.50        16.87        21.30         9.34 
TCGA-DX-AATS TCGA-DX-AB2O TCGA-IE-A4EJ TCGA-IS-A3KA TCGA-K1-A42X TCGA-K1-A6RU 
        1.15        86.10         3.22        13.58       123.78        23.38 
TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A8VH TCGA-X6-A7W8 TCGA-X6-A8C3 
       13.08        18.08        10.52        26.43        19.17 

$`11P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        17.95        14.07        15.85        40.60        12.07 
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-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       32.15        16.60        37.02        12.62        52.11        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 
       52.27        28.21       159.29        22.62        17.75         8.28 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
        6.35        20.94       188.15        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       35.08        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX 
       36.03        18.64        26.56         0.56        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        45.11        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       66.94        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM 
       78.28        86.30        64.21       101.23        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       30.35       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       45.14        47.87        38.17        40.77       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E 
       40.44        36.69        60.66        19.43         6.58        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       12.00        15.72        65.98        66.74         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      106.55        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       34.88         4.57        33.30         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
       19.53         1.38        19.89        37.12        25.22       171.09 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
       53.33        62.17        17.36         5.19        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       35.28        30.31        25.41         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 
      122.96        37.55        38.63        81.01        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       46.82        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       64.77         0.72        16.77        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       25.35        32.75         8.61        19.63        13.22        13.41 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX 
       10.72        12.46        11.93         4.80        84.79        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46        22.62         8.58        63.35        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       45.34        30.84        35.18        20.65        50.86        29.46 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        36.43         4.37        13.38        15.95        15.98 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.15               0.49 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            123.78             188.15 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             18.08              32.73 
[1] "1.1 - 123.8 (18.1)" "0.5 - 188.2 (32.7)"
[1] "hr=" "2.2"
D21V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  11P GAIN MUTATED                0                  2                   0
  11P GAIN WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  11P GAIN MUTATED                     0                             1
  11P GAIN WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  11P GAIN MUTATED                       0                      3
  11P GAIN WILD-TYPE                     1                     25
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  11P GAIN MUTATED                      1                    0
  11P GAIN WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  11P GAIN MUTATED                                       0
  11P GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  11P GAIN MUTATED                                  0
  11P GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  11P GAIN MUTATED                                                0
  11P GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  11P GAIN MUTATED                                 0
  11P GAIN WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  11P GAIN MUTATED                                         0
  11P GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  11P GAIN MUTATED                              0                       0
  11P GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  11P GAIN MUTATED                                  2
  11P GAIN WILD-TYPE                               15
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  11P GAIN MUTATED                                         0
  11P GAIN WILD-TYPE                                       5
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  11P GAIN MUTATED                              7
  11P GAIN WILD-TYPE                           37
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  11P GAIN MUTATED                                         0
  11P GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  11P GAIN MUTATED                                           0
  11P GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  11P GAIN MUTATED                                                  0
  11P GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  11P GAIN MUTATED                                          0
  11P GAIN WILD-TYPE                                        8
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  11P GAIN MUTATED                                                         0
  11P GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  11P GAIN MUTATED                                            0
  11P GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  11P GAIN MUTATED                                                   5
  11P GAIN WILD-TYPE                                                68
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  11P GAIN MUTATED                                                    0
  11P GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  11P GAIN MUTATED                                    1
  11P GAIN WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  11P GAIN MUTATED                          0                           0
  11P GAIN WILD-TYPE                        5                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  11P GAIN MUTATED                           0
  11P GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  11P GAIN MUTATED                                   0
  11P GAIN WILD-TYPE                                 7
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  11P GAIN MUTATED                                   1
  11P GAIN WILD-TYPE                                 4
D21V3, multiclass
                                                         clus
vv                                                        11P GAIN MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     2
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 3
  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                                       2
  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                      5
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  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                                                        11P GAIN 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                                                     1
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  5
  LOWER EXTREMITY - THIGH/KNEE                                            37
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 8
  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                                       1
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  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"
D21V4, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    14   9
  11P GAIN WILD-TYPE 125 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     14    9
  11P GAIN WILD-TYPE  125  109
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               14                125
  MALE                  9                109
[1] 2 2
[1] FALSE
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    12  10
  11P GAIN WILD-TYPE 167  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     12   10
  11P GAIN WILD-TYPE  167   62
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                12                167
  YES               10                 62
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  11P GAIN MUTATED                              4             0
  11P GAIN WILD-TYPE                           55             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  11P GAIN MUTATED                                                                          0
  11P GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  11P GAIN MUTATED                      4
  11P GAIN WILD-TYPE                   99
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  11P GAIN MUTATED                                                  1
  11P GAIN WILD-TYPE                                                8
                    vv
clus                 MYXOFIBROSARCOMA
  11P GAIN MUTATED                  6
  11P GAIN WILD-TYPE               18
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  11P GAIN MUTATED                                                          7
  11P GAIN WILD-TYPE                                                       21
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  11P GAIN MUTATED                                          0
  11P GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  11P GAIN MUTATED                             0                             0
  11P GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  11P GAIN MUTATED                                            1
  11P GAIN WILD-TYPE                                         20
D21V6, multiclass
                                                                          clus
vv                                                                         11P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            4
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    4
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                        6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              1
                                                                          clus
vv                                                                         11P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             55
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     99
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          8
  MYXOFIBROSARCOMA                                                                         18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 21
  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
  11P GAIN MUTATED    10   8   1   4
  11P GAIN WILD-TYPE 142  61   8  22
D21V7, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               10                142
  R1                8                 61
  R2                1                  8
  RX                4                 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
  11P GAIN MUTATED       1                         0    21
  11P GAIN WILD-TYPE     5                        18   203
D21V8, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   21                203
[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"
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  20
  11P GAIN WILD-TYPE   5 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   20
  11P GAIN WILD-TYPE    5  200
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               20                200
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     8  13
  11Q GAIN WILD-TYPE 151  85
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                21                236 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 85 
$`11Q GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A8BH TCGA-DX-AB2W TCGA-DX-AB2X TCGA-HB-A43Z TCGA-IE-A4EH 
       34.68        14.43       106.45        13.28        37.02        26.93 
TCGA-KF-A41W TCGA-PC-A5DP TCGA-3B-A9HI TCGA-DX-A1KU TCGA-DX-A6YV TCGA-DX-A6YX 
       11.70        18.08        50.01        14.04        50.50        16.87 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A8BJ TCGA-DX-AATS TCGA-K1-A42X TCGA-QC-A7B5 
       64.21        21.30         9.34         1.15       123.78        13.08 
TCGA-QQ-A5VA TCGA-QQ-A8VH TCGA-X6-A7W8 
       18.08        10.52        26.43 

$`11Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        16.18        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        17.95        14.07        15.85        40.60        12.07 
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-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       16.60        12.62        52.11        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB 
       22.62        17.75         8.28         6.35        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP 
       17.52        26.17        41.49        35.08        19.69        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       68.55        88.57        44.91        54.74        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        38.47        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        32.71        68.61        12.85        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      136.44        33.44        44.68        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        73.87        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        85.45         9.73        45.99        24.26        35.28 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        37.41        82.68        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YZ 
       36.85        26.99         3.06        41.00        78.28        86.30 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
      101.23        34.49        62.20        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       48.20        20.05        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       40.77       150.35        27.95        40.44        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       19.43         6.58        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        66.74         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       19.89        15.48         8.05        67.63        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       33.30         0.72         9.80        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA 
        1.38        19.89        37.12        25.22       171.09        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       85.97         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS 
       53.33        62.17        17.36        23.38         5.19        63.81 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       16.41        35.28        30.31        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N 
        7.36       122.96        37.55        38.63        81.01        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
        1.84        46.82        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
      111.98        64.77         0.72        16.77        18.94         3.88 
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        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       38.27        65.46        22.62         8.58        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       18.08        45.34        30.84        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.15               0.49 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            123.78             188.15 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            18.080             32.055 
[1] "1.1 - 123.8 (18.1)" "0.5 - 188.2 (32.1)"
[1] "hr=" "2.1"
D22V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  11Q GAIN MUTATED                0                  1                   0
  11Q GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  11Q GAIN MUTATED                     0                             1
  11Q GAIN WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  11Q GAIN MUTATED                       0                      4
  11Q GAIN WILD-TYPE                     1                     24
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  11Q GAIN MUTATED                      1                    0
  11Q GAIN WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  11Q GAIN MUTATED                                       0
  11Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  11Q GAIN MUTATED                                  0
  11Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  11Q GAIN MUTATED                                                0
  11Q GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  11Q GAIN MUTATED                                 0
  11Q GAIN WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  11Q GAIN MUTATED                                         0
  11Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  11Q GAIN MUTATED                              0                       0
  11Q GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  11Q GAIN MUTATED                                  1
  11Q GAIN WILD-TYPE                               16
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  11Q GAIN MUTATED                                         0
  11Q GAIN WILD-TYPE                                       5
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  11Q GAIN MUTATED                              6
  11Q GAIN WILD-TYPE                           38
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  11Q GAIN MUTATED                                         0
  11Q GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  11Q GAIN MUTATED                                           0
  11Q GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  11Q GAIN MUTATED                                                  0
  11Q GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  11Q GAIN MUTATED                                          0
  11Q GAIN WILD-TYPE                                        8
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  11Q GAIN MUTATED                                                         0
  11Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  11Q GAIN MUTATED                                            0
  11Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  11Q GAIN MUTATED                                                   5
  11Q GAIN WILD-TYPE                                                68
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  11Q GAIN MUTATED                                                    0
  11Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  11Q GAIN MUTATED                                    1
  11Q GAIN WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  11Q GAIN MUTATED                          0                           0
  11Q GAIN WILD-TYPE                        5                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  11Q GAIN MUTATED                           0
  11Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  11Q GAIN MUTATED                                   0
  11Q GAIN WILD-TYPE                                 7
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  11Q GAIN MUTATED                                   1
  11Q GAIN WILD-TYPE                                 4
D22V3, multiclass
                                                         clus
vv                                                        11Q GAIN 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                                                 4
  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                                       1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                0
  LOWER EXTREMITY - THIGH/KNEE                                           6
  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                      5
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  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                                                        11Q GAIN 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                                                  24
  HEAD AND NECK - HEAD                                                     1
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  5
  LOWER EXTREMITY - THIGH/KNEE                                            38
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 8
  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                                       1
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  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
  11Q GAIN MUTATED    12   9
  11Q GAIN WILD-TYPE 127 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12    9
  11Q GAIN WILD-TYPE  127  109
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               12                127
  MALE                  9                109
[1] 2 2
[1] FALSE
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    12   9
  11Q GAIN WILD-TYPE 167  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12    9
  11Q GAIN WILD-TYPE  167   63
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                12                167
  YES                9                 63
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  11Q GAIN MUTATED                              4             0
  11Q GAIN WILD-TYPE                           55             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  11Q GAIN MUTATED                                                                          0
  11Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  11Q GAIN MUTATED                      5
  11Q GAIN WILD-TYPE                   98
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  11Q GAIN MUTATED                                                  1
  11Q GAIN WILD-TYPE                                                8
                    vv
clus                 MYXOFIBROSARCOMA
  11Q GAIN MUTATED                  4
  11Q GAIN WILD-TYPE               20
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  11Q GAIN MUTATED                                                          7
  11Q GAIN WILD-TYPE                                                       21
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  11Q GAIN MUTATED                                          0
  11Q GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  11Q GAIN MUTATED                             0                             0
  11Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  11Q GAIN MUTATED                                            0
  11Q GAIN WILD-TYPE                                         21
D22V6, multiclass
                                                                          clus
vv                                                                         11Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            4
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    5
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                        4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              0
                                                                          clus
vv                                                                         11Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             55
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     98
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          8
  MYXOFIBROSARCOMA                                                                         20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    10   6   1   4
  11Q GAIN WILD-TYPE 142  63   8  22
D22V7, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               10                142
  R1                6                 63
  R2                1                  8
  RX                4                 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
  11Q GAIN MUTATED       0                         0    20
  11Q GAIN WILD-TYPE     6                        18   204
D22V8, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   20                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"
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  18
  11Q GAIN WILD-TYPE   5 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   18
  11Q GAIN WILD-TYPE    5  202
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               18                202
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    18  23
  12P GAIN WILD-TYPE 141  75
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                41                216 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                23                 75 
$`12P GAIN MUTATED`
TCGA-DX-A8BH TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB3A TCGA-MB-A5Y9 
       14.43        40.60       106.45        13.28        32.15         8.28 
TCGA-SG-A849 TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A3LS TCGA-DX-A6YS 
       17.52        14.04        68.61        12.85         9.04        78.28 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BX TCGA-DX-AATS 
       16.87        64.21        34.49         9.34        19.43         1.15 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IF-A4AJ 
       86.10        66.74       106.55         4.57         0.72        25.22 
TCGA-IW-A3M5 TCGA-K1-A42W TCGA-MB-A5Y8 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QQ-A5VA 
        5.92        62.17        25.41        10.45        37.55        18.08 
TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU 
      111.98        10.52        16.77        25.35         8.61        13.41 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-AAPF 
       35.18        20.65        27.32        36.43        15.95 

$`12P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2P 
       75.32        15.22        17.95        14.07        15.85        12.07 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK 
       22.85       101.98        30.51        60.00        84.66        16.60 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       37.02        12.62        52.11        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP 
      159.29        22.62        11.70        17.75         6.35        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
       20.94       188.15        26.17        41.49        35.08        50.01 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       19.69        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 
       18.64        26.56         0.56        32.71        45.11        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        95.38        79.17        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        73.87        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       85.45         9.73        45.99        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       108.82        59.84        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 
       26.99         3.06        41.00        50.50        86.30       101.23 
TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       20.05        61.97        45.14        47.87        38.17        40.77 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ 
      150.35        27.95        40.44        36.69        60.66         6.58 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2T 
       17.79        12.00        15.72        65.98         9.21        77.88 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32        19.89        15.48         8.05        67.63        34.88 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       33.30         9.80        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE 
       19.89        37.12       171.09        13.58        85.97        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91       101.26        53.33       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
       23.38         5.19        63.81        16.41        35.28        30.31 
TCGA-MB-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-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
       11.57         7.36       122.96        38.63        81.01        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
       17.65         1.84        46.82        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
      130.32        64.77         0.72        18.94         3.88        22.82 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       32.75        19.63        13.22        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
        4.80        84.79        38.27        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       63.35        26.43        35.90        18.08        45.34        30.84 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       19.17        50.86        29.46         4.37        13.38        15.98 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.72               0.49 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            111.98             188.15 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            19.430             33.025 
[1] "0.7 - 112.0 (19.4)" "0.5 - 188.2 (33.0)"
[1] "hr=" "2"  
D23V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  12P GAIN MUTATED                0                  1                   0
  12P GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  12P GAIN MUTATED                     0                             1
  12P GAIN WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  12P GAIN MUTATED                       0                      2
  12P GAIN WILD-TYPE                     1                     26
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  12P GAIN MUTATED                      0                    0
  12P GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  12P GAIN MUTATED                                       0
  12P GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  12P GAIN MUTATED                                  0
  12P GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  12P GAIN MUTATED                                                0
  12P GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  12P GAIN MUTATED                                 3
  12P GAIN WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  12P GAIN MUTATED                                         0
  12P GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  12P GAIN MUTATED                              0                       0
  12P GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  12P GAIN MUTATED                                  9
  12P GAIN WILD-TYPE                                8
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  12P GAIN MUTATED                                         1
  12P GAIN WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  12P GAIN MUTATED                              4
  12P GAIN WILD-TYPE                           40
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  12P GAIN MUTATED                                         0
  12P GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  12P GAIN MUTATED                                           0
  12P GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  12P GAIN MUTATED                                                  1
  12P GAIN WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  12P GAIN MUTATED                                          1
  12P GAIN WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  12P GAIN MUTATED                                                         0
  12P GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  12P GAIN MUTATED                                            1
  12P GAIN WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  12P GAIN MUTATED                                                   9
  12P GAIN WILD-TYPE                                                64
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  12P GAIN MUTATED                                                    0
  12P GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  12P GAIN MUTATED                                    1
  12P GAIN WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  12P GAIN MUTATED                          1                           0
  12P GAIN WILD-TYPE                        4                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  12P GAIN MUTATED                           0
  12P GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  12P GAIN MUTATED                                   3
  12P GAIN WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  12P GAIN MUTATED                                   2
  12P GAIN WILD-TYPE                                 3
D23V3, multiclass
                                                         clus
vv                                                        12P GAIN 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                                                 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                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                           4
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  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                                     1
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        12P GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            1
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  26
  HEAD AND NECK - HEAD                                                     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                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                         8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            40
  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                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       64
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        4
  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"
D23V4, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    22  19
  12P GAIN WILD-TYPE 117  99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     22   19
  12P GAIN WILD-TYPE  117   99
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               22                117
  MALE                 19                 99
[1] 2 2
[1] FALSE
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    26  15
  12P GAIN WILD-TYPE 153  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     26   15
  12P GAIN WILD-TYPE  153   57
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                26                153
  YES               15                 57
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  12P GAIN MUTATED                              7             0
  12P GAIN WILD-TYPE                           52             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  12P GAIN MUTATED                                                                          0
  12P GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  12P GAIN MUTATED                      8
  12P GAIN WILD-TYPE                   95
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  12P GAIN MUTATED                                                  3
  12P GAIN WILD-TYPE                                                6
                    vv
clus                 MYXOFIBROSARCOMA
  12P GAIN MUTATED                  4
  12P GAIN WILD-TYPE               20
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  12P GAIN MUTATED                                                          9
  12P GAIN WILD-TYPE                                                       19
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  12P GAIN MUTATED                                          1
  12P GAIN WILD-TYPE                                        1
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  12P GAIN MUTATED                             0                             0
  12P GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  12P GAIN MUTATED                                            9
  12P GAIN WILD-TYPE                                         12
D23V6, multiclass
                                                                          clus
vv                                                                         12P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            7
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    8
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        3
  MYXOFIBROSARCOMA                                                                        4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                1
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              9
                                                                          clus
vv                                                                         12P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             52
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     95
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          6
  MYXOFIBROSARCOMA                                                                         20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  1
  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
  12P GAIN MUTATED    21  12   2   5
  12P GAIN WILD-TYPE 131  57   7  21
D23V7, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               21                131
  R1               12                 57
  R2                2                  7
  RX                5                 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
  12P GAIN MUTATED       2                         0    37
  12P GAIN WILD-TYPE     4                        18   187
D23V8, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   37                187
[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
  12P GAIN MUTATED     2  32
  12P GAIN WILD-TYPE   3 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   32
  12P GAIN WILD-TYPE    3  188
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               32                188
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    17  14
  12Q GAIN WILD-TYPE 142  84
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                31                226 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                14                 84 
$`12Q GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A8BH TCGA-DX-AB2J TCGA-DX-AB2W TCGA-HS-A5N9 TCGA-SG-A849 
       34.68        14.43        40.60       106.45        52.11        17.52 
TCGA-DX-A1KX TCGA-DX-A6YS TCGA-DX-A6Z0 TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BO 
       68.61        78.28        64.21         9.34        45.14        40.77 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-HB-A3YV 
       60.66        19.43         1.15        66.74       106.55         4.57 
TCGA-HS-A5N8 TCGA-IF-A4AJ TCGA-MO-A47R TCGA-PC-A5DL TCGA-QQ-A8VF TCGA-QQ-A8VH 
        0.72        25.22        10.45        37.55       111.98        10.52 
TCGA-RN-AAAQ TCGA-SI-A71O TCGA-SI-A71P TCGA-UE-A6QU TCGA-X6-A8C3 TCGA-X9-A973 
       16.77        22.82        25.35        13.41        19.17        36.43 
TCGA-Z4-AAPF 
       15.95 

$`12Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        16.18        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB2X 
       15.22        17.95        14.07        15.85        12.07        13.28 
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-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       16.60        37.02        12.62        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
      159.29        22.62        11.70        17.75         8.28         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       18.08        20.94       188.15        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       50.01        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        45.11        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       66.94        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF 
       41.00        50.50        16.87        86.30       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS 
       20.05        61.97        47.87        38.17       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       40.44        36.69         6.58        17.79        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B 
       65.98        86.10         9.21        77.88        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA 
       15.48         8.05        67.63        34.88        33.30         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48        19.53         3.22         1.38        19.89        37.12 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
      171.09        13.58        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
       23.38         5.19        63.81        16.41        35.28        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57         7.36       122.96        38.63        81.01 
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-RN-A68Q TCGA-SG-A6Z4 
       35.90        37.12       130.32        64.77         0.72        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G 
        3.88        32.75         8.61        19.63        13.22        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       12.46        11.93         4.80        84.79        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       22.62         8.58        63.35        26.43        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       45.34        30.84        35.18        20.65        50.86        29.46 
TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       27.32         4.37        13.38        15.98 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.72               0.49 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            111.98             188.15 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             25.35              31.33 
[1] "0.7 - 112.0 (25.4)" "0.5 - 188.2 (31.3)"
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  12Q GAIN MUTATED                0                  1                   0
  12Q GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  12Q GAIN MUTATED                     0                             1
  12Q GAIN WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  12Q GAIN MUTATED                       0                      2
  12Q GAIN WILD-TYPE                     1                     26
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  12Q GAIN MUTATED                      0                    0
  12Q GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  12Q GAIN MUTATED                                       0
  12Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  12Q GAIN MUTATED                                  0
  12Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  12Q GAIN MUTATED                                                0
  12Q GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  12Q GAIN MUTATED                                 3
  12Q GAIN WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  12Q GAIN MUTATED                                         0
  12Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  12Q GAIN MUTATED                              0                       0
  12Q GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  12Q GAIN MUTATED                                  5
  12Q GAIN WILD-TYPE                               12
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  12Q GAIN MUTATED                                         2
  12Q GAIN WILD-TYPE                                       3
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  12Q GAIN MUTATED                              2
  12Q GAIN WILD-TYPE                           42
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  12Q GAIN MUTATED                                         0
  12Q GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  12Q GAIN MUTATED                                           0
  12Q GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  12Q GAIN MUTATED                                                  1
  12Q GAIN WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  12Q GAIN MUTATED                                          1
  12Q GAIN WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  12Q GAIN MUTATED                                                         0
  12Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  12Q GAIN MUTATED                                            0
  12Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  12Q GAIN MUTATED                                                   5
  12Q GAIN WILD-TYPE                                                68
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  12Q GAIN MUTATED                                                    0
  12Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  12Q GAIN MUTATED                                    1
  12Q GAIN WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  12Q GAIN MUTATED                          1                           0
  12Q GAIN WILD-TYPE                        4                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  12Q GAIN MUTATED                           0
  12Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  12Q GAIN MUTATED                                   3
  12Q GAIN WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  12Q GAIN MUTATED                                   2
  12Q GAIN WILD-TYPE                                 3
D24V3, multiclass
                                                         clus
vv                                                        12Q GAIN 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                                                 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                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                2
  LOWER EXTREMITY - THIGH/KNEE                                           2
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      5
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        12Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            1
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  26
  HEAD AND NECK - HEAD                                                     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                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        12
  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                       68
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        4
  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"
D24V4, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    13  18
  12Q GAIN WILD-TYPE 126 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     13   18
  12Q GAIN WILD-TYPE  126  100
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               13                126
  MALE                 18                100
[1] 2 2
[1] FALSE
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    17  14
  12Q GAIN WILD-TYPE 162  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     17   14
  12Q GAIN WILD-TYPE  162   58
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                17                162
  YES               14                 58
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  12Q GAIN MUTATED                              2             0
  12Q GAIN WILD-TYPE                           57             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  12Q GAIN MUTATED                                                                          0
  12Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  12Q GAIN MUTATED                      6
  12Q GAIN WILD-TYPE                   97
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  12Q GAIN MUTATED                                                  4
  12Q GAIN WILD-TYPE                                                5
                    vv
clus                 MYXOFIBROSARCOMA
  12Q GAIN MUTATED                  5
  12Q GAIN WILD-TYPE               19
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  12Q GAIN MUTATED                                                          9
  12Q GAIN WILD-TYPE                                                       19
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  12Q GAIN MUTATED                                          1
  12Q GAIN WILD-TYPE                                        1
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  12Q GAIN MUTATED                             0                             0
  12Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  12Q GAIN MUTATED                                            4
  12Q GAIN WILD-TYPE                                         17
D24V6, multiclass
                                                                          clus
vv                                                                         12Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            2
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    6
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        4
  MYXOFIBROSARCOMA                                                                        5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                1
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              4
                                                                          clus
vv                                                                         12Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             57
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     97
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          5
  MYXOFIBROSARCOMA                                                                         19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  1
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               17
[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
  12Q GAIN MUTATED    16   8   1   5
  12Q GAIN WILD-TYPE 136  61   8  21
D24V7, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               16                136
  R1                8                 61
  R2                1                  8
  RX                5                 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
  12Q GAIN MUTATED       3                         0    26
  12Q GAIN WILD-TYPE     3                        18   198
D24V8, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    3                  3
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   26                198
[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"
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  24
  12Q GAIN WILD-TYPE   3 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   24
  12Q GAIN WILD-TYPE    3  196
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               24                196
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     9   6
  13Q GAIN WILD-TYPE 150  92
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                242 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 92 
$`13Q GAIN MUTATED`
TCGA-DX-AB2P TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-LI-A9QH TCGA-PC-A5DP TCGA-3B-A9HV 
       12.07        52.11        52.27        17.75        18.08        14.37 
TCGA-DX-A6YR TCGA-DX-A8BS TCGA-DX-AB2T TCGA-JV-A5VE TCGA-K1-A6RV TCGA-MJ-A68H 
       41.00        27.95        77.88        16.41         5.19        14.99 
TCGA-WP-A9GB TCGA-X9-A971 TCGA-Z4-AAPF 
        8.58        27.32        15.95 

$`13Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       75.32        15.22        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       40.60       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 
       26.93        28.21       159.29        22.62        11.70         8.28 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
        6.35        20.94       188.15        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       35.08        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       44.91        54.74        25.25        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       79.17         9.04        49.05        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       82.68        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        78.28        50.50        16.87        86.30        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
      101.23        21.30        34.49        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       29.49        48.20        20.05         9.34        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU 
       47.87        38.17        40.77       150.35        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        17.79        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V 
       15.72        65.98        86.10        66.74         9.21       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32        19.89        15.48         8.05        67.63        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
        4.57        33.30         0.72         9.80        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
        3.22         1.38        19.89        37.12        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       13.58        85.97         5.92         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS 
       53.33        62.17       123.78        17.36        23.38        63.81 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       16.41        35.28        30.31        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       19.73        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
      122.96        37.55        38.63        81.01        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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       19.63        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
        4.80        84.79        38.27        65.46        22.62        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       26.43        35.90        18.08        45.34        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        20.65        50.86        29.46        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPG 
       13.38        15.98 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              5.19               0.49 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             77.88             188.15 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            17.750             32.055 
[1] "5.2 - 77.9 (17.8)"  "0.5 - 188.2 (32.1)"
[1] "hr=" "1.5"
D25V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  13Q GAIN MUTATED                0                  1                   0
  13Q GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  13Q GAIN MUTATED                     0                             0
  13Q GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  13Q GAIN MUTATED                       0                      3
  13Q GAIN WILD-TYPE                     1                     25
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  13Q GAIN MUTATED                      0                    0
  13Q GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  13Q GAIN MUTATED                                       0
  13Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  13Q GAIN MUTATED                                  0
  13Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  13Q GAIN MUTATED                                                1
  13Q GAIN WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  13Q GAIN MUTATED                                 1
  13Q GAIN WILD-TYPE                               9
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  13Q GAIN MUTATED                                         0
  13Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  13Q GAIN MUTATED                              0                       0
  13Q GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  13Q GAIN MUTATED                                  1
  13Q GAIN WILD-TYPE                               16
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  13Q GAIN MUTATED                                         0
  13Q GAIN WILD-TYPE                                       5
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  13Q GAIN MUTATED                              5
  13Q GAIN WILD-TYPE                           39
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  13Q GAIN MUTATED                                         0
  13Q GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  13Q GAIN MUTATED                                           0
  13Q GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  13Q GAIN MUTATED                                                  0
  13Q GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  13Q GAIN MUTATED                                          0
  13Q GAIN WILD-TYPE                                        8
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  13Q GAIN MUTATED                                                         0
  13Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  13Q GAIN MUTATED                                            0
  13Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  13Q GAIN MUTATED                                                   1
  13Q GAIN WILD-TYPE                                                72
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  13Q GAIN MUTATED                                                    0
  13Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  13Q GAIN MUTATED                                    0
  13Q GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  13Q GAIN MUTATED                          0                           0
  13Q GAIN WILD-TYPE                        5                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  13Q GAIN MUTATED                           0
  13Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  13Q GAIN MUTATED                                   1
  13Q GAIN WILD-TYPE                                 6
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  13Q GAIN MUTATED                                   1
  13Q GAIN WILD-TYPE                                 4
D25V3, multiclass
                                                         clus
vv                                                        13Q GAIN 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                                                 3
  HEAD AND NECK - HEAD                                                   0
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  0
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         1
  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                                       1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                0
  LOWER EXTREMITY - THIGH/KNEE                                           5
  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                                      1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        13Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  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                           1
  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                                        16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  5
  LOWER EXTREMITY - THIGH/KNEE                                            39
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       72
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       2
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        6
  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"
D25V4, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    12   3
  13Q GAIN WILD-TYPE 127 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12    3
  13Q GAIN WILD-TYPE  127  115
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               12                127
  MALE                  3                115
[1] 2 2
[1] FALSE
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    10   5
  13Q GAIN WILD-TYPE 169  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     10    5
  13Q GAIN WILD-TYPE  169   67
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                10                169
  YES                5                 67
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  13Q GAIN MUTATED                              0             0
  13Q GAIN WILD-TYPE                           59             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  13Q GAIN MUTATED                                                                          0
  13Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  13Q GAIN MUTATED                      9
  13Q GAIN WILD-TYPE                   94
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  13Q GAIN MUTATED                                                  0
  13Q GAIN WILD-TYPE                                                9
                    vv
clus                 MYXOFIBROSARCOMA
  13Q GAIN MUTATED                  2
  13Q GAIN WILD-TYPE               22
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  13Q GAIN MUTATED                                                          3
  13Q GAIN WILD-TYPE                                                       25
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  13Q GAIN MUTATED                                          1
  13Q GAIN WILD-TYPE                                        1
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  13Q GAIN MUTATED                             0                             0
  13Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  13Q GAIN MUTATED                                            0
  13Q GAIN WILD-TYPE                                         21
D25V6, multiclass
                                                                          clus
vv                                                                         13Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            0
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    9
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        0
  MYXOFIBROSARCOMA                                                                        2
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                1
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              0
                                                                          clus
vv                                                                         13Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             59
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     94
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          9
  MYXOFIBROSARCOMA                                                                         22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 25
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  1
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    10   2   1   2
  13Q GAIN WILD-TYPE 142  67   8  24
D25V7, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               10                142
  R1                2                 67
  R2                1                  8
  RX                2                 24
[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
  13Q GAIN MUTATED       0                         4    10
  13Q GAIN WILD-TYPE     6                        14   214
D25V8, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   10                214
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  14
  13Q GAIN WILD-TYPE   5 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   14
  13Q GAIN WILD-TYPE    5  206
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               14                206
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    26  30
  14Q GAIN WILD-TYPE 133  68
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                56                201 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                30                 68 
$`14Q GAIN MUTATED`
TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-HB-A5W3 
       67.20        75.32        15.22        17.95        14.43        12.62 
TCGA-IF-A4AK TCGA-KF-A41W TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 
       52.27        11.70         6.35        18.08        20.94        17.52 
TCGA-3B-A9HI TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1L1 TCGA-DX-A23Y 
       50.01        88.57        18.64         0.56        54.21         6.28 
TCGA-DX-A240 TCGA-DX-A3LW TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6YQ 
       60.30       136.44        14.99        85.45        24.26         3.06 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BJ 
       50.50        16.87        64.21        21.30        34.49         9.34 
TCGA-DX-A8BV TCGA-DX-AB2E TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-HB-A3YV 
       60.66        17.79        66.74       106.55        50.40         4.57 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-K1-A6RU TCGA-K1-A6RV TCGA-MB-A8JL 
       25.22        13.58         5.92        23.38         5.19        19.73 
TCGA-MJ-A68H TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-SG-A6Z7 
       14.99        48.59        35.90        37.12       111.98         3.88 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C3 
       22.82        32.75        84.79        22.62        26.43        19.17 
TCGA-X9-A971 TCGA-Z4-AAPG 
       27.32        15.98 

$`14Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A8BP 
       36.30        31.53        34.68        16.18        34.36        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       15.85        40.60        12.07       106.45        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
      101.98        30.51        60.00        84.66        32.15        16.60 
TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       37.02        52.11        26.93        28.21       159.29        22.62 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       17.75         8.28       188.15        26.17        41.49        35.08 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       19.69        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 
       14.37        42.84        10.32        38.47        36.03        26.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04        32.71        68.61        12.85        45.11        18.54 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       85.02        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        49.05        86.83        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77        51.02         4.54        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       50.43        34.88         9.73        45.99        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       108.82        59.84        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EM 
       26.99        41.00        78.28        86.30       101.23        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       30.35       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       45.14        47.87        38.17        40.77       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F 
       40.44        36.69        19.43         6.58         1.15        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B 
       15.72        65.98        86.10         9.21        77.88        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 
       15.48         8.05        67.63        34.88        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
        9.80        80.48        19.53         3.22         1.38        19.89 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       37.12       171.09        85.97        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-KD-A5QS 
      101.26        53.33        62.17       123.78        17.36        63.81 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       16.41        35.28        30.31        25.41         0.49        21.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        81.01        13.08        17.65         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       46.82        18.08       130.32        64.77        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       16.77        18.94        25.35         8.61        19.63        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX 
       13.41        10.72        12.46        11.93         4.80        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       65.46         8.58        63.35        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       30.84        35.18        20.65        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.56               0.49 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            136.44             188.15 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             22.72              33.30 
[1] "0.6 - 136.4 (22.7)" "0.5 - 188.2 (33.3)"
[1] "hr=" "1.8"
D26V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  14Q GAIN MUTATED                1                  3                   0
  14Q GAIN WILD-TYPE              0                  4                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  14Q GAIN MUTATED                     0                             0
  14Q GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  14Q GAIN MUTATED                       0                      4
  14Q GAIN WILD-TYPE                     1                     24
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  14Q GAIN MUTATED                      0                    0
  14Q GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  14Q GAIN MUTATED                                       0
  14Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  14Q GAIN MUTATED                                  0
  14Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  14Q GAIN MUTATED                                                2
  14Q GAIN WILD-TYPE                                              0
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  14Q GAIN MUTATED                                 0
  14Q GAIN WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  14Q GAIN MUTATED                                         1
  14Q GAIN WILD-TYPE                                       1
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  14Q GAIN MUTATED                              1                       1
  14Q GAIN WILD-TYPE                            3                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  14Q GAIN MUTATED                                  5
  14Q GAIN WILD-TYPE                               12
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  14Q GAIN MUTATED                                         3
  14Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  14Q GAIN MUTATED                             13
  14Q GAIN WILD-TYPE                           31
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  14Q GAIN MUTATED                                         0
  14Q GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  14Q GAIN MUTATED                                           1
  14Q GAIN WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  14Q GAIN MUTATED                                                  0
  14Q GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  14Q GAIN MUTATED                                          3
  14Q GAIN WILD-TYPE                                        5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  14Q GAIN MUTATED                                                         1
  14Q GAIN WILD-TYPE                                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  14Q GAIN MUTATED                                            0
  14Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  14Q GAIN MUTATED                                                   9
  14Q GAIN WILD-TYPE                                                64
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  14Q GAIN MUTATED                                                    0
  14Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  14Q GAIN MUTATED                                    2
  14Q GAIN WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  14Q GAIN MUTATED                          2                           0
  14Q GAIN WILD-TYPE                        3                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  14Q GAIN MUTATED                           0
  14Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  14Q GAIN MUTATED                                   2
  14Q GAIN WILD-TYPE                                 5
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  14Q GAIN MUTATED                                   2
  14Q GAIN WILD-TYPE                                 3
D26V3, multiclass
                                                         clus
vv                                                        14Q GAIN MUTATED
  CHEST - BREAST                                                         1
  CHEST - CHEST WALL                                                     3
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          0
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 4
  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                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                1
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                       5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                3
  LOWER EXTREMITY - THIGH/KNEE                                          13
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      9
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        14Q GAIN WILD-TYPE
  CHEST - BREAST                                                           0
  CHEST - CHEST WALL                                                       4
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  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                           0
  LOWER ABDOMINAL/PELVIC - PELVIC                                         10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  1
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  1
  LOWER EXTREMITY - LOWER LEG/CALF                                        12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  2
  LOWER EXTREMITY - THIGH/KNEE                                            31
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       64
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  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"
D26V4, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    32  24
  14Q GAIN WILD-TYPE 107  94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     32   24
  14Q GAIN WILD-TYPE  107   94
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               32                107
  MALE                 24                 94
[1] 2 2
[1] FALSE
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    34  22
  14Q GAIN WILD-TYPE 145  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     34   22
  14Q GAIN WILD-TYPE  145   50
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                34                145
  YES               22                 50
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  14Q GAIN MUTATED                              8             0
  14Q GAIN WILD-TYPE                           51             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  14Q GAIN MUTATED                                                                          0
  14Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  14Q GAIN MUTATED                     23
  14Q GAIN WILD-TYPE                   80
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  14Q GAIN MUTATED                                                  2
  14Q GAIN WILD-TYPE                                                7
                    vv
clus                 MYXOFIBROSARCOMA
  14Q GAIN MUTATED                 12
  14Q GAIN WILD-TYPE               12
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  14Q GAIN MUTATED                                                          7
  14Q GAIN WILD-TYPE                                                       21
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  14Q GAIN MUTATED                                          0
  14Q GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  14Q GAIN MUTATED                             0                             0
  14Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  14Q GAIN MUTATED                                            4
  14Q GAIN WILD-TYPE                                         17
D26V6, multiclass
                                                                          clus
vv                                                                         14Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            8
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   23
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        2
  MYXOFIBROSARCOMA                                                                       12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              4
                                                                          clus
vv                                                                         14Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             51
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     80
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          7
  MYXOFIBROSARCOMA                                                                         12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               17
[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
  14Q GAIN MUTATED    34  16   1   5
  14Q GAIN WILD-TYPE 118  53   8  21
D26V7, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               34                118
  R1               16                 53
  R2                1                  8
  RX                5                 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
  14Q GAIN MUTATED       1                         5    47
  14Q GAIN WILD-TYPE     5                        13   177
D26V8, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   47                177
[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"
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  48
  14Q GAIN WILD-TYPE   4 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   48
  14Q GAIN WILD-TYPE    4  172
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               48                172
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    35  27
  15Q GAIN WILD-TYPE 124  71
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                62                195 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                27                 71 
$`15Q GAIN MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A8BG TCGA-DX-AB2P TCGA-DX-AB2X TCGA-HB-A43Z 
       31.53        67.20        17.95        12.07        13.28        37.02 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-PC-A5DP TCGA-SG-A849 TCGA-3B-A9HQ 
       12.62        52.11        52.27        18.08        17.52        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-DX-A1KX TCGA-DX-A1L4 
       88.57        44.91        42.84        38.47        68.61        66.94 
TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UF 
        6.28         8.58        51.02        14.99        68.55        85.45 
TCGA-DX-A48L TCGA-DX-A6BA TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EI 
       24.26        82.68        78.28        16.87        64.21        34.49 
TCGA-DX-A8BO TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AB2Q TCGA-IE-A4EI TCGA-IE-A4EJ 
       40.77        36.69        19.43        66.74        19.53         3.22 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-JV-A75J TCGA-K1-A42W TCGA-KD-A5QS 
       19.89        25.22        13.58         3.91        62.17        63.81 
TCGA-LI-A67I TCGA-MJ-A68H TCGA-PC-A5DL TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       30.31        14.99        37.55        46.82        18.08        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P 
       37.12       111.98        16.77        18.94         3.88        25.35 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8XS TCGA-X6-A7W8 TCGA-X6-A8C3 
       32.75         8.61        13.41        84.79        26.43        19.17 
TCGA-X6-A8C4 TCGA-X9-A971 
       20.65        27.32 

$`15Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        34.68        16.18        34.36        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB30 
       14.43        14.07        15.85        40.60       106.45        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
      101.98        30.51        60.00        84.66        32.15        16.60 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH 
       26.93        28.21       159.29        22.62        11.70        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT 
        8.28         6.35        20.94       188.15        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HU 
       35.08        50.01        19.69        53.49        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       14.37        10.32        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        45.11        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       85.02        33.53        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE 
       35.77         4.54        10.68        73.87        50.43        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        45.99        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB 
      108.82        59.84        37.58        15.95        37.41        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN 
       50.50        86.30       101.23        21.30        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       45.14        47.87        38.17       150.35        27.95        40.44 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       60.66         6.58         1.15        17.79        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       65.98        86.10         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31        49.15        31.13        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       19.89        15.48         8.05        67.63        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EK TCGA-IF-A3RQ 
       33.30         0.72         9.80        80.48         1.38        37.12 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN 
      171.09        85.97         5.92        16.41         1.05       101.26 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT 
       53.33       123.78        17.36        23.38         5.19        16.41 
TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
       35.28        25.41         0.49        21.73        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN 
       22.39        11.57        10.45         7.36       122.96        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A8VD 
       81.01        13.08        17.65         1.84        48.59       130.32 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SI-A71O TCGA-SI-AA8C TCGA-UE-A6QT 
       64.77        10.52         0.72        22.82        19.63        13.22 
TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY 
       10.72        12.46        11.93         4.80        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62         8.58        63.35        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB 
       30.84        35.18        50.86        29.46        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              3.22               0.49 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            111.98             188.15 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             30.92              31.13 
[1] "3.2 - 112.0 (30.9)" "0.5 - 188.2 (31.1)"
[1] "hr=" "1.2"
D27V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  15Q GAIN MUTATED                0                  1                   0
  15Q GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  15Q GAIN MUTATED                     1                             0
  15Q GAIN WILD-TYPE                   0                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  15Q GAIN MUTATED                       0                      5
  15Q GAIN WILD-TYPE                     1                     23
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  15Q GAIN MUTATED                      0                    0
  15Q GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  15Q GAIN MUTATED                                       0
  15Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  15Q GAIN MUTATED                                  0
  15Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  15Q GAIN MUTATED                                                2
  15Q GAIN WILD-TYPE                                              0
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  15Q GAIN MUTATED                                 2
  15Q GAIN WILD-TYPE                               8
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  15Q GAIN MUTATED                                         0
  15Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  15Q GAIN MUTATED                              1                       0
  15Q GAIN WILD-TYPE                            3                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  15Q GAIN MUTATED                                  8
  15Q GAIN WILD-TYPE                                9
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  15Q GAIN MUTATED                                         1
  15Q GAIN WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  15Q GAIN MUTATED                             16
  15Q GAIN WILD-TYPE                           28
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  15Q GAIN MUTATED                                         1
  15Q GAIN WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  15Q GAIN MUTATED                                           1
  15Q GAIN WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  15Q GAIN MUTATED                                                  1
  15Q GAIN WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  15Q GAIN MUTATED                                          2
  15Q GAIN WILD-TYPE                                        6
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  15Q GAIN MUTATED                                                         0
  15Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  15Q GAIN MUTATED                                            1
  15Q GAIN WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  15Q GAIN MUTATED                                                  13
  15Q GAIN WILD-TYPE                                                60
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  15Q GAIN MUTATED                                                    0
  15Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  15Q GAIN MUTATED                                    0
  15Q GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  15Q GAIN MUTATED                          0                           1
  15Q GAIN WILD-TYPE                        5                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  15Q GAIN MUTATED                           0
  15Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  15Q GAIN MUTATED                                   3
  15Q GAIN WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  15Q GAIN MUTATED                                   1
  15Q GAIN WILD-TYPE                                 4
D27V3, multiclass
                                                         clus
vv                                                        15Q GAIN 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                                                 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                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     13
  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                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        15Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      0
  CHEST - OTHER (PLEASE SPECIFY                                            2
  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                           0
  LOWER ABDOMINAL/PELVIC - PELVIC                                          8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                         9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            28
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       60
  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                                        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"
D27V4, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   40 22
  15Q GAIN WILD-TYPE 99 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     40   22
  15Q GAIN WILD-TYPE   99   96
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               40                 99
  MALE                 22                 96
[1] 2 2
[1] FALSE
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    40  21
  15Q GAIN WILD-TYPE 139  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     40   21
  15Q GAIN WILD-TYPE  139   51
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                40                139
  YES               21                 51
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  15Q GAIN MUTATED                              8             0
  15Q GAIN WILD-TYPE                           51             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  15Q GAIN MUTATED                                                                          0
  15Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  15Q GAIN MUTATED                     29
  15Q GAIN WILD-TYPE                   74
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  15Q GAIN MUTATED                                                  3
  15Q GAIN WILD-TYPE                                                6
                    vv
clus                 MYXOFIBROSARCOMA
  15Q GAIN MUTATED                  8
  15Q GAIN WILD-TYPE               16
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  15Q GAIN MUTATED                                                          7
  15Q GAIN WILD-TYPE                                                       21
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  15Q GAIN MUTATED                                          0
  15Q GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  15Q GAIN MUTATED                             0                             0
  15Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  15Q GAIN MUTATED                                            7
  15Q GAIN WILD-TYPE                                         14
D27V6, multiclass
                                                                          clus
vv                                                                         15Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            8
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   29
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        3
  MYXOFIBROSARCOMA                                                                        8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              7
                                                                          clus
vv                                                                         15Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             51
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     74
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          6
  MYXOFIBROSARCOMA                                                                         16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               14
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    36  17   1   7
  15Q GAIN WILD-TYPE 116  52   8  19
D27V7, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               36                116
  R1               17                 52
  R2                1                  8
  RX                7                 19
[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
  15Q GAIN MUTATED       2                         3    55
  15Q GAIN WILD-TYPE     4                        15   169
D27V8, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                3                 15
  WHITE                                   55                169
[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"
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3  53
  15Q GAIN WILD-TYPE   2 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   53
  15Q GAIN WILD-TYPE    2  167
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               53                167
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    18  22
  16P GAIN WILD-TYPE 141  76
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                40                217 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                 76 
$`16P GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A8BH TCGA-DX-AB2P TCGA-DX-AB2X TCGA-IE-A4EH TCGA-IF-A4AK 
       34.36        14.43        12.07        13.28        26.93        52.27 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HX TCGA-DX-A1KU 
       50.01        19.69        44.91        54.74        42.84        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A2J0 TCGA-DX-A3U5 TCGA-DX-A3U9 TCGA-DX-A48L 
       32.71        68.61         9.70        31.86        14.99        24.26 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BK TCGA-DX-A8BL 
       78.28        50.50        21.30        34.49        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-AB2E TCGA-DX-AB2O TCGA-FX-A2QS TCGA-IE-A3OV 
       47.87        27.95        17.79        86.10        49.15        80.48 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-K1-A6RU TCGA-LI-A67I TCGA-MO-A47R 
       25.22        13.58         5.92        23.38        30.31        10.45 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-X2-A95T TCGA-X6-A7W8 
       18.94         3.88        63.35        26.43 

$`16P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W 
       15.22        17.95        14.07        15.85        40.60       106.45 
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-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IS-A3K6 TCGA-IS-A3K8 
       16.60        37.02        12.62        52.11        28.21       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP 
       22.62        11.70        17.75         8.28         6.35        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       20.94       188.15        17.52        26.17        41.49        35.08 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY 
       53.49        68.55        88.57        25.25        14.37        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KY 
       38.47        36.03        18.64        26.56         0.56        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       45.11        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         8.58        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 
       86.83       136.44        33.44        44.68        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        10.68        73.87        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       85.45         9.73        45.99        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       82.68        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
        3.06        41.00        16.87        86.30        64.21       101.23 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU 
        9.34        38.17        40.77       150.35        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G 
       60.66        19.43         6.58         1.15        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       65.98        66.74         9.21        77.88       106.55        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       50.89        71.31        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       15.48         8.05        67.63        34.88         4.57        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
        0.72         9.80        19.53         3.22         1.38        19.89 
TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       37.12       171.09        85.97        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
      101.26        53.33        62.17       123.78        17.36         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       63.81        16.41        35.28        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        22.39        11.57         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
      122.96        37.55        38.63        81.01        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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
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        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46        22.62         8.58        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       45.34        30.84        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.88               0.49 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             86.10             188.15 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             29.13              31.53 
[1] "3.9 - 86.1 (29.1)"  "0.5 - 188.2 (31.5)"
[1] "hr=" "1.7"
D28V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  16P GAIN MUTATED                0                  1                   0
  16P GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  16P GAIN MUTATED                     0                             0
  16P GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  16P GAIN MUTATED                       0                      4
  16P GAIN WILD-TYPE                     1                     24
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  16P GAIN MUTATED                      0                    0
  16P GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  16P GAIN MUTATED                                       1
  16P GAIN WILD-TYPE                                     1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  16P GAIN MUTATED                                  0
  16P GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  16P GAIN MUTATED                                                1
  16P GAIN WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  16P GAIN MUTATED                                 1
  16P GAIN WILD-TYPE                               9
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  16P GAIN MUTATED                                         0
  16P GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  16P GAIN MUTATED                              0                       0
  16P GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  16P GAIN MUTATED                                  4
  16P GAIN WILD-TYPE                               13
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  16P GAIN MUTATED                                         1
  16P GAIN WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  16P GAIN MUTATED                             12
  16P GAIN WILD-TYPE                           32
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  16P GAIN MUTATED                                         1
  16P GAIN WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  16P GAIN MUTATED                                           0
  16P GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  16P GAIN MUTATED                                                  1
  16P GAIN WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  16P GAIN MUTATED                                          1
  16P GAIN WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  16P GAIN MUTATED                                                         1
  16P GAIN WILD-TYPE                                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  16P GAIN MUTATED                                            0
  16P GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  16P GAIN MUTATED                                                   7
  16P GAIN WILD-TYPE                                                66
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  16P GAIN MUTATED                                                    0
  16P GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  16P GAIN MUTATED                                    1
  16P GAIN WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  16P GAIN MUTATED                          0                           0
  16P GAIN WILD-TYPE                        5                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  16P GAIN MUTATED                           0
  16P GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  16P GAIN MUTATED                                   2
  16P GAIN WILD-TYPE                                 5
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  16P GAIN MUTATED                                   1
  16P GAIN WILD-TYPE                                 4
D28V3, multiclass
                                                         clus
vv                                                        16P GAIN 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                                                 4
  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                         1
  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                                       4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      7
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               0
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        16P GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  24
  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                           1
  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                                        13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       66
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    20  20
  16P GAIN WILD-TYPE 119  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     20   20
  16P GAIN WILD-TYPE  119   98
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               20                119
  MALE                 20                 98
[1] 2 2
[1] FALSE
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    26  14
  16P GAIN WILD-TYPE 153  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     26   14
  16P GAIN WILD-TYPE  153   58
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                26                153
  YES               14                 58
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  16P GAIN MUTATED                             10             0
  16P GAIN WILD-TYPE                           49             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  16P GAIN MUTATED                                                                          0
  16P GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  16P GAIN MUTATED                     13
  16P GAIN WILD-TYPE                   90
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  16P GAIN MUTATED                                                  0
  16P GAIN WILD-TYPE                                                9
                    vv
clus                 MYXOFIBROSARCOMA
  16P GAIN MUTATED                  7
  16P GAIN WILD-TYPE               17
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  16P GAIN MUTATED                                                         10
  16P GAIN WILD-TYPE                                                       18
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  16P GAIN MUTATED                                          0
  16P GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  16P GAIN MUTATED                             0                             0
  16P GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  16P GAIN MUTATED                                            0
  16P GAIN WILD-TYPE                                         21
D28V6, multiclass
                                                                          clus
vv                                                                         16P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           10
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   13
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        0
  MYXOFIBROSARCOMA                                                                        7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              0
                                                                          clus
vv                                                                         16P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             49
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     90
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          9
  MYXOFIBROSARCOMA                                                                         17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               21
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    27  10   1   2
  16P GAIN WILD-TYPE 125  59   8  24
D28V7, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               27                125
  R1               10                 59
  R2                1                  8
  RX                2                 24
[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
  16P GAIN MUTATED       1                         1    38
  16P GAIN WILD-TYPE     5                        17   186
D28V8, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                 17
  WHITE                                   38                186
[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"
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  36
  16P GAIN WILD-TYPE   5 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   36
  16P GAIN WILD-TYPE    5  184
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               36                184
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    11   8
  16Q GAIN WILD-TYPE 148  90
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                19                238 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                 90 
$`16Q GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A8BG TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HX TCGA-DX-A1KW 
       34.36        17.95        44.91        54.74        42.84        32.71 
TCGA-DX-A3U5 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BK TCGA-DX-A8BS TCGA-DX-AB2E 
       31.86        21.30        34.49        61.97        27.95        17.79 
TCGA-DX-AB2O TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-WK-A8Y0 
       86.10       171.09         5.92        18.94         3.88        22.62 
TCGA-Z4-AAPG 
       15.98 

$`16Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       84.66        32.15        16.60        37.02        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       17.75         8.28         6.35        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       17.52        26.17        41.49        35.08        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY 
       53.49        68.55        88.57        25.25        14.37        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-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       79.17         9.04        49.05        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       44.68        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       41.00        78.28        50.50        16.87        86.30        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
      101.23        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       20.05         9.34        45.14        47.87        38.17        40.77 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
      150.35        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S 
        1.15        12.00        15.72        65.98        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       77.88       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       67.63        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       25.22        13.58        85.97        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
      101.26        53.33        62.17       123.78        17.36        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
        5.19        63.81        16.41        35.28        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       81.01        13.08        17.65         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        35.90        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       10.52         0.72        16.77        22.82        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D 
        8.61        19.63        13.22        13.41        10.72        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB 
       11.93         4.80        84.79        38.27        65.46         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       63.35        26.43        35.90        18.08        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       35.18        19.17        20.65        50.86        29.46        27.32 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       36.43         4.37        13.38        15.95 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.88               0.49 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            171.09             188.15 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            31.860             30.985 
[1] "3.9 - 171.1 (31.9)" "0.5 - 188.2 (31.0)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  16Q GAIN MUTATED                0                  2                   0
  16Q GAIN WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  16Q GAIN MUTATED                     0                             0
  16Q GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  16Q GAIN MUTATED                       0                      2
  16Q GAIN WILD-TYPE                     1                     26
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  16Q GAIN MUTATED                      0                    0
  16Q GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  16Q GAIN MUTATED                                       1
  16Q GAIN WILD-TYPE                                     1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  16Q GAIN MUTATED                                  0
  16Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  16Q GAIN MUTATED                                                0
  16Q GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  16Q GAIN MUTATED                                 0
  16Q GAIN WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  16Q GAIN MUTATED                                         0
  16Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  16Q GAIN MUTATED                              0                       0
  16Q GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  16Q GAIN MUTATED                                  1
  16Q GAIN WILD-TYPE                               16
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  16Q GAIN MUTATED                                         0
  16Q GAIN WILD-TYPE                                       5
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  16Q GAIN MUTATED                              5
  16Q GAIN WILD-TYPE                           39
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  16Q GAIN MUTATED                                         1
  16Q GAIN WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  16Q GAIN MUTATED                                           0
  16Q GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  16Q GAIN MUTATED                                                  0
  16Q GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  16Q GAIN MUTATED                                          1
  16Q GAIN WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  16Q GAIN MUTATED                                                         0
  16Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  16Q GAIN MUTATED                                            0
  16Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  16Q GAIN MUTATED                                                   5
  16Q GAIN WILD-TYPE                                                68
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  16Q GAIN MUTATED                                                    0
  16Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  16Q GAIN MUTATED                                    0
  16Q GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  16Q GAIN MUTATED                          0                           0
  16Q GAIN WILD-TYPE                        5                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  16Q GAIN MUTATED                           0
  16Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  16Q GAIN MUTATED                                   1
  16Q GAIN WILD-TYPE                                 6
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  16Q GAIN MUTATED                                   0
  16Q GAIN WILD-TYPE                                 5
D29V3, multiclass
                                                         clus
vv                                                        16Q GAIN 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                                                 2
  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                                           5
  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                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      5
  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                                      1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      0
                                                         clus
vv                                                        16Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  26
  HEAD AND NECK - HEAD                                                     2
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  5
  LOWER EXTREMITY - THIGH/KNEE                                            39
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  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                                              4
  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"
D29V4, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    13   6
  16Q GAIN WILD-TYPE 126 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     13    6
  16Q GAIN WILD-TYPE  126  112
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               13                126
  MALE                  6                112
[1] 2 2
[1] FALSE
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    11   8
  16Q GAIN WILD-TYPE 168  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     11    8
  16Q GAIN WILD-TYPE  168   64
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                11                168
  YES                8                 64
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  16Q GAIN MUTATED                              4             0
  16Q GAIN WILD-TYPE                           55             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  16Q GAIN MUTATED                                                                          0
  16Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  16Q GAIN MUTATED                      5
  16Q GAIN WILD-TYPE                   98
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  16Q GAIN MUTATED                                                  0
  16Q GAIN WILD-TYPE                                                9
                    vv
clus                 MYXOFIBROSARCOMA
  16Q GAIN MUTATED                  3
  16Q GAIN WILD-TYPE               21
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  16Q GAIN MUTATED                                                          5
  16Q GAIN WILD-TYPE                                                       23
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  16Q GAIN MUTATED                                          0
  16Q GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  16Q GAIN MUTATED                             0                             0
  16Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  16Q GAIN MUTATED                                            2
  16Q GAIN WILD-TYPE                                         19
D29V6, multiclass
                                                                          clus
vv                                                                         16Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            4
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    5
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        0
  MYXOFIBROSARCOMA                                                                        3
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              2
                                                                          clus
vv                                                                         16Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             55
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     98
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          9
  MYXOFIBROSARCOMA                                                                         21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 23
  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
  16Q GAIN MUTATED    14   4   0   1
  16Q GAIN WILD-TYPE 138  65   9  25
D29V7, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               14                138
  R1                4                 65
  R2                0                  9
  RX                1                 25
[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
  16Q GAIN MUTATED       0                         1    18
  16Q GAIN WILD-TYPE     6                        17   206
D29V8, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                 17
  WHITE                                   18                206
[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"
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  16
  16Q GAIN WILD-TYPE   5 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   16
  16Q GAIN WILD-TYPE    5  204
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               16                204
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    30  31
  17P GAIN WILD-TYPE 129  67
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                61                196 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                31                 67 
$`17P GAIN MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB37 TCGA-HB-A5W3 
       16.18        67.20       106.45        13.28        84.66        12.62 
TCGA-LI-A9QH TCGA-PC-A5DP TCGA-SG-A849 TCGA-X6-A8C6 TCGA-3B-A9HS TCGA-3B-A9HT 
       17.75        18.08        17.52        35.08        44.91        54.74 
TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 
       42.84        18.64         0.56        32.71        12.85        54.21 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48R TCGA-DX-A6B8 
       85.02         6.28        85.45        45.99        26.47        15.95 
TCGA-DX-A6BF TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       31.96        50.50        86.30        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BV TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A3RE TCGA-FX-A3TO 
       40.77        60.66        77.88       106.55        21.70        20.32 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-JV-A75J TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU 
       19.89         4.57         3.91        23.38        63.81        35.28 
TCGA-LI-A67I TCGA-MO-A47R TCGA-N1-A6IA TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       30.31        10.45         7.36        13.08        46.82        18.08 
TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8Y0 
       18.94        25.35        13.41        10.72        84.79        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X9-A971 
        8.58        26.43        45.34        35.18        19.17        27.32 
TCGA-Z4-AAPG 
       15.98 

$`17P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        34.68        34.36        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       17.95        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK 
       22.85       101.98        30.51        60.00        32.15        16.60 
TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       37.02        52.11        26.93        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB 
       22.62        11.70         8.28         6.35        20.94       188.15 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       26.17        41.49        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       88.57        25.25        14.37        10.32        38.47        36.03 
TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 
       26.56        14.04        68.61        45.11        18.54        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       66.94        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       35.77        51.02         4.54        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       68.55        50.43        34.88         9.73        24.26        35.28 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       52.77        46.03       108.82        59.84        37.58        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       82.68        36.33        28.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       41.00        78.28        16.87        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       20.05         9.34        61.97       150.35        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       36.69        19.43         6.58         1.15        17.79        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2Z 
       15.72        65.98        86.10        66.74         9.21        50.40 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO 
       50.89        71.31        49.15        31.13        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       67.63        34.88        33.30         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       19.53         3.22         1.38        19.89        37.12        25.22 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
      171.09        13.58        85.97         5.92        16.41         1.05 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
      101.26        53.33        62.17       123.78        17.36         5.19 
TCGA-KD-A5QT TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       16.41        25.41         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       17.98        22.39        11.57       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
       81.01        17.65         1.84        48.59        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
        3.88        22.82        32.75         8.61        19.63        13.22 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
       12.46        11.93         4.80        38.27        65.46        63.35 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       35.90        18.08        30.84        20.65        50.86        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       36.43         4.37        13.38        15.95 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.56               0.49 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            106.55             188.15 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            26.470             32.005 
[1] "0.6 - 106.5 (26.5)" "0.5 - 188.2 (32.0)"
[1] "hr=" "1.6"
D30V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  17P GAIN MUTATED                0                  1                   0
  17P GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  17P GAIN MUTATED                     0                             0
  17P GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  17P GAIN MUTATED                       1                      7
  17P GAIN WILD-TYPE                     0                     21
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  17P GAIN MUTATED                      1                    0
  17P GAIN WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  17P GAIN MUTATED                                       1
  17P GAIN WILD-TYPE                                     1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  17P GAIN MUTATED                                  0
  17P GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  17P GAIN MUTATED                                                0
  17P GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  17P GAIN MUTATED                                 0
  17P GAIN WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  17P GAIN MUTATED                                         0
  17P GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  17P GAIN MUTATED                              0                       0
  17P GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  17P GAIN MUTATED                                  6
  17P GAIN WILD-TYPE                               11
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  17P GAIN MUTATED                                         1
  17P GAIN WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  17P GAIN MUTATED                             14
  17P GAIN WILD-TYPE                           30
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  17P GAIN MUTATED                                         1
  17P GAIN WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  17P GAIN MUTATED                                           1
  17P GAIN WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  17P GAIN MUTATED                                                  1
  17P GAIN WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  17P GAIN MUTATED                                          2
  17P GAIN WILD-TYPE                                        6
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  17P GAIN MUTATED                                                         0
  17P GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  17P GAIN MUTATED                                            0
  17P GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  17P GAIN MUTATED                                                  17
  17P GAIN WILD-TYPE                                                56
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  17P GAIN MUTATED                                                    0
  17P GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  17P GAIN MUTATED                                    0
  17P GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  17P GAIN MUTATED                          1                           0
  17P GAIN WILD-TYPE                        4                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  17P GAIN MUTATED                           0
  17P GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  17P GAIN MUTATED                                   4
  17P GAIN WILD-TYPE                                 3
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  17P GAIN MUTATED                                   1
  17P GAIN WILD-TYPE                                 4
D30V3, multiclass
                                                         clus
vv                                                        17P GAIN MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     1
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          0
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                 7
  HEAD AND NECK - HEAD                                                   1
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  1
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         0
  LOWER ABDOMINAL/PELVIC - PELVIC                                        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          14
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     17
  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                                      4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        17P GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    0
  GYNECOLOGICAL - UTERUS                                                  21
  HEAD AND NECK - HEAD                                                     1
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            30
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       56
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       2
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        3
  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"
D30V4, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    32  29
  17P GAIN WILD-TYPE 107  89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     32   29
  17P GAIN WILD-TYPE  107   89
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               32                107
  MALE                 29                 89
[1] 2 2
[1] FALSE
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    38  23
  17P GAIN WILD-TYPE 141  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     38   23
  17P GAIN WILD-TYPE  141   49
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                38                141
  YES               23                 49
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  17P GAIN MUTATED                             10             0
  17P GAIN WILD-TYPE                           49             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  17P GAIN MUTATED                                                                          0
  17P GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  17P GAIN MUTATED                     21
  17P GAIN WILD-TYPE                   82
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  17P GAIN MUTATED                                                  1
  17P GAIN WILD-TYPE                                                8
                    vv
clus                 MYXOFIBROSARCOMA
  17P GAIN MUTATED                 11
  17P GAIN WILD-TYPE               13
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  17P GAIN MUTATED                                                          9
  17P GAIN WILD-TYPE                                                       19
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  17P GAIN MUTATED                                          0
  17P GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  17P GAIN MUTATED                             0                             0
  17P GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  17P GAIN MUTATED                                            9
  17P GAIN WILD-TYPE                                         12
D30V6, multiclass
                                                                          clus
vv                                                                         17P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           10
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   21
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                       11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              9
                                                                          clus
vv                                                                         17P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             49
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     82
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          8
  MYXOFIBROSARCOMA                                                                         13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 19
  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
  17P GAIN MUTATED    29  19   3  10
  17P GAIN WILD-TYPE 123  50   6  16
D30V7, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               29                123
  R1               19                 50
  R2                3                  6
  RX               10                 16
[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
  17P GAIN MUTATED       3                         3    54
  17P GAIN WILD-TYPE     3                        15   170
D30V8, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    3                  3
  BLACK OR AFRICAN AMERICAN                3                 15
  WHITE                                   54                170
[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"
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  56
  17P GAIN WILD-TYPE   4 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   56
  17P GAIN WILD-TYPE    4  164
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               56                164
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    34  22
  17Q GAIN WILD-TYPE 125  76
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                56                201 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                22                 76 
$`17Q GAIN MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-AB2X TCGA-HB-A5W3 TCGA-LI-A9QH 
       16.18        67.20        34.36        13.28        12.62        17.75 
TCGA-PC-A5DP TCGA-SG-A849 TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX 
       18.08        17.52        54.74        42.84        18.64         0.56 
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A6BF TCGA-DX-A6YV 
       32.71        85.02        10.68        45.99        31.96        50.50 
TCGA-DX-A6YZ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BV 
       86.30        45.14        47.87        38.17        40.77        60.66 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       66.74        77.88       106.55        21.70        20.32        19.89 
TCGA-IE-A6BZ TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT 
       19.89        85.97         3.91        23.38        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MO-A47R TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       35.28        30.31        10.45        13.08        18.08        35.90 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G 
       16.77        18.94        25.35         8.61        13.41        10.72 
TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 
       84.79        22.62         8.58        26.43        35.18        19.17 
TCGA-X9-A971 TCGA-Z4-AAPG 
       27.32        15.98 

$`17Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG 
       36.30        31.53        34.68        75.32        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W 
       14.43        14.07        15.85        40.60        12.07       106.45 
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-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       16.60        37.02        52.11        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX 
      159.29        22.62        11.70         8.28         6.35        20.94 
TCGA-QQ-A8VB TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
      188.15        26.17        41.49        35.08        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV 
       53.49        68.55        88.57        44.91        25.25        14.37 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KX 
       10.32        38.47        36.03        26.56        14.04        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       12.85        45.11        18.54        54.21        33.53        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77        51.02         4.54        14.99        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       50.43        34.88        85.45         9.73        24.26        35.28 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       15.95        37.41        82.68        36.33        28.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z0 
       26.99         3.06        41.00        78.28        16.87        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
      101.23        21.30        34.49        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BR 
       29.49        48.20        20.05         9.34        61.97       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       27.95        40.44        36.69        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S 
       17.79        12.00        15.72        65.98        86.10         9.21 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y 
       50.40        50.89        71.31        49.15        31.13        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
        8.05        67.63        34.88         4.57        33.30         0.72 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
        9.80        80.48        19.53         3.22         1.38        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
       25.22       171.09        13.58         5.92        16.41         1.05 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
      101.26        53.33        62.17       123.78        17.36         5.19 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       22.39        11.57         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD 
       81.01        17.65         1.84        46.82        48.59        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
      130.32       111.98        64.77        10.52         0.72         3.88 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-AB3D TCGA-WK-A8XO 
       22.82        32.75        19.63        13.22        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
        4.80        38.27        65.46        63.35        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       45.34        30.84        20.65        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.56               0.49 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            106.55             188.15 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            24.365             32.750 
[1] "0.6 - 106.5 (24.4)" "0.5 - 188.2 (32.8)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  17Q GAIN MUTATED                0                  2                   0
  17Q GAIN WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  17Q GAIN MUTATED                     0                             0
  17Q GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  17Q GAIN MUTATED                       1                      8
  17Q GAIN WILD-TYPE                     0                     20
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  17Q GAIN MUTATED                      1                    0
  17Q GAIN WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  17Q GAIN MUTATED                                       1
  17Q GAIN WILD-TYPE                                     1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  17Q GAIN MUTATED                                  0
  17Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  17Q GAIN MUTATED                                                0
  17Q GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  17Q GAIN MUTATED                                 0
  17Q GAIN WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  17Q GAIN MUTATED                                         0
  17Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  17Q GAIN MUTATED                              1                       0
  17Q GAIN WILD-TYPE                            3                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  17Q GAIN MUTATED                                  7
  17Q GAIN WILD-TYPE                               10
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  17Q GAIN MUTATED                                         1
  17Q GAIN WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  17Q GAIN MUTATED                             12
  17Q GAIN WILD-TYPE                           32
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  17Q GAIN MUTATED                                         1
  17Q GAIN WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  17Q GAIN MUTATED                                           1
  17Q GAIN WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  17Q GAIN MUTATED                                                  1
  17Q GAIN WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  17Q GAIN MUTATED                                          1
  17Q GAIN WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  17Q GAIN MUTATED                                                         0
  17Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  17Q GAIN MUTATED                                            0
  17Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  17Q GAIN MUTATED                                                  10
  17Q GAIN WILD-TYPE                                                63
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  17Q GAIN MUTATED                                                    0
  17Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  17Q GAIN MUTATED                                    0
  17Q GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  17Q GAIN MUTATED                          1                           1
  17Q GAIN WILD-TYPE                        4                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  17Q GAIN MUTATED                           0
  17Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  17Q GAIN MUTATED                                   4
  17Q GAIN WILD-TYPE                                 3
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  17Q GAIN MUTATED                                   1
  17Q GAIN WILD-TYPE                                 4
D31V3, multiclass
                                                         clus
vv                                                        17Q GAIN MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     2
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          0
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                 8
  HEAD AND NECK - HEAD                                                   1
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  1
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         0
  LOWER ABDOMINAL/PELVIC - PELVIC                                        0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     10
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            1
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        17Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    0
  GYNECOLOGICAL - UTERUS                                                  20
  HEAD AND NECK - HEAD                                                     1
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  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                       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                                        3
  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"
D31V4, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    36  20
  17Q GAIN WILD-TYPE 103  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     36   20
  17Q GAIN WILD-TYPE  103   98
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               36                103
  MALE                 20                 98
[1] 2 2
[1] FALSE
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    36  19
  17Q GAIN WILD-TYPE 143  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     36   19
  17Q GAIN WILD-TYPE  143   53
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                36                143
  YES               19                 53
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  17Q GAIN MUTATED                              6             0
  17Q GAIN WILD-TYPE                           53             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  17Q GAIN MUTATED                                                                          0
  17Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  17Q GAIN MUTATED                     19
  17Q GAIN WILD-TYPE                   84
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  17Q GAIN MUTATED                                                  2
  17Q GAIN WILD-TYPE                                                7
                    vv
clus                 MYXOFIBROSARCOMA
  17Q GAIN MUTATED                 11
  17Q GAIN WILD-TYPE               13
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  17Q GAIN MUTATED                                                          9
  17Q GAIN WILD-TYPE                                                       19
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  17Q GAIN MUTATED                                          0
  17Q GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  17Q GAIN MUTATED                             0                             0
  17Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  17Q GAIN MUTATED                                            9
  17Q GAIN WILD-TYPE                                         12
D31V6, multiclass
                                                                          clus
vv                                                                         17Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            6
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   19
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        2
  MYXOFIBROSARCOMA                                                                       11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              9
                                                                          clus
vv                                                                         17Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             53
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     84
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          7
  MYXOFIBROSARCOMA                                                                         13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 19
  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
  17Q GAIN MUTATED    29  14   3   9
  17Q GAIN WILD-TYPE 123  55   6  17
D31V7, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               29                123
  R1               14                 55
  R2                3                  6
  RX                9                 17
[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
  17Q GAIN MUTATED       3                         2    49
  17Q GAIN WILD-TYPE     3                        16   175
D31V8, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    3                  3
  BLACK OR AFRICAN AMERICAN                2                 16
  WHITE                                   49                175
[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"
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     2  51
  17Q GAIN WILD-TYPE   3 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   51
  17Q GAIN WILD-TYPE    3  169
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               51                169
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    28  24
  18P GAIN WILD-TYPE 131  74
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                52                205 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                24                 74 
$`18P GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2W TCGA-HB-A43Z TCGA-LI-A9QH TCGA-MB-A5Y9 
       34.36        17.95       106.45        37.02        17.75         8.28 
TCGA-PC-A5DM TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HV TCGA-3B-A9I1 
        6.35        50.01        53.49        88.57        14.37        18.64 
TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3UE TCGA-DX-A6B8 
       32.71        33.53         6.28        51.02        34.88        15.95 
TCGA-DX-A6BA TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO 
       82.68        16.87        64.21        61.97        47.87        40.77 
TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2V 
       27.95        60.66         1.15        12.00        86.10       106.55 
TCGA-DX-AB2Z TCGA-FX-A3TO TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IS-A3KA 
       50.40        20.32         0.72        19.53        19.89        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-K1-A6RV TCGA-KD-A5QS TCGA-MO-A47R TCGA-QC-AA9N 
        5.92        16.41         5.19        63.81        10.45        17.65 
TCGA-QQ-A5V9 TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-VT-AB3D TCGA-X6-A7WC 
       46.82        16.77        18.94        22.82        12.46        45.34 
TCGA-X6-A8C3 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-AAPG 
       19.17        27.32        36.43        15.98 

$`18P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        14.43        14.07        15.85        40.60        12.07 
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-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       32.15        16.60        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DP TCGA-QC-A6FX 
       28.21       159.29        22.62        11.70        18.08        20.94 
TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL 
      188.15        17.52        26.17        41.49        35.08        19.69 
TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       68.55        44.91        54.74        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX 
       38.47        36.03        26.56         0.56        14.04        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L4 
       12.85        45.11        18.54        54.21        85.02        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        73.87        68.55        50.43 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       85.45         9.73        45.99        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       46.03        26.47       108.82        59.84        37.58        37.41 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF 
       41.00        78.28        50.50        86.30       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT 
       20.05         9.34        45.14        38.17       150.35        40.44 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L 
       36.69        19.43         6.58        17.79        15.72        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       66.74         9.21        77.88        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       31.13        21.70        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ 
       34.88         4.57        33.30         9.80        80.48         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VF 
        1.38        37.12        25.22       171.09        85.97         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       23.38        16.41        35.28        30.31        25.41         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
       21.73        19.73        14.99        17.98        22.39        11.57 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
        7.36       122.96        37.55        38.63        81.01        13.08 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
        1.84        18.08        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71P 
      111.98        64.77        10.52         0.72         3.88        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-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        84.79        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
        8.58        63.35        26.43        35.90        18.08        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       35.18        20.65        50.86        29.46         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.72               0.49 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            106.55             188.15 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             21.57              31.96 
[1] "0.7 - 106.5 (21.6)" "0.5 - 188.2 (32.0)"
[1] "hr=" "1.5"
D32V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  18P GAIN MUTATED                0                  1                   0
  18P GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  18P GAIN MUTATED                     0                             0
  18P GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  18P GAIN MUTATED                       0                      7
  18P GAIN WILD-TYPE                     1                     21
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  18P GAIN MUTATED                      0                    0
  18P GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  18P GAIN MUTATED                                       0
  18P GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  18P GAIN MUTATED                                  0
  18P GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  18P GAIN MUTATED                                                0
  18P GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  18P GAIN MUTATED                                 3
  18P GAIN WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  18P GAIN MUTATED                                         0
  18P GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  18P GAIN MUTATED                              0                       0
  18P GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  18P GAIN MUTATED                                  5
  18P GAIN WILD-TYPE                               12
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  18P GAIN MUTATED                                         2
  18P GAIN WILD-TYPE                                       3
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  18P GAIN MUTATED                             14
  18P GAIN WILD-TYPE                           30
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  18P GAIN MUTATED                                         0
  18P GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  18P GAIN MUTATED                                           0
  18P GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  18P GAIN MUTATED                                                  1
  18P GAIN WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  18P GAIN MUTATED                                          0
  18P GAIN WILD-TYPE                                        8
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  18P GAIN MUTATED                                                         0
  18P GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  18P GAIN MUTATED                                            0
  18P GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  18P GAIN MUTATED                                                  10
  18P GAIN WILD-TYPE                                                63
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  18P GAIN MUTATED                                                    0
  18P GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  18P GAIN MUTATED                                    0
  18P GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  18P GAIN MUTATED                          2                           2
  18P GAIN WILD-TYPE                        3                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  18P GAIN MUTATED                           0
  18P GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  18P GAIN MUTATED                                   3
  18P GAIN WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  18P GAIN MUTATED                                   2
  18P GAIN WILD-TYPE                                 3
D32V3, multiclass
                                                         clus
vv                                                        18P GAIN 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                                                 7
  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                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                2
  LOWER EXTREMITY - THIGH/KNEE                                          14
  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                     10
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        18P GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  21
  HEAD AND NECK - HEAD                                                     2
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  3
  LOWER EXTREMITY - THIGH/KNEE                                            30
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 8
  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                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        4
  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"
D32V4, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    32  20
  18P GAIN WILD-TYPE 107  98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     32   20
  18P GAIN WILD-TYPE  107   98
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               32                107
  MALE                 20                 98
[1] 2 2
[1] FALSE
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    28  24
  18P GAIN WILD-TYPE 151  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     28   24
  18P GAIN WILD-TYPE  151   48
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                28                151
  YES               24                 48
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  18P GAIN MUTATED                              5             0
  18P GAIN WILD-TYPE                           54             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  18P GAIN MUTATED                                                                          0
  18P GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  18P GAIN MUTATED                     20
  18P GAIN WILD-TYPE                   83
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  18P GAIN MUTATED                                                  2
  18P GAIN WILD-TYPE                                                7
                    vv
clus                 MYXOFIBROSARCOMA
  18P GAIN MUTATED                  7
  18P GAIN WILD-TYPE               17
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  18P GAIN MUTATED                                                         10
  18P GAIN WILD-TYPE                                                       18
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  18P GAIN MUTATED                                          0
  18P GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  18P GAIN MUTATED                             0                             0
  18P GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  18P GAIN MUTATED                                            8
  18P GAIN WILD-TYPE                                         13
D32V6, multiclass
                                                                          clus
vv                                                                         18P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            5
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   20
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        2
  MYXOFIBROSARCOMA                                                                        7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              8
                                                                          clus
vv                                                                         18P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             54
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     83
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          7
  MYXOFIBROSARCOMA                                                                         17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 18
  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
  18P GAIN MUTATED    30  14   2   5
  18P GAIN WILD-TYPE 122  55   7  21
D32V7, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               30                122
  R1               14                 55
  R2                2                  7
  RX                5                 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
  18P GAIN MUTATED       2                         5    43
  18P GAIN WILD-TYPE     4                        13   181
D32V8, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   43                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"
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  47
  18P GAIN WILD-TYPE   5 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   47
  18P GAIN WILD-TYPE    5  173
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               47                173
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    21  16
  18Q GAIN WILD-TYPE 138  82
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                37                220 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                16                 82 
$`18Q GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A8BG TCGA-HB-A43Z TCGA-MB-A5Y9 TCGA-3B-A9HI TCGA-3B-A9HP 
       34.36        17.95        37.02         8.28        50.01        53.49 
TCGA-3B-A9HR TCGA-3B-A9HV TCGA-3B-A9I1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A3U7 
       88.57        14.37        18.64        85.02        33.53        51.02 
TCGA-DX-A3UE TCGA-DX-A6YZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2V 
       34.88        86.30         1.15        12.00        86.10       106.55 
TCGA-DX-AB2Z TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A6BZ 
       50.40        49.15        20.32         0.72        19.53        19.89 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-K1-A6RV TCGA-MO-A47R TCGA-PC-A5DL 
       13.58         5.92        16.41         5.19        10.45        37.55 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-SI-A71O TCGA-VT-AB3D TCGA-WP-A9GB TCGA-X9-A971 
       17.65        46.82        22.82        12.46         8.58        27.32 
TCGA-Z4-AAPF 
       15.95 

$`18Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       84.66        32.15        16.60        12.62        52.11        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH 
       52.27        28.21       159.29        22.62        11.70        17.75 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
        6.35        18.08        20.94       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       41.49        35.08        19.69        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 
       25.25        42.84        10.32        38.47        36.03        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
        0.56        14.04        32.71        68.61        12.85        45.11 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       18.54        54.21        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       33.44        44.68        31.86        35.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J 
       10.68        73.87        68.55        50.43        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       41.00        78.28        50.50        16.87        64.21       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       21.30        34.49        62.20        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.20        20.05         9.34        61.97        45.14        47.87 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       38.17        40.77       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L 
       60.66        19.43         6.58        17.79        15.72        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
       66.74         9.21        77.88        50.89        71.31        31.13 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       21.70        19.89        15.48         8.05        67.63        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK 
        4.57        33.30         9.80        80.48         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-JV-A75J 
       37.12        25.22       171.09        85.97         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
      101.26        53.33        62.17       123.78        17.36        23.38 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       63.81        16.41        35.28        30.31        25.41         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
       21.73        19.73        14.99        17.98        22.39        11.57 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 
        7.36       122.96        38.63        81.01        13.08         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
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-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-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       10.72        11.93         4.80        84.79        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62        63.35        26.43        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       30.84        35.18        19.17        20.65        50.86        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.98 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.72               0.49 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            106.55             188.15 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             20.32              31.91 
[1] "0.7 - 106.5 (20.3)" "0.5 - 188.2 (31.9)"
[1] "hr=" "1.3"
D33V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  18Q GAIN MUTATED                0                  1                   0
  18Q GAIN WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  18Q GAIN MUTATED                     0                             0
  18Q GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  18Q GAIN MUTATED                       0                      7
  18Q GAIN WILD-TYPE                     1                     21
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  18Q GAIN MUTATED                      0                    0
  18Q GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  18Q GAIN MUTATED                                       0
  18Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  18Q GAIN MUTATED                                  0
  18Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  18Q GAIN MUTATED                                                0
  18Q GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  18Q GAIN MUTATED                                 1
  18Q GAIN WILD-TYPE                               9
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  18Q GAIN MUTATED                                         0
  18Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  18Q GAIN MUTATED                              0                       0
  18Q GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  18Q GAIN MUTATED                                  2
  18Q GAIN WILD-TYPE                               15
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  18Q GAIN MUTATED                                         1
  18Q GAIN WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  18Q GAIN MUTATED                              7
  18Q GAIN WILD-TYPE                           37
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  18Q GAIN MUTATED                                         0
  18Q GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  18Q GAIN MUTATED                                           0
  18Q GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  18Q GAIN MUTATED                                                  1
  18Q GAIN WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  18Q GAIN MUTATED                                          0
  18Q GAIN WILD-TYPE                                        8
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  18Q GAIN MUTATED                                                         1
  18Q GAIN WILD-TYPE                                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  18Q GAIN MUTATED                                            0
  18Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  18Q GAIN MUTATED                                                   8
  18Q GAIN WILD-TYPE                                                65
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  18Q GAIN MUTATED                                                    0
  18Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  18Q GAIN MUTATED                                    0
  18Q GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  18Q GAIN MUTATED                          2                           2
  18Q GAIN WILD-TYPE                        3                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  18Q GAIN MUTATED                           0
  18Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  18Q GAIN MUTATED                                   1
  18Q GAIN WILD-TYPE                                 6
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  18Q GAIN MUTATED                                   3
  18Q GAIN WILD-TYPE                                 2
D33V3, multiclass
                                                         clus
vv                                                        18Q GAIN 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                                                 7
  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                                       2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                           7
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      8
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      3
                                                         clus
vv                                                        18Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  21
  HEAD AND NECK - HEAD                                                     2
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                          9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            37
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       65
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       2
  SUPERFICIAL TRUNK - BACK                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        2
[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"
D33V4, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    24  13
  18Q GAIN WILD-TYPE 115 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     24   13
  18Q GAIN WILD-TYPE  115  105
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               24                115
  MALE                 13                105
[1] 2 2
[1] FALSE
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    26  11
  18Q GAIN WILD-TYPE 153  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     26   11
  18Q GAIN WILD-TYPE  153   61
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                26                153
  YES               11                 61
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  18Q GAIN MUTATED                              5             0
  18Q GAIN WILD-TYPE                           54             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  18Q GAIN MUTATED                                                                          0
  18Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  18Q GAIN MUTATED                     17
  18Q GAIN WILD-TYPE                   86
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  18Q GAIN MUTATED                                                  1
  18Q GAIN WILD-TYPE                                                8
                    vv
clus                 MYXOFIBROSARCOMA
  18Q GAIN MUTATED                  4
  18Q GAIN WILD-TYPE               20
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  18Q GAIN MUTATED                                                          3
  18Q GAIN WILD-TYPE                                                       25
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  18Q GAIN MUTATED                                          1
  18Q GAIN WILD-TYPE                                        1
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  18Q GAIN MUTATED                             0                             0
  18Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  18Q GAIN MUTATED                                            6
  18Q GAIN WILD-TYPE                                         15
D33V6, multiclass
                                                                          clus
vv                                                                         18Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            5
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   17
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                        4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                1
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              6
                                                                          clus
vv                                                                         18Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             54
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     86
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          8
  MYXOFIBROSARCOMA                                                                         20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 25
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  1
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               15
[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
  18Q GAIN MUTATED    23   7   1   6
  18Q GAIN WILD-TYPE 129  62   8  20
D33V7, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               23                129
  R1                7                 62
  R2                1                  8
  RX                6                 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
  18Q GAIN MUTATED       1                         4    31
  18Q GAIN WILD-TYPE     5                        14   193
D33V8, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   31                193
[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"
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  35
  18Q GAIN WILD-TYPE   5 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   35
  18Q GAIN WILD-TYPE    5  185
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               35                185
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    47  41
  19P GAIN WILD-TYPE 112  57
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                88                169 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                41                 57 
$`19P GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2X TCGA-DX-AB35 
       34.68        67.20        17.95        14.43        13.28        30.51 
TCGA-DX-AB3A TCGA-LI-A9QH TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-3B-A9HI 
       32.15        17.75        20.94       188.15        17.52        50.01 
TCGA-3B-A9HR TCGA-3B-A9HV TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       88.57        14.37        18.64         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R 
       68.61        12.85        18.54        54.21        85.02        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF 
        6.28         9.70        51.02        14.99        50.43        85.45 
TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ 
       35.28        15.95        41.00        78.28        50.50        86.30 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7ES 
       64.21       101.23        21.30        34.49        62.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT 
        9.34        45.14        47.87        40.77        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q 
       36.69        19.43         1.15        17.79        86.10        66.74 
TCGA-DX-AB2V TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HS-A5NA 
      106.55        21.70        20.32        19.89         4.57         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IW-A3M5 TCGA-JV-A5VF 
       80.48        19.53         3.22        19.89         5.92         1.05 
TCGA-JV-A75J TCGA-K1-A42W TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A8JK TCGA-QQ-A5V9 
        3.91        62.17        16.41        35.28        21.73        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SI-A71O TCGA-SI-A71P TCGA-UE-A6QT 
       18.08        35.90       111.98        22.82        25.35        13.22 
TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WB 
       13.41        12.46        84.79        38.27         8.58        18.08 
TCGA-X6-A7WC TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-AAPG 
       45.34        27.32        36.43        15.98 

$`19P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        34.36        75.32        15.22 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 
       14.07        15.85        40.60        12.07       106.45        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
      101.98        60.00        84.66        16.60        37.02        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       52.11        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-VT-A80J TCGA-WK-A8XT 
       11.70         8.28         6.35        18.08        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       35.08        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 
       25.25        42.84        10.32        38.47        36.03        26.56 
TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       45.11        33.53        66.94         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       49.05        86.83       136.44        33.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       35.77         4.54        10.68        73.87        68.55        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        45.99        24.26        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
      108.82        59.84        37.58        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YX 
       28.96        31.96        36.85        26.99         3.06        16.87 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BK TCGA-DX-A8BN 
       30.35       152.12        29.49        48.20        61.97        38.17 
TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
      150.35        60.66         6.58        12.00        15.72        65.98 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21        77.88        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 
       31.13        15.48         8.05        67.63        34.88        33.30 
TCGA-HS-A5N8 TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA 
        0.72         1.38        37.12        25.22       171.09        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
       85.97        16.41       101.26        53.33       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       23.38         5.19        63.81        30.31        25.41         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
        7.36       122.96        37.55        38.63        81.01        13.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
       17.65         1.84        48.59        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71Q 
       10.52         0.72        16.77        18.94         3.88        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY 
        8.61        19.63        10.72        11.93         4.80        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 
       22.62        63.35        26.43        35.90        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       19.17        20.65        50.86        29.46         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.56               0.49 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            188.15             171.09 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            26.335             31.960 
[1] "0.6 - 188.2 (26.3)" "0.5 - 171.1 (32.0)"
[1] "hr=" "1.4"
D34V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  19P GAIN MUTATED                0                  2                   0
  19P GAIN WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  19P GAIN MUTATED                     0                             0
  19P GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  19P GAIN MUTATED                       1                     10
  19P GAIN WILD-TYPE                     0                     18
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  19P GAIN MUTATED                      1                    0
  19P GAIN WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  19P GAIN MUTATED                                       0
  19P GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  19P GAIN MUTATED                                  0
  19P GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  19P GAIN MUTATED                                                1
  19P GAIN WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  19P GAIN MUTATED                                 3
  19P GAIN WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  19P GAIN MUTATED                                         0
  19P GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  19P GAIN MUTATED                              0                       0
  19P GAIN WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  19P GAIN MUTATED                                  6
  19P GAIN WILD-TYPE                               11
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  19P GAIN MUTATED                                         2
  19P GAIN WILD-TYPE                                       3
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  19P GAIN MUTATED                             17
  19P GAIN WILD-TYPE                           27
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  19P GAIN MUTATED                                         0
  19P GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  19P GAIN MUTATED                                           1
  19P GAIN WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  19P GAIN MUTATED                                                  0
  19P GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  19P GAIN MUTATED                                          2
  19P GAIN WILD-TYPE                                        6
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  19P GAIN MUTATED                                                         0
  19P GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  19P GAIN MUTATED                                            1
  19P GAIN WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  19P GAIN MUTATED                                                  26
  19P GAIN WILD-TYPE                                                47
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  19P GAIN MUTATED                                                    0
  19P GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  19P GAIN MUTATED                                    1
  19P GAIN WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  19P GAIN MUTATED                          2                           2
  19P GAIN WILD-TYPE                        3                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  19P GAIN MUTATED                           0
  19P GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  19P GAIN MUTATED                                   6
  19P GAIN WILD-TYPE                                 1
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  19P GAIN MUTATED                                   3
  19P GAIN WILD-TYPE                                 2
D34V3, multiclass
                                                         clus
vv                                                        19P GAIN MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     2
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          0
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                10
  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                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                2
  LOWER EXTREMITY - THIGH/KNEE                                          17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     26
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      3
                                                         clus
vv                                                        19P GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    0
  GYNECOLOGICAL - UTERUS                                                  18
  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                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  3
  LOWER EXTREMITY - THIGH/KNEE                                            27
  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                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       47
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        2
[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"
D34V4, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   42 46
  19P GAIN WILD-TYPE 97 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     42   46
  19P GAIN WILD-TYPE   97   72
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               42                 97
  MALE                 46                 72
[1] 2 2
[1] FALSE
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    60  26
  19P GAIN WILD-TYPE 119  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     60   26
  19P GAIN WILD-TYPE  119   46
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                60                119
  YES               26                 46
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  19P GAIN MUTATED                             19             0
  19P GAIN WILD-TYPE                           40             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  19P GAIN MUTATED                                                                          0
  19P GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  19P GAIN MUTATED                     29
  19P GAIN WILD-TYPE                   74
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  19P GAIN MUTATED                                                  3
  19P GAIN WILD-TYPE                                                6
                    vv
clus                 MYXOFIBROSARCOMA
  19P GAIN MUTATED                  9
  19P GAIN WILD-TYPE               15
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  19P GAIN MUTATED                                                         17
  19P GAIN WILD-TYPE                                                       11
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  19P GAIN MUTATED                                          0
  19P GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  19P GAIN MUTATED                             0                             0
  19P GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  19P GAIN MUTATED                                           11
  19P GAIN WILD-TYPE                                         10
D34V6, multiclass
                                                                          clus
vv                                                                         19P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           19
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   29
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        3
  MYXOFIBROSARCOMA                                                                        9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             11
                                                                          clus
vv                                                                         19P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             40
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     74
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          6
  MYXOFIBROSARCOMA                                                                         15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               10
[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
  19P GAIN MUTATED    49  22   5  12
  19P GAIN WILD-TYPE 103  47   4  14
D34V7, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               49                103
  R1               22                 47
  R2                5                  4
  RX               12                 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
  19P GAIN MUTATED       2                         4    79
  19P GAIN WILD-TYPE     4                        14   145
D34V8, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   79                145
[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"
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  75
  19P GAIN WILD-TYPE   2 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   75
  19P GAIN WILD-TYPE    2  145
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               75                145
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    38  26
  19Q GAIN WILD-TYPE 121  72
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                64                193 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                26                 72 
$`19Q GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2X TCGA-DX-AB35 
       34.68        67.20        34.36        17.95        13.28        30.51 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-3B-A9HI 
       11.70        17.75        20.94        17.52        26.17        50.01 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HV TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       88.57        44.91        14.37        14.04        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3U9 
       12.85        54.21        85.02        74.66         6.28        14.99 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       85.45        35.28        15.95        41.00        78.28        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL 
       86.30        64.21        21.30        20.05         9.34        45.14 
TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2V 
       27.95        36.69        19.43         1.15        17.79       106.55 
TCGA-FX-A3TO TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-JV-A5VF 
       20.32         9.80        19.53         3.22        19.89         1.05 
TCGA-K1-A6RV TCGA-KD-A5QU TCGA-MB-A8JK TCGA-MJ-A68H TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.19        35.28        21.73        14.99        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WP-A9GB 
       35.90       111.98        13.41        12.46        84.79         8.58 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X9-A971 TCGA-X9-A973 
       45.34        19.17        27.32        36.43 

$`19Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH 
       36.30        31.53        16.18        75.32        15.22        14.43 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 
       14.07        15.85        40.60        12.07       106.45        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
      101.98        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       12.62        52.11        26.93        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-WK-A8XT 
       22.62         8.28         6.35        18.08       188.15        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU 
       35.08        19.69        53.49        68.55        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        38.47        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
        0.56        45.11        18.54        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        73.87        68.55        50.43        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       45.99        24.26        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       59.84        37.58        37.41        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A6Z2 
       31.96        36.85        26.99         3.06        16.87       101.23 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT 
       61.97        47.87        38.17        40.77       150.35        40.44 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
       60.66         6.58        12.00        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
       66.74         9.21        77.88        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        21.70        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV 
       67.63        34.88         4.57        33.30         0.72        80.48 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        37.12        25.22       171.09        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        5.92        16.41         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I 
      123.78        17.36        23.38        63.81        16.41        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
       25.41         0.49        19.73        17.98        22.39        11.57 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       10.45         7.36       122.96        37.55        38.63        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-QQ-A8VD 
       13.08        17.65         1.84        46.82        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-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-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       10.72        11.93         4.80        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        26.43        35.90        18.08        30.84        35.18 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       20.65        50.86        29.46         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.05               0.49 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            111.98             188.15 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             23.95              32.15 
[1] "1.1 - 112.0 (24.0)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  19Q GAIN MUTATED                0                  3                   0
  19Q GAIN WILD-TYPE              1                  4                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  19Q GAIN MUTATED                     0                             0
  19Q GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  19Q GAIN MUTATED                       0                      5
  19Q GAIN WILD-TYPE                     1                     23
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  19Q GAIN MUTATED                      0                    0
  19Q GAIN WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  19Q GAIN MUTATED                                       0
  19Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  19Q GAIN MUTATED                                  0
  19Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  19Q GAIN MUTATED                                                2
  19Q GAIN WILD-TYPE                                              0
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  19Q GAIN MUTATED                                 3
  19Q GAIN WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  19Q GAIN MUTATED                                         0
  19Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  19Q GAIN MUTATED                              0                       1
  19Q GAIN WILD-TYPE                            4                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  19Q GAIN MUTATED                                  5
  19Q GAIN WILD-TYPE                               12
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  19Q GAIN MUTATED                                         1
  19Q GAIN WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  19Q GAIN MUTATED                             15
  19Q GAIN WILD-TYPE                           29
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  19Q GAIN MUTATED                                         0
  19Q GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  19Q GAIN MUTATED                                           1
  19Q GAIN WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  19Q GAIN MUTATED                                                  0
  19Q GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  19Q GAIN MUTATED                                          0
  19Q GAIN WILD-TYPE                                        8
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  19Q GAIN MUTATED                                                         0
  19Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  19Q GAIN MUTATED                                            0
  19Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  19Q GAIN MUTATED                                                  17
  19Q GAIN WILD-TYPE                                                56
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  19Q GAIN MUTATED                                                    0
  19Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  19Q GAIN MUTATED                                    0
  19Q GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  19Q GAIN MUTATED                          2                           1
  19Q GAIN WILD-TYPE                        3                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  19Q GAIN MUTATED                           0
  19Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  19Q GAIN MUTATED                                   5
  19Q GAIN WILD-TYPE                                 2
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  19Q GAIN MUTATED                                   3
  19Q GAIN WILD-TYPE                                 2
D35V3, multiclass
                                                         clus
vv                                                        19Q GAIN MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     3
  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                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                       5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          15
  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                     17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            1
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      3
                                                         clus
vv                                                        19Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       4
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  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                           0
  LOWER ABDOMINAL/PELVIC - PELVIC                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  1
  LOWER EXTREMITY - LOWER LEG/CALF                                        12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       56
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       2
  SUPERFICIAL TRUNK - BACK                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              3
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        2
[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"
D35V4, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    31  33
  19Q GAIN WILD-TYPE 108  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     31   33
  19Q GAIN WILD-TYPE  108   85
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               31                108
  MALE                 33                 85
[1] 2 2
[1] FALSE
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    40  23
  19Q GAIN WILD-TYPE 139  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     40   23
  19Q GAIN WILD-TYPE  139   49
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                40                139
  YES               23                 49
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  19Q GAIN MUTATED                             14             0
  19Q GAIN WILD-TYPE                           45             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  19Q GAIN MUTATED                                                                          0
  19Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  19Q GAIN MUTATED                     20
  19Q GAIN WILD-TYPE                   83
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  19Q GAIN MUTATED                                                  0
  19Q GAIN WILD-TYPE                                                9
                    vv
clus                 MYXOFIBROSARCOMA
  19Q GAIN MUTATED                 11
  19Q GAIN WILD-TYPE               13
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  19Q GAIN MUTATED                                                         11
  19Q GAIN WILD-TYPE                                                       17
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  19Q GAIN MUTATED                                          0
  19Q GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  19Q GAIN MUTATED                             0                             0
  19Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  19Q GAIN MUTATED                                            8
  19Q GAIN WILD-TYPE                                         13
D35V6, multiclass
                                                                          clus
vv                                                                         19Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           14
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   20
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        0
  MYXOFIBROSARCOMA                                                                       11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              8
                                                                          clus
vv                                                                         19Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             45
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     83
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          9
  MYXOFIBROSARCOMA                                                                         13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 17
  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
  19Q GAIN MUTATED    36  18   3   7
  19Q GAIN WILD-TYPE 116  51   6  19
D35V7, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               36                116
  R1               18                 51
  R2                3                  6
  RX                7                 19
[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
  19Q GAIN MUTATED       2                         4    57
  19Q GAIN WILD-TYPE     4                        14   167
D35V8, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   57                167
[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"
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  57
  19Q GAIN WILD-TYPE   4 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   57
  19Q GAIN WILD-TYPE    4  163
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               57                163
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    29  33
  20P GAIN WILD-TYPE 130  65
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                62                195 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                33                 65 
$`20P GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A8BH TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 TCGA-HB-A5W3 
       34.36        14.43       106.45        22.85        30.51        12.62 
TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-VT-A80J 
       52.11        52.27        11.70        17.75         8.28        26.17 
TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       35.08        19.69        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3U7 
       68.61        18.54        54.21        74.66         6.28        51.02 
TCGA-DX-A3UA TCGA-DX-A48P TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6Z0 
       10.68        46.03        36.33         3.06        41.00        64.21 
TCGA-DX-A7EI TCGA-DX-A8BL TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS 
       34.49        45.14        27.95        36.69        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2V TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-IE-A3OV 
       17.79       106.55        31.13        20.32        19.89        80.48 
TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-K1-A42W TCGA-K1-A6RV 
        3.22        25.22        13.58         5.92        62.17         5.19 
TCGA-KD-A5QU TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-RN-AAAQ TCGA-SG-A6Z7 
       35.28         7.36        37.55        13.08        16.77         3.88 
TCGA-SI-A71O TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XX TCGA-X6-A7W8 
       22.82        25.35        13.41        10.72        38.27        26.43 
TCGA-X6-A7WC TCGA-X6-A8C3 
       45.34        19.17 

$`20P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        17.95        14.07        15.85        40.60        12.07 
TCGA-DX-AB2X TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
       13.28       101.98        60.00        84.66        32.15        16.60 
TCGA-HB-A43Z TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-PC-A5DM 
       37.02        26.93        28.21       159.29        22.62         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-WK-A8XT TCGA-3B-A9HI 
       18.08        20.94       188.15        17.52        41.49        50.01 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       53.49        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       14.37        42.84        10.32        38.47        36.03        18.64 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       12.85        45.11        85.02        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       33.44        44.68        31.86        35.77         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U 
       45.99        24.26        35.28        52.77        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE 
       59.84        37.58        15.95        37.41        82.68        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX 
       31.96        36.85        26.99        78.28        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       86.30       101.23        21.30        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM 
       29.49        48.20        20.05         9.34        61.97        47.87 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ 
       38.17        40.77       150.35        40.44        60.66         6.58 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.00        15.72        65.98        86.10        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE 
       77.88        50.40        50.89        71.31        49.15        21.70 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       15.48         8.05        67.63        34.88         4.57        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
        0.72         9.80        19.53         1.38        19.89        37.12 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
      171.09        85.97        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT 
       53.33       123.78        17.36        23.38        63.81        16.41 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       30.31        25.41         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN 
       17.98        22.39        11.57        10.45       122.96        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       81.01        17.65         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90        37.12       130.32       111.98        64.77        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
        0.72        18.94        32.75         8.61        19.63        13.22 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 
       12.46        11.93         4.80        84.79        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
        8.58        63.35        35.90        18.08        30.84        35.18 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       20.65        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.56               0.49 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            106.55             188.15 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            25.285             33.440 
[1] "0.6 - 106.5 (25.3)" "0.5 - 188.2 (33.4)"
[1] "hr=" "2.1"
D36V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  20P GAIN MUTATED                0                  2                   0
  20P GAIN WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  20P GAIN MUTATED                     0                             0
  20P GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  20P GAIN MUTATED                       0                      7
  20P GAIN WILD-TYPE                     1                     21
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  20P GAIN MUTATED                      1                    0
  20P GAIN WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  20P GAIN MUTATED                                       0
  20P GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  20P GAIN MUTATED                                  0
  20P GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  20P GAIN MUTATED                                                0
  20P GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  20P GAIN MUTATED                                 2
  20P GAIN WILD-TYPE                               8
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  20P GAIN MUTATED                                         0
  20P GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  20P GAIN MUTATED                              1                       0
  20P GAIN WILD-TYPE                            3                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  20P GAIN MUTATED                                  5
  20P GAIN WILD-TYPE                               12
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  20P GAIN MUTATED                                         3
  20P GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  20P GAIN MUTATED                             13
  20P GAIN WILD-TYPE                           31
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  20P GAIN MUTATED                                         0
  20P GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  20P GAIN MUTATED                                           0
  20P GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  20P GAIN MUTATED                                                  0
  20P GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  20P GAIN MUTATED                                          3
  20P GAIN WILD-TYPE                                        5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  20P GAIN MUTATED                                                         0
  20P GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  20P GAIN MUTATED                                            1
  20P GAIN WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  20P GAIN MUTATED                                                  17
  20P GAIN WILD-TYPE                                                56
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  20P GAIN MUTATED                                                    0
  20P GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  20P GAIN MUTATED                                    1
  20P GAIN WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  20P GAIN MUTATED                          1                           0
  20P GAIN WILD-TYPE                        4                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  20P GAIN MUTATED                           0
  20P GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  20P GAIN MUTATED                                   4
  20P GAIN WILD-TYPE                                 3
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  20P GAIN MUTATED                                   0
  20P GAIN WILD-TYPE                                 5
D36V3, multiclass
                                                         clus
vv                                                        20P GAIN 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                                                 7
  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                                        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                3
  LOWER EXTREMITY - THIGH/KNEE                                          13
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      0
                                                         clus
vv                                                        20P GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  21
  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                                          8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  2
  LOWER EXTREMITY - THIGH/KNEE                                            31
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       56
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        3
  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"
D36V4, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    27  35
  20P GAIN WILD-TYPE 112  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     27   35
  20P GAIN WILD-TYPE  112   83
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               27                112
  MALE                 35                 83
[1] 2 2
[1] FALSE
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    43  17
  20P GAIN WILD-TYPE 136  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     43   17
  20P GAIN WILD-TYPE  136   55
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                43                136
  YES               17                 55
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  20P GAIN MUTATED                             12             0
  20P GAIN WILD-TYPE                           47             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  20P GAIN MUTATED                                                                          0
  20P GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  20P GAIN MUTATED                     22
  20P GAIN WILD-TYPE                   81
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  20P GAIN MUTATED                                                  3
  20P GAIN WILD-TYPE                                                6
                    vv
clus                 MYXOFIBROSARCOMA
  20P GAIN MUTATED                 10
  20P GAIN WILD-TYPE               14
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  20P GAIN MUTATED                                                          9
  20P GAIN WILD-TYPE                                                       19
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  20P GAIN MUTATED                                          0
  20P GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  20P GAIN MUTATED                             0                             0
  20P GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  20P GAIN MUTATED                                            6
  20P GAIN WILD-TYPE                                         15
D36V6, multiclass
                                                                          clus
vv                                                                         20P GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           12
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   22
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        3
  MYXOFIBROSARCOMA                                                                       10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              6
                                                                          clus
vv                                                                         20P GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             47
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     81
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          6
  MYXOFIBROSARCOMA                                                                         14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               15
[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
  20P GAIN MUTATED    32  18   3   8
  20P GAIN WILD-TYPE 120  51   6  18
D36V7, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               32                120
  R1               18                 51
  R2                3                  6
  RX                8                 18
[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
  20P GAIN MUTATED       2                         2    55
  20P GAIN WILD-TYPE     4                        16   169
D36V8, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                2                 16
  WHITE                                   55                169
[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"
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1  55
  20P GAIN WILD-TYPE   4 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   55
  20P GAIN WILD-TYPE    4  165
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               55                165
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    41  42
  20Q GAIN WILD-TYPE 118  56
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                83                174 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                42                 56 
$`20Q GAIN MUTATED`
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 
       34.36        15.22        14.43        12.07       106.45        22.85 
TCGA-DX-AB35 TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       30.51        12.62        52.27        11.70        17.75         8.28 
TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HR 
       20.94        17.52        26.17        35.08        19.69        88.57 
TCGA-3B-A9HS TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       44.91        26.56         0.56        14.04        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LW 
       12.85        18.54        54.21        74.66         6.28       136.44 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A48P TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6YQ 
       51.02        10.68        46.03        15.95        36.33         3.06 
TCGA-DX-A6YR TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BL 
       41.00        86.30        64.21        21.30        34.49        45.14 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS 
       47.87        40.77        27.95        36.69        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G 
       17.79        66.74       106.55        31.13        20.32        19.89 
TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IS-A3KA 
        4.57        80.48        19.53         3.22       171.09        13.58 
TCGA-IW-A3M5 TCGA-K1-A42W TCGA-K1-A6RV TCGA-KD-A5QS TCGA-LI-A67I TCGA-N1-A6IA 
        5.92        62.17         5.19        63.81        30.31         7.36 
TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VF 
       37.55        13.08        46.82        18.08        37.12       111.98 
TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU 
       16.77         3.88        22.82        25.35         8.61        13.41 
TCGA-VT-A80G TCGA-WK-A8XX TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C3 
       10.72        38.27        26.43        45.34        19.17 

$`20Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2X TCGA-DX-AB32 
       17.95        14.07        15.85        40.60        13.28       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 
       60.00        84.66        32.15        16.60        37.02        52.11 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-PC-A5DM TCGA-PC-A5DP 
       26.93        28.21       159.29        22.62         6.35        18.08 
TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT 
      188.15        41.49        50.01        53.49        68.55        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       18.64        45.11        85.02        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
       95.38        79.17         9.04        49.05        86.83        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       44.68        31.86        35.77         4.54        14.99        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       68.55        50.43        34.88        85.45         9.73        45.99 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        35.28        52.77        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.58        37.41        82.68        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EM 
       26.99        78.28        50.50        16.87       101.23        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ 
       61.97        38.17       150.35        40.44        60.66         6.58 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T 
       12.00        15.72        65.98        86.10         9.21        77.88 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A76Y 
       50.40        50.89        71.31        49.15        21.70        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        8.05        67.63        34.88        33.30         0.72         9.80 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IW-A3M4 TCGA-JV-A5VE 
        1.38        19.89        37.12        25.22        85.97        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91       101.26        53.33       123.78        17.36 
TCGA-K1-A6RU TCGA-KD-A5QT TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       23.38        16.41        35.28        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB 
      122.96        38.63        81.01        17.65         1.84        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 
       35.90       130.32        64.77        10.52         0.72        18.94 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       32.75        19.63        13.22        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       84.79        65.46        22.62         8.58        63.35        35.90 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       18.08        30.84        35.18        20.65        50.86        29.46 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        36.43         4.37        13.38        15.95        15.98 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.56               0.49 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            171.09             188.15 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            25.350             33.485 
[1] "0.6 - 171.1 (25.4)" "0.5 - 188.2 (33.5)"
[1] "hr=" "1.9"
D37V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  20Q GAIN MUTATED                0                  2                   0
  20Q GAIN WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  20Q GAIN MUTATED                     0                             0
  20Q GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  20Q GAIN MUTATED                       0                      7
  20Q GAIN WILD-TYPE                     1                     21
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  20Q GAIN MUTATED                      1                    0
  20Q GAIN WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  20Q GAIN MUTATED                                       0
  20Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  20Q GAIN MUTATED                                  0
  20Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  20Q GAIN MUTATED                                                0
  20Q GAIN WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  20Q GAIN MUTATED                                 2
  20Q GAIN WILD-TYPE                               8
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  20Q GAIN MUTATED                                         0
  20Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  20Q GAIN MUTATED                              2                       0
  20Q GAIN WILD-TYPE                            2                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  20Q GAIN MUTATED                                  7
  20Q GAIN WILD-TYPE                               10
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  20Q GAIN MUTATED                                         3
  20Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  20Q GAIN MUTATED                             21
  20Q GAIN WILD-TYPE                           23
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  20Q GAIN MUTATED                                         0
  20Q GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  20Q GAIN MUTATED                                           0
  20Q GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  20Q GAIN MUTATED                                                  0
  20Q GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  20Q GAIN MUTATED                                          4
  20Q GAIN WILD-TYPE                                        4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  20Q GAIN MUTATED                                                         0
  20Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  20Q GAIN MUTATED                                            1
  20Q GAIN WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  20Q GAIN MUTATED                                                  22
  20Q GAIN WILD-TYPE                                                51
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  20Q GAIN MUTATED                                                    0
  20Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  20Q GAIN MUTATED                                    2
  20Q GAIN WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  20Q GAIN MUTATED                          2                           0
  20Q GAIN WILD-TYPE                        3                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  20Q GAIN MUTATED                           0
  20Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  20Q GAIN MUTATED                                   5
  20Q GAIN WILD-TYPE                                 2
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  20Q GAIN MUTATED                                   1
  20Q GAIN WILD-TYPE                                 4
D37V3, multiclass
                                                         clus
vv                                                        20Q GAIN 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                                                 7
  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                                        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           2
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                3
  LOWER EXTREMITY - THIGH/KNEE                                          21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     22
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        20Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  21
  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                                          8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             2
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  2
  LOWER EXTREMITY - THIGH/KNEE                                            23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       51
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        2
  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"
D37V4, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    35  48
  20Q GAIN WILD-TYPE 104  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     35   48
  20Q GAIN WILD-TYPE  104   70
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               35                104
  MALE                 48                 70
[1] 2 2
[1] FALSE
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    52  29
  20Q GAIN WILD-TYPE 127  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     52   29
  20Q GAIN WILD-TYPE  127   43
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                52                127
  YES               29                 43
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  20Q GAIN MUTATED                             15             0
  20Q GAIN WILD-TYPE                           44             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  20Q GAIN MUTATED                                                                          0
  20Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  20Q GAIN MUTATED                     27
  20Q GAIN WILD-TYPE                   76
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  20Q GAIN MUTATED                                                  3
  20Q GAIN WILD-TYPE                                                6
                    vv
clus                 MYXOFIBROSARCOMA
  20Q GAIN MUTATED                 12
  20Q GAIN WILD-TYPE               12
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  20Q GAIN MUTATED                                                         16
  20Q GAIN WILD-TYPE                                                       12
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  20Q GAIN MUTATED                                          0
  20Q GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  20Q GAIN MUTATED                             0                             0
  20Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  20Q GAIN MUTATED                                           10
  20Q GAIN WILD-TYPE                                         11
D37V6, multiclass
                                                                          clus
vv                                                                         20Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           15
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   27
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        3
  MYXOFIBROSARCOMA                                                                       12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             10
                                                                          clus
vv                                                                         20Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             44
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     76
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          6
  MYXOFIBROSARCOMA                                                                         12
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               11
[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
  20Q GAIN MUTATED    43  24   3  12
  20Q GAIN WILD-TYPE 109  45   6  14
D37V7, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               43                109
  R1               24                 45
  R2                3                  6
  RX               12                 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
  20Q GAIN MUTATED       2                         4    75
  20Q GAIN WILD-TYPE     4                        14   149
D37V8, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   75                149
[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"
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     2  74
  20Q GAIN WILD-TYPE   3 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2   74
  20Q GAIN WILD-TYPE    3  146
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               74                146
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    30  29
  21Q GAIN WILD-TYPE 129  69
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                59                198 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                29                 69 
$`21Q GAIN MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB2W TCGA-DX-AB35 
       34.68        34.36        15.22        14.43       106.45        30.51 
TCGA-HS-A5N9 TCGA-PC-A5DM TCGA-3B-A9HI TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 
       52.11         6.35        50.01        44.91        42.84        18.64 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3U9 
       32.71        12.85        54.21         8.58       136.44        14.99 
TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EM 
       45.99        15.95        41.00        50.50        86.30        62.20 
TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-AB2E TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A3OV 
       27.95        60.66        17.79         4.57         0.72        80.48 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF 
        3.22        19.89        25.22        13.58         5.92         1.05 
TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       23.38        63.81        16.41        30.31        25.41         0.49 
TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 
       14.99         7.36        37.55        13.08        17.65        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU 
       48.59        35.90       111.98        32.75        13.22        13.41 
TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X9-A971 
       38.27        22.62         8.58        26.43        27.32 

$`21Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        31.53        16.18        67.20        75.32        17.95 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 
       14.07        15.85        40.60        12.07        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
      101.98        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       11.70        17.75         8.28        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP 
       17.52        26.17        41.49        35.08        19.69        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY 
       68.55        88.57        54.74        25.25        14.37        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX 
       38.47        36.03        26.56         0.56        14.04        68.61 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       45.11        18.54        85.02        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
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-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
      108.82        59.84        37.58        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YS 
       28.96        31.96        36.85        26.99         3.06        78.28 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN 
       16.87        64.21       101.23        21.30        34.49        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT 
       45.14        47.87        38.17        40.77       150.35        40.44 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G 
       36.69        19.43         6.58         1.15        12.00        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       65.98        86.10        66.74         9.21        77.88       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32        19.89        15.48         8.05        67.63        34.88 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K7 
       33.30         9.80        19.53         1.38        37.12       171.09 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       85.97        16.41         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QU TCGA-MB-A8JK TCGA-MB-A8JL 
      123.78        17.36         5.19        35.28        21.73        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN 
       17.98        22.39        11.57        10.45       122.96        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
       81.01         1.84        18.08        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       10.52         0.72        16.77        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       25.35         8.61        19.63        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
        4.80        84.79        65.46        63.35        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       45.34        30.84        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       29.46        36.43         4.37        13.38        15.95        15.98 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.49               0.56 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            136.44             188.15 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            26.430             32.725 
[1] "0.5 - 136.4 (26.4)" "0.6 - 188.2 (32.7)"
[1] "hr=" "1.7"
D38V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  21Q GAIN MUTATED                0                  4                   0
  21Q GAIN WILD-TYPE              1                  3                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  21Q GAIN MUTATED                     0                             0
  21Q GAIN WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  21Q GAIN MUTATED                       0                      9
  21Q GAIN WILD-TYPE                     1                     19
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  21Q GAIN MUTATED                      2                    0
  21Q GAIN WILD-TYPE                    0                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  21Q GAIN MUTATED                                       0
  21Q GAIN WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  21Q GAIN MUTATED                                  0
  21Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  21Q GAIN MUTATED                                                2
  21Q GAIN WILD-TYPE                                              0
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  21Q GAIN MUTATED                                 1
  21Q GAIN WILD-TYPE                               9
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  21Q GAIN MUTATED                                         0
  21Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  21Q GAIN MUTATED                              0                       1
  21Q GAIN WILD-TYPE                            4                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  21Q GAIN MUTATED                                  4
  21Q GAIN WILD-TYPE                               13
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  21Q GAIN MUTATED                                         1
  21Q GAIN WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  21Q GAIN MUTATED                             10
  21Q GAIN WILD-TYPE                           34
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  21Q GAIN MUTATED                                         2
  21Q GAIN WILD-TYPE                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  21Q GAIN MUTATED                                           0
  21Q GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  21Q GAIN MUTATED                                                  0
  21Q GAIN WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  21Q GAIN MUTATED                                          1
  21Q GAIN WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  21Q GAIN MUTATED                                                         0
  21Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  21Q GAIN MUTATED                                            0
  21Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  21Q GAIN MUTATED                                                  13
  21Q GAIN WILD-TYPE                                                60
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  21Q GAIN MUTATED                                                    0
  21Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  21Q GAIN MUTATED                                    2
  21Q GAIN WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  21Q GAIN MUTATED                          0                           2
  21Q GAIN WILD-TYPE                        5                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  21Q GAIN MUTATED                           0
  21Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  21Q GAIN MUTATED                                   4
  21Q GAIN WILD-TYPE                                 3
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  21Q GAIN MUTATED                                   1
  21Q GAIN WILD-TYPE                                 4
D38V3, multiclass
                                                         clus
vv                                                        21Q GAIN MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     4
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          0
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 9
  HEAD AND NECK - HEAD                                                   2
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  0
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                       4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          10
  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                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     13
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               0
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        21Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       3
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  19
  HEAD AND NECK - HEAD                                                     0
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           0
  LOWER ABDOMINAL/PELVIC - PELVIC                                          9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  1
  LOWER EXTREMITY - LOWER LEG/CALF                                        13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            34
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  2
  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                       60
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        3
  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"
D38V4, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    28  31
  21Q GAIN WILD-TYPE 111  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     28   31
  21Q GAIN WILD-TYPE  111   87
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               28                111
  MALE                 31                 87
[1] 2 2
[1] FALSE
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    41  16
  21Q GAIN WILD-TYPE 138  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     41   16
  21Q GAIN WILD-TYPE  138   56
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                41                138
  YES               16                 56
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  21Q GAIN MUTATED                              8             0
  21Q GAIN WILD-TYPE                           51             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  21Q GAIN MUTATED                                                                          0
  21Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  21Q GAIN MUTATED                     27
  21Q GAIN WILD-TYPE                   76
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  21Q GAIN MUTATED                                                  1
  21Q GAIN WILD-TYPE                                                8
                    vv
clus                 MYXOFIBROSARCOMA
  21Q GAIN MUTATED                  9
  21Q GAIN WILD-TYPE               15
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  21Q GAIN MUTATED                                                          5
  21Q GAIN WILD-TYPE                                                       23
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  21Q GAIN MUTATED                                          0
  21Q GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  21Q GAIN MUTATED                             0                             0
  21Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  21Q GAIN MUTATED                                            9
  21Q GAIN WILD-TYPE                                         12
D38V6, multiclass
                                                                          clus
vv                                                                         21Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            8
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   27
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                        9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              9
                                                                          clus
vv                                                                         21Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             51
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     76
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          8
  MYXOFIBROSARCOMA                                                                         15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 23
  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
  21Q GAIN MUTATED    36  12   2   9
  21Q GAIN WILD-TYPE 116  57   7  17
D38V7, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               36                116
  R1               12                 57
  R2                2                  7
  RX                9                 17
[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
  21Q GAIN MUTATED       2                         8    46
  21Q GAIN WILD-TYPE     4                        10   178
D38V8, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                8                 10
  WHITE                                   46                178
[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"
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  53
  21Q GAIN WILD-TYPE   5 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   53
  21Q GAIN WILD-TYPE    5  167
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               53                167
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    34  24
  22Q GAIN WILD-TYPE 125  74
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                58                199 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                 74 
$`22Q GAIN MUTATED`
TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-HB-A43Z 
       31.53        34.68        12.07       106.45        13.28        37.02 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
       12.62        52.11        52.27        17.75         8.28         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-X6-A8C6 TCGA-3B-A9HT TCGA-DX-A1KU 
       18.08        20.94        17.52        35.08        54.74        14.04 
TCGA-DX-A1KY TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A6BB 
       12.85        10.68        45.99        52.77        46.03        36.33 
TCGA-DX-A6YR TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BS 
       41.00        64.21       101.23        34.49         9.34        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2S 
       40.44        36.69        17.79        12.00        66.74         9.21 
TCGA-DX-AB2V TCGA-HB-A2OT TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-JV-A5VE TCGA-JV-A75J 
      106.55        67.63        19.53         3.22        16.41         3.91 
TCGA-KD-A5QU TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A5V9 
       35.28        14.99         7.36        37.55        13.08        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-VT-A80G 
       48.59        35.90       111.98        18.94        22.82        10.72 
TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A8C3 TCGA-X6-A8C4 
       22.62        35.90        19.17        20.65 

$`22Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        16.18        67.20        34.36        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB30 
       17.95        14.43        14.07        15.85        40.60        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
      101.98        30.51        60.00        84.66        32.15        16.60 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-QQ-A8VB 
       26.93        28.21       159.29        22.62        11.70       188.15 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       26.17        41.49        50.01        19.69        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-A1KW 
       38.47        36.03        18.64        26.56         0.56        32.71 
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       68.61        45.11        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       66.94        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       31.86        35.77        51.02         4.54        14.99        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       68.55        50.43        34.88        85.45         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       35.28        26.47       108.82        59.84        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       37.41        82.68        28.96        31.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF 
        3.06        78.28        50.50        16.87        86.30        21.30 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       61.97        45.14        47.87        38.17        40.77       150.35 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2G TCGA-DX-AB2L 
       60.66        19.43         6.58         1.15        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       86.10        77.88        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       34.88         4.57        33.30         0.72         9.80        80.48 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA 
        1.38        19.89        37.12        25.22       171.09        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       85.97         5.92         1.05       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT 
      123.78        17.36        23.38         5.19        63.81        16.41 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
       30.31        25.41         0.49        21.73        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       22.39        11.57        10.45       122.96        38.63        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG 
       17.65         1.84        18.08        37.12       130.32        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q 
       10.52         0.72        16.77         3.88        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO 
        8.61        19.63        13.22        13.41        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
        4.80        84.79        38.27        65.46         8.58        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 
       26.43        18.08        45.34        30.84        35.18        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              3.22               0.49 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            111.98             188.15 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            25.385             31.860 
[1] "3.2 - 112.0 (25.4)" "0.5 - 188.2 (31.9)"
[1] "hr=" "1.3"
D39V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  22Q GAIN MUTATED                0                  3                   0
  22Q GAIN WILD-TYPE              1                  4                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  22Q GAIN MUTATED                     0                             1
  22Q GAIN WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  22Q GAIN MUTATED                       0                      5
  22Q GAIN WILD-TYPE                     1                     23
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  22Q GAIN MUTATED                      1                    0
  22Q GAIN WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  22Q GAIN MUTATED                                       1
  22Q GAIN WILD-TYPE                                     1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  22Q GAIN MUTATED                                  0
  22Q GAIN WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  22Q GAIN MUTATED                                                1
  22Q GAIN WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  22Q GAIN MUTATED                                 2
  22Q GAIN WILD-TYPE                               8
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  22Q GAIN MUTATED                                         0
  22Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  22Q GAIN MUTATED                              1                       1
  22Q GAIN WILD-TYPE                            3                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  22Q GAIN MUTATED                                  8
  22Q GAIN WILD-TYPE                                9
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  22Q GAIN MUTATED                                         3
  22Q GAIN WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  22Q GAIN MUTATED                             12
  22Q GAIN WILD-TYPE                           32
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  22Q GAIN MUTATED                                         0
  22Q GAIN WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  22Q GAIN MUTATED                                           0
  22Q GAIN WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  22Q GAIN MUTATED                                                  1
  22Q GAIN WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  22Q GAIN MUTATED                                          1
  22Q GAIN WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  22Q GAIN MUTATED                                                         0
  22Q GAIN WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  22Q GAIN MUTATED                                            0
  22Q GAIN WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  22Q GAIN MUTATED                                                  11
  22Q GAIN WILD-TYPE                                                62
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  22Q GAIN MUTATED                                                    0
  22Q GAIN WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  22Q GAIN MUTATED                                    0
  22Q GAIN WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  22Q GAIN MUTATED                          3                           0
  22Q GAIN WILD-TYPE                        2                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  22Q GAIN MUTATED                           0
  22Q GAIN WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  22Q GAIN MUTATED                                   2
  22Q GAIN WILD-TYPE                                 5
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  22Q GAIN MUTATED                                   1
  22Q GAIN WILD-TYPE                                 4
D39V3, multiclass
                                                         clus
vv                                                        22Q GAIN MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     3
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 5
  HEAD AND NECK - HEAD                                                   1
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  1
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                       8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                3
  LOWER EXTREMITY - THIGH/KNEE                                          12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     11
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               3
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        22Q GAIN WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       4
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            1
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  23
  HEAD AND NECK - HEAD                                                     1
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  1
  LOWER EXTREMITY - LOWER LEG/CALF                                         9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  2
  LOWER EXTREMITY - THIGH/KNEE                                            32
  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                       62
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       2
  SUPERFICIAL TRUNK - BACK                                                 2
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    33  25
  22Q GAIN WILD-TYPE 106  93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     33   25
  22Q GAIN WILD-TYPE  106   93
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               33                106
  MALE                 25                 93
[1] 2 2
[1] FALSE
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    32  25
  22Q GAIN WILD-TYPE 147  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     32   25
  22Q GAIN WILD-TYPE  147   47
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                32                147
  YES               25                 47
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  22Q GAIN MUTATED                              6             0
  22Q GAIN WILD-TYPE                           53             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  22Q GAIN MUTATED                                                                          0
  22Q GAIN WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  22Q GAIN MUTATED                     24
  22Q GAIN WILD-TYPE                   79
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  22Q GAIN MUTATED                                                  1
  22Q GAIN WILD-TYPE                                                8
                    vv
clus                 MYXOFIBROSARCOMA
  22Q GAIN MUTATED                  7
  22Q GAIN WILD-TYPE               17
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  22Q GAIN MUTATED                                                         12
  22Q GAIN WILD-TYPE                                                       16
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  22Q GAIN MUTATED                                          0
  22Q GAIN WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  22Q GAIN MUTATED                             0                             0
  22Q GAIN WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  22Q GAIN MUTATED                                            8
  22Q GAIN WILD-TYPE                                         13
D39V6, multiclass
                                                                          clus
vv                                                                         22Q GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            6
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   24
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                        7
  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                                                                         22Q GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             53
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     79
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          8
  MYXOFIBROSARCOMA                                                                         17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 16
  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
  22Q GAIN MUTATED    31  19   3   5
  22Q GAIN WILD-TYPE 121  50   6  21
D39V7, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               31                121
  R1               19                 50
  R2                3                  6
  RX                5                 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
  22Q GAIN MUTATED       1                         5    51
  22Q GAIN WILD-TYPE     5                        13   173
D39V8, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   51                173
[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"
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  50
  22Q GAIN WILD-TYPE   2 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   50
  22Q GAIN WILD-TYPE    2  170
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               50                170
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    49  25
  XP GAIN WILD-TYPE 110  73
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               74               183 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               25                73 
$`XP GAIN MUTATED`
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2H TCGA-DX-AB2W TCGA-DX-AB2X 
       67.20        34.36        17.95        15.85       106.45        13.28 
TCGA-DX-AB30 TCGA-HS-A5N9 TCGA-IW-A3M6 TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
       22.85        52.11        22.62        20.94        17.52        26.17 
TCGA-3B-A9HL TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-DX-A1KX TCGA-DX-A1KZ 
       19.69        25.25        42.84        38.47        68.61        45.11 
TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A3LW TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UE 
        6.28        60.30       136.44        10.68        68.55        34.88 
TCGA-DX-A3UF TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YS TCGA-DX-A6YV 
       85.45        15.95        82.68        36.33        78.28        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM 
       86.30        64.21        62.20         9.34        45.14        47.87 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O 
       27.95        40.44        19.43         1.15        12.00        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-FX-A3TO TCGA-HB-A2OT TCGA-IE-A3OV TCGA-IE-A4EI 
       66.74        77.88        20.32        67.63        80.48        19.53 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-JV-A75J TCGA-K1-A42W TCGA-KD-A5QS 
       19.89        37.12        13.58         3.91        62.17        63.81 
TCGA-LI-A67I TCGA-MJ-A68H TCGA-PC-A5DN TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF 
       30.31        14.99        38.63        18.08        35.90       111.98 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS 
       10.52         3.88        13.41        10.72        12.46        84.79 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X9-A971 
        8.58        26.43        35.90        45.34        35.18        27.32 
TCGA-X9-A973 TCGA-Z4-AAPF 
       36.43        15.95 

$`XP GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        34.68        16.18        75.32        15.22 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB35 
       14.43        14.07        40.60        12.07       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-KF-A41W TCGA-LI-A9QH 
       26.93        52.27        28.21       159.29        11.70        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-X6-A8C6 
        8.28         6.35        18.08       188.15        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       50.01        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       14.37        10.32        36.03        18.64        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        32.71        12.85        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05        86.83        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J 
       51.02         4.54        14.99        73.87        50.43         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF 
      108.82        59.84        37.58        37.41        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6Z2 
       36.85        26.99         3.06        41.00        16.87       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        34.49        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BU 
       20.05        61.97        38.17        40.77       150.35        36.69 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S 
       60.66         6.58        17.79        15.72        65.98         9.21 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      106.55        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV 
       21.70        19.89        15.48         8.05        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ 
       33.30         0.72         9.80         3.22         1.38        25.22 
TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN 
      171.09        85.97         5.92        16.41         1.05       101.26 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT 
       53.33       123.78        17.36        23.38         5.19        16.41 
TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
       35.28        25.41         0.49        21.73        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       81.01        13.08        17.65         1.84        46.82        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
       37.12       130.32        64.77         0.72        16.77        18.94 
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-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
       11.93         4.80        38.27        65.46        22.62        63.35 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       18.08        30.84        19.17        20.65        50.86        29.46 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
        4.37        13.38        15.98 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             1.15              0.49 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           136.44            188.15 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            35.03             30.51 
[1] "1.1 - 136.4 (35.0)" "0.5 - 188.2 (30.5)"
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  XP GAIN MUTATED                0                  2                   0
  XP GAIN WILD-TYPE              1                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  XP GAIN MUTATED                     1                             2
  XP GAIN WILD-TYPE                   0                             0
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  XP GAIN MUTATED                       0                      6
  XP GAIN WILD-TYPE                     1                     22
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  XP GAIN MUTATED                      0                    0
  XP GAIN WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  XP GAIN MUTATED                                       0
  XP GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  XP GAIN MUTATED                                  0
  XP GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  XP GAIN MUTATED                                                1
  XP GAIN WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  XP GAIN MUTATED                                 4
  XP GAIN WILD-TYPE                               6
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  XP GAIN MUTATED                                         1
  XP GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  XP GAIN MUTATED                              1                       0
  XP GAIN WILD-TYPE                            3                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  XP GAIN MUTATED                                  6
  XP GAIN WILD-TYPE                               11
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  XP GAIN MUTATED                                         2
  XP GAIN WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  XP GAIN MUTATED                             17
  XP GAIN WILD-TYPE                           27
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  XP GAIN MUTATED                                         1
  XP GAIN WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  XP GAIN MUTATED                                           1
  XP GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  XP GAIN MUTATED                                                  0
  XP GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  XP GAIN MUTATED                                          1
  XP GAIN WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  XP GAIN MUTATED                                                         0
  XP GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  XP GAIN MUTATED                                            1
  XP GAIN WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  XP GAIN MUTATED                                                  16
  XP GAIN WILD-TYPE                                                57
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  XP GAIN MUTATED                                                    0
  XP GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  XP GAIN MUTATED                                    0                        2
  XP GAIN WILD-TYPE                                  2                        3
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  XP GAIN MUTATED                             1                         0
  XP GAIN WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  XP GAIN MUTATED                                   5
  XP GAIN WILD-TYPE                                 2
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  XP GAIN MUTATED                                   3
  XP GAIN WILD-TYPE                                 2
D40V3, multiclass
                                                         clus
vv                                                        XP GAIN MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    2
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                         2
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                6
  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                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               1
  LOWER EXTREMITY - FOOT/ANKLE                                          1
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                         17
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  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                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              2
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     3
                                                         clus
vv                                                        XP GAIN WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     0
  CHEST - OTHER (PLEASE SPECIFY                                           0
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 22
  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                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 1
  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                                           27
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  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                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      57
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                3
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       2
[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"
D40V4, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   46 28
  XP GAIN WILD-TYPE 93 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     46   28
  XP GAIN WILD-TYPE   93   90
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              46                93
  MALE                28                90
[1] 2 2
[1] FALSE
D40V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    50  24
  XP GAIN WILD-TYPE 129  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     50   24
  XP GAIN WILD-TYPE  129   48
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               50               129
  YES              24                48
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  XP GAIN MUTATED                             11             0
  XP GAIN WILD-TYPE                           48             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  XP GAIN MUTATED                                                                          0
  XP GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  XP GAIN MUTATED                     28
  XP GAIN WILD-TYPE                   75
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  XP GAIN MUTATED                                                  1
  XP GAIN WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  XP GAIN MUTATED                 11
  XP GAIN WILD-TYPE               13
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  XP GAIN MUTATED                                                         12
  XP GAIN WILD-TYPE                                                       16
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  XP GAIN MUTATED                                          1
  XP GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  XP GAIN MUTATED                             0                             0
  XP GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  XP GAIN MUTATED                                           10
  XP GAIN WILD-TYPE                                         11
D40V6, multiclass
                                                                          clus
vv                                                                         XP GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          11
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  28
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                      11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            10
                                                                          clus
vv                                                                         XP GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            48
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    75
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              11
[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
  XP GAIN MUTATED    50  16   1   7
  XP GAIN WILD-TYPE 102  53   8  19
D40V7, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              50               102
  R1              16                53
  R2               1                 8
  RX               7                19
[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
  XP GAIN MUTATED       2                         5    66
  XP GAIN WILD-TYPE     4                        13   158
D40V8, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  66               158
[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"
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     3  67
  XP GAIN WILD-TYPE   2 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3   67
  XP GAIN WILD-TYPE    2  153
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              67               153
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    20  14
  XQ GAIN WILD-TYPE 139  84
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34               223 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               14                84 
$`XQ GAIN MUTATED`
TCGA-DX-AB2H TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-HS-A5N9 TCGA-QC-A6FX 
       15.85       106.45        13.28        22.85        52.11        20.94 
TCGA-SG-A849 TCGA-VT-A80J TCGA-3R-A8YX TCGA-DX-A1KZ TCGA-DX-A23Y TCGA-DX-A240 
       17.52        26.17         0.56        45.11         6.28        60.30 
TCGA-DX-A3LW TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6Z0 TCGA-DX-A8BX TCGA-DX-AB2Q 
      136.44        78.28        50.50        64.21        19.43        66.74 
TCGA-DX-AB2T TCGA-HB-A2OT TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IS-A3KA TCGA-JV-A75J 
       77.88        67.63        80.48        19.53        13.58         3.91 
TCGA-K1-A42W TCGA-LI-A67I TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z7 
       62.17        30.31        18.08       111.98        10.52         3.88 
TCGA-WK-A8XS TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-Z4-AAPF 
       84.79        26.43        45.34        15.95 

$`XQ GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2J 
       75.32        15.22        17.95        14.43        14.07        40.60 
TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       12.07       101.98        30.51        60.00        84.66        32.15 
TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       16.60        37.02        12.62        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
      159.29        22.62        11.70        17.75         8.28         6.35 
TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL 
       18.08       188.15        41.49        35.08        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       53.49        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       14.37        42.84        10.32        38.47        36.03        18.64 
TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 
       26.56        14.04        32.71        68.61        12.85        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       76.41        66.87        27.81         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 
       79.17         9.04        49.05        86.83        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       31.86        35.77        51.02         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       41.00        16.87        86.30       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        61.97        45.14        47.87        38.17        40.77 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ 
      150.35        27.95        40.44        36.69        60.66         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        1.15        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ 
       34.88         4.57        33.30         0.72         9.80         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 
        1.38        19.89        37.12        25.22       171.09        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
        5.92        16.41         1.05       101.26        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        63.81        16.41        35.28 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       25.41         0.49        21.73        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        81.01        13.08        17.65         1.84        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q 
       48.59        35.90        37.12       130.32        64.77         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       16.77        18.94        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       19.63        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
        4.80        38.27        65.46        22.62         8.58        63.35 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       35.90        18.08        30.84        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPG 
       15.98 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.56              0.49 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           136.44            188.15 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            28.37             31.53 
[1] "0.6 - 136.4 (28.4)" "0.5 - 188.2 (31.5)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  XQ GAIN MUTATED                0                  0                   0
  XQ GAIN WILD-TYPE              1                  7                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  XQ GAIN MUTATED                     0                             1
  XQ GAIN WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  XQ GAIN MUTATED                       0                      3
  XQ GAIN WILD-TYPE                     1                     25
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  XQ GAIN MUTATED                      0                    0
  XQ GAIN WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  XQ GAIN MUTATED                                       0
  XQ GAIN WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  XQ GAIN MUTATED                                  0
  XQ GAIN WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  XQ GAIN MUTATED                                                0
  XQ GAIN WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  XQ GAIN MUTATED                                 0
  XQ GAIN WILD-TYPE                              10
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  XQ GAIN MUTATED                                         1
  XQ GAIN WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  XQ GAIN MUTATED                              0                       0
  XQ GAIN WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  XQ GAIN MUTATED                                  4
  XQ GAIN WILD-TYPE                               13
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  XQ GAIN MUTATED                                         1
  XQ GAIN WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  XQ GAIN MUTATED                             11
  XQ GAIN WILD-TYPE                           33
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  XQ GAIN MUTATED                                         0
  XQ GAIN WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  XQ GAIN MUTATED                                           1
  XQ GAIN WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  XQ GAIN MUTATED                                                  0
  XQ GAIN WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  XQ GAIN MUTATED                                          1
  XQ GAIN WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  XQ GAIN MUTATED                                                         0
  XQ GAIN WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  XQ GAIN MUTATED                                            1
  XQ GAIN WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  XQ GAIN MUTATED                                                   7
  XQ GAIN WILD-TYPE                                                66
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  XQ GAIN MUTATED                                                    0
  XQ GAIN WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  XQ GAIN MUTATED                                    0                        1
  XQ GAIN WILD-TYPE                                  2                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  XQ GAIN MUTATED                             0                         0
  XQ GAIN WILD-TYPE                           4                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  XQ GAIN MUTATED                                   0
  XQ GAIN WILD-TYPE                                 7
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  XQ GAIN MUTATED                                   2
  XQ GAIN WILD-TYPE                                 3
D41V3, multiclass
                                                         clus
vv                                                        XQ GAIN 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                                                3
  HEAD AND NECK - HEAD                                                  0
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                       0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               1
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  LOWER EXTREMITY - THIGH/KNEE                                         11
  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                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     7
  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                                     2
                                                         clus
vv                                                        XQ GAIN 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                                        10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 1
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           33
  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                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      66
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             4
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       7
  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"
D41V4, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    20  14
  XQ GAIN WILD-TYPE 119 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     20   14
  XQ GAIN WILD-TYPE  119  104
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              20               119
  MALE                14               104
[1] 2 2
[1] FALSE
D41V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    22  12
  XQ GAIN WILD-TYPE 157  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     22   12
  XQ GAIN WILD-TYPE  157   60
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               22               157
  YES              12                60
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  XQ GAIN MUTATED                              8             0
  XQ GAIN WILD-TYPE                           51             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  XQ GAIN MUTATED                                                                          0
  XQ GAIN WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  XQ GAIN MUTATED                      9
  XQ GAIN WILD-TYPE                   94
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  XQ GAIN MUTATED                                                  1
  XQ GAIN WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  XQ GAIN MUTATED                  7
  XQ GAIN WILD-TYPE               17
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  XQ GAIN MUTATED                                                          5
  XQ GAIN WILD-TYPE                                                       23
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  XQ GAIN MUTATED                                          1
  XQ GAIN WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  XQ GAIN MUTATED                             0                             0
  XQ GAIN WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  XQ GAIN MUTATED                                            3
  XQ GAIN WILD-TYPE                                         18
D41V6, multiclass
                                                                          clus
vv                                                                         XQ GAIN MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           8
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                   9
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             3
                                                                          clus
vv                                                                         XQ GAIN WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            51
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    94
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                23
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 1
  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
  XQ GAIN MUTATED    21   6   2   5
  XQ GAIN WILD-TYPE 131  63   7  21
D41V7, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              21               131
  R1               6                63
  R2               2                 7
  RX               5                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
  XQ GAIN MUTATED       0                         2    30
  XQ GAIN WILD-TYPE     6                        16   194
D41V8, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  30               194
[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"
D41V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3  27
  XQ GAIN WILD-TYPE   2 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   27
  XQ GAIN WILD-TYPE    2  193
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              27               193
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    23   9
  1P LOSS WILD-TYPE 136  89
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               225 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9                89 
$`1P LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-QQ-A8VB TCGA-WK-A8XT 
       31.53        67.20       159.29        22.62       188.15        41.49 
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A6B9 
       68.61        45.11        18.54        10.68        85.45        37.41 
TCGA-DX-A6BA TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BV TCGA-DX-AB2V TCGA-DX-AB2Z 
       82.68        78.28        21.30        60.66       106.55        50.40 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-K1-A42X TCGA-MO-A47R 
       21.70        19.89       171.09        85.97       123.78        10.45 
TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8Y0 TCGA-X6-A7WD 
       18.94        25.35        32.75        19.63        22.62        30.84 
TCGA-X9-A971 TCGA-Z4-AAPG 
       27.32        15.98 

$`1P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        34.68        16.18        34.36        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       17.95        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       84.66        32.15        16.60        37.02        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       26.93        52.27        28.21        11.70        17.75         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 
        6.35        18.08        20.94        17.52        26.17        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       50.01        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       12.85        54.21        85.02        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       51.02         4.54        14.99        73.87        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88         9.73        45.99        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       108.82        59.84        37.58        15.95 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       41.00        50.50        16.87        86.30        64.21       101.23 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       20.05         9.34        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX 
       40.77       150.35        27.95        40.44        36.69        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
        6.58         1.15        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B TCGA-DX-AB3C 
       86.10        66.74         9.21        77.88        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       49.15        31.13        20.32        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       34.88         4.57        33.30         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       19.53         3.22         1.38        19.89        37.12        25.22 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       13.58         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS 
       53.33        62.17        17.36        23.38         5.19        63.81 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       16.41        35.28        30.31        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        22.39        11.57         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
      122.96        37.55        38.63        81.01        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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
        3.88        22.82         8.61        13.22        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       12.46        11.93         4.80        84.79        38.27        65.46 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
        8.58        63.35        26.43        35.90        18.08        45.34 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       35.18        19.17        20.65        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            10.45              0.49 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           188.15            152.12 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            35.08             30.35 
[1] "10.4 - 188.2 (35.1)" "0.5 - 152.1 (30.4)" 
[1] "hr=" "1.9"
D42V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  1P LOSS MUTATED                0                  2                   0
  1P LOSS WILD-TYPE              1                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  1P LOSS MUTATED                     0                             0
  1P LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  1P LOSS MUTATED                       1                      6
  1P LOSS WILD-TYPE                     0                     22
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  1P LOSS MUTATED                      0                    0
  1P LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  1P LOSS MUTATED                                       0
  1P LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  1P LOSS MUTATED                                  0
  1P LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  1P LOSS MUTATED                                                0
  1P LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  1P LOSS MUTATED                                 2
  1P LOSS WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  1P LOSS MUTATED                                         0
  1P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  1P LOSS MUTATED                              1                       0
  1P LOSS WILD-TYPE                            3                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  1P LOSS MUTATED                                  1
  1P LOSS WILD-TYPE                               16
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  1P LOSS MUTATED                                         1
  1P LOSS WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  1P LOSS MUTATED                              5
  1P LOSS WILD-TYPE                           39
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  1P LOSS MUTATED                                         1
  1P LOSS WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  1P LOSS MUTATED                                           0
  1P LOSS WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  1P LOSS MUTATED                                                  2
  1P LOSS WILD-TYPE                                                3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  1P LOSS MUTATED                                          1
  1P LOSS WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  1P LOSS MUTATED                                                         0
  1P LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  1P LOSS MUTATED                                            0
  1P LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  1P LOSS MUTATED                                                   5
  1P LOSS WILD-TYPE                                                68
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  1P LOSS MUTATED                                                    0
  1P LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  1P LOSS MUTATED                                    0                        1
  1P LOSS WILD-TYPE                                  2                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  1P LOSS MUTATED                             1                         0
  1P LOSS WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  1P LOSS MUTATED                                   1
  1P LOSS WILD-TYPE                                 6
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  1P LOSS MUTATED                                   0
  1P LOSS WILD-TYPE                                 5
D42V3, multiclass
                                                         clus
vv                                                        1P LOSS MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    2
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                                6
  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                                          1
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  LOWER EXTREMITY - THIGH/KNEE                                          5
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     5
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     0
                                                         clus
vv                                                        1P LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   0
  GYNECOLOGICAL - UTERUS                                                 22
  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                                         8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            3
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           39
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        3
  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                                                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"
D42V4, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    24   8
  1P LOSS WILD-TYPE 115 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     24    8
  1P LOSS WILD-TYPE  115  110
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              24               115
  MALE                 8               110
[1] 2 2
[1] FALSE
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    23   9
  1P LOSS WILD-TYPE 156  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     23    9
  1P LOSS WILD-TYPE  156   63
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               23               156
  YES               9                63
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  1P LOSS MUTATED                              4             0
  1P LOSS WILD-TYPE                           55             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  1P LOSS MUTATED                                                                          0
  1P LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  1P LOSS MUTATED                     14
  1P LOSS WILD-TYPE                   89
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  1P LOSS MUTATED                                                  4
  1P LOSS WILD-TYPE                                                5
                   vv
clus                MYXOFIBROSARCOMA
  1P LOSS MUTATED                  4
  1P LOSS WILD-TYPE               20
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  1P LOSS MUTATED                                                          3
  1P LOSS WILD-TYPE                                                       25
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  1P LOSS MUTATED                                          0
  1P LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  1P LOSS MUTATED                             0                             1
  1P LOSS WILD-TYPE                           2                             5
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  1P LOSS MUTATED                                            2
  1P LOSS WILD-TYPE                                         19
D42V6, multiclass
                                                                          clus
vv                                                                         1P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           4
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  14
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       4
  MYXOFIBROSARCOMA                                                                       4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             2
                                                                          clus
vv                                                                         1P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            55
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    89
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         5
  MYXOFIBROSARCOMA                                                                        20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                25
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            5
  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
  1P LOSS MUTATED    22   6   0   4
  1P LOSS WILD-TYPE 130  63   9  22
D42V7, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              22               130
  R1               6                63
  R2               0                 9
  RX               4                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
  1P LOSS MUTATED       2                         2    28
  1P LOSS WILD-TYPE     4                        16   196
D42V8, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  28               196
[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"
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  27
  1P LOSS WILD-TYPE   5 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   27
  1P LOSS WILD-TYPE    5  193
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              27               193
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    24  16
  1Q LOSS WILD-TYPE 135  82
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               40               217 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               16                82 
$`1Q LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A8BH TCGA-DX-AB2P TCGA-HB-A5W3 TCGA-IS-A3K8 TCGA-LI-A9QH 
       31.53        14.43        12.07        12.62       159.29        17.75 
TCGA-3B-A9HI TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A2J0 
       50.01        68.61        45.11        18.54        85.02         9.70 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A7EF 
       15.95        82.68        31.96        78.28        16.87        21.30 
TCGA-DX-A8BV TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A2QS 
       60.66        86.10        66.74       106.55        50.40        49.15 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-IS-A3K7 TCGA-K1-A42X TCGA-MB-A8JK TCGA-N1-A6IA 
       19.89         4.57       171.09       123.78        21.73         7.36 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-AA8B 
       81.01        17.65        16.77        18.94        25.35         8.61 
TCGA-SI-AA8C TCGA-WK-A8Y0 TCGA-X6-A7WD TCGA-Z4-AAPG 
       19.63        22.62        30.84        15.98 

$`1Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        34.68        16.18        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W 
       15.22        17.95        14.07        15.85        40.60       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-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       32.15        16.60        37.02        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP 
       28.21        22.62        11.70         8.28         6.35        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       20.94       188.15        17.52        26.17        41.49        35.08 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       19.69        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY 
       18.64        26.56         0.56        14.04        32.71        12.85 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       54.21        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 
       66.87         6.28        27.81        60.30         8.58        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       79.17         9.04        49.05        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB 
       26.47       108.82        59.84        37.58        37.41        36.33 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV 
       28.96        36.85        26.99         3.06        41.00        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN 
       86.30        64.21       101.23        34.49        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       45.14        47.87        38.17        40.77       150.35        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       40.44        36.69        19.43         6.58         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3B 
       12.00        15.72        65.98         9.21        77.88        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO 
       71.31        31.13        21.70        20.32        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       67.63        34.88        33.30         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       19.53         3.22         1.38        19.89        37.12        25.22 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        85.97         5.92        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
      101.26        53.33        62.17        17.36        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       63.81        16.41        35.28        30.31        25.41         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 
      122.96        37.55        38.63        13.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q 
       64.77        10.52         0.72         3.88        22.82        32.75 
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-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       84.79        38.27        65.46         8.58        63.35        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       35.90        18.08        45.34        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             4.57              0.49 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           171.09            188.15 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           23.985            32.150 
[1] "4.6 - 171.1 (24.0)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1"  
D43V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  1Q LOSS MUTATED                0                  1                   0
  1Q LOSS WILD-TYPE              1                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  1Q LOSS MUTATED                     0                             0
  1Q LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  1Q LOSS MUTATED                       0                      5
  1Q LOSS WILD-TYPE                     1                     23
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  1Q LOSS MUTATED                      0                    0
  1Q LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  1Q LOSS MUTATED                                       0
  1Q LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  1Q LOSS MUTATED                                  0
  1Q LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  1Q LOSS MUTATED                                                0
  1Q LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  1Q LOSS MUTATED                                 2
  1Q LOSS WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  1Q LOSS MUTATED                                         0
  1Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  1Q LOSS MUTATED                              0                       0
  1Q LOSS WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  1Q LOSS MUTATED                                  4
  1Q LOSS WILD-TYPE                               13
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  1Q LOSS MUTATED                                         1
  1Q LOSS WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  1Q LOSS MUTATED                              8
  1Q LOSS WILD-TYPE                           36
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  1Q LOSS MUTATED                                         0
  1Q LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  1Q LOSS MUTATED                                           0
  1Q LOSS WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  1Q LOSS MUTATED                                                  1
  1Q LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  1Q LOSS MUTATED                                          2
  1Q LOSS WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  1Q LOSS MUTATED                                                         1
  1Q LOSS WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  1Q LOSS MUTATED                                            0
  1Q LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  1Q LOSS MUTATED                                                   8
  1Q LOSS WILD-TYPE                                                65
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  1Q LOSS MUTATED                                                    0
  1Q LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  1Q LOSS MUTATED                                    1                        1
  1Q LOSS WILD-TYPE                                  1                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  1Q LOSS MUTATED                             1                         0
  1Q LOSS WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  1Q LOSS MUTATED                                   2
  1Q LOSS WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  1Q LOSS MUTATED                                   1
  1Q LOSS WILD-TYPE                                 4
D43V3, multiclass
                                                         clus
vv                                                        1Q LOSS 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                                      4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  LOWER EXTREMITY - THIGH/KNEE                                          8
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     8
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        1Q LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      6
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  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                                         8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           36
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      65
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    23  17
  1Q LOSS WILD-TYPE 116 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     23   17
  1Q LOSS WILD-TYPE  116  101
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              23               116
  MALE                17               101
[1] 2 2
[1] FALSE
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    23  17
  1Q LOSS WILD-TYPE 156  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     23   17
  1Q LOSS WILD-TYPE  156   55
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               23               156
  YES              17                55
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  1Q LOSS MUTATED                              9             0
  1Q LOSS WILD-TYPE                           50             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  1Q LOSS MUTATED                                                                          0
  1Q LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  1Q LOSS MUTATED                     10
  1Q LOSS WILD-TYPE                   93
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  1Q LOSS MUTATED                                                  3
  1Q LOSS WILD-TYPE                                                6
                   vv
clus                MYXOFIBROSARCOMA
  1Q LOSS MUTATED                  4
  1Q LOSS WILD-TYPE               20
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  1Q LOSS MUTATED                                                          9
  1Q LOSS WILD-TYPE                                                       19
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  1Q LOSS MUTATED                                          0
  1Q LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  1Q LOSS MUTATED                             0                             0
  1Q LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  1Q LOSS MUTATED                                            5
  1Q LOSS WILD-TYPE                                         16
D43V6, multiclass
                                                                          clus
vv                                                                         1Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           9
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  10
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       3
  MYXOFIBROSARCOMA                                                                       4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             5
                                                                          clus
vv                                                                         1Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            50
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    93
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         6
  MYXOFIBROSARCOMA                                                                        20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              16
[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
  1Q LOSS MUTATED    22  11   1   5
  1Q LOSS WILD-TYPE 130  58   8  21
D43V7, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              22               130
  R1              11                58
  R2               1                 8
  RX               5                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
  1Q LOSS MUTATED       0                         2    37
  1Q LOSS WILD-TYPE     6                        16   187
D43V8, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  37               187
[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"
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  33
  1Q LOSS WILD-TYPE   4 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   33
  1Q LOSS WILD-TYPE    4  187
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              33               187
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    50  42
  2P LOSS WILD-TYPE 109  56
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               92               165 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               42                56 
$`2P LOSS MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       34.68        67.20        34.36        15.22        17.95        14.43 
TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A43Z 
       15.85        12.07        30.51        84.66        32.15        37.02 
TCGA-HB-A5W3 TCGA-IF-A4AK TCGA-LI-A9QH TCGA-PC-A5DP TCGA-3B-A9HI TCGA-3B-A9HL 
       12.62        52.27        17.75        18.08        50.01        19.69 
TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1L0 
       88.57        25.25        14.37        18.64        26.56        18.54 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC 
       85.02         6.28        44.68        51.02        14.99        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R 
       50.43        34.88        85.45        24.26        46.03        26.47 
TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX 
       59.84        15.95        82.68         3.06        41.00        16.87 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       62.20        30.35        61.97        47.87        38.17        40.77 
TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2T 
       27.95        36.69        60.66         1.15        12.00        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 
      106.55        50.40        20.32        67.63        34.88        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
        0.72         9.80        80.48         3.22        19.89        37.12 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W TCGA-KD-A5QS 
       25.22        13.58        16.41       101.26        62.17        63.81 
TCGA-KD-A5QT TCGA-MJ-A68H TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-SG-A6Z4 
       16.41        14.99        81.01        17.65        46.82        18.94 
TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX 
       22.82         8.61        10.72        12.46        84.79        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB 
       65.46        22.62         8.58        63.35        26.43        18.08 
TCGA-X6-A8C2 TCGA-X9-A971 
       35.18        27.32 

$`2P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A8BP TCGA-DX-AB2J 
       36.30        31.53        16.18        75.32        14.07        40.60 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-FX-A3NK 
      106.45        13.28        22.85       101.98        60.00        16.60 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       52.11        26.93        28.21       159.29        22.62        11.70 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
        8.28         6.35        20.94       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       41.49        35.08        53.49        68.55        44.91        54.74 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU 
       42.84        10.32        38.47        36.03         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
       32.71        68.61        12.85        45.11        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       66.94        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05        86.83       136.44        33.44        31.86        35.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
        4.54        10.68        73.87         9.73        45.99        35.28 
TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       52.77       108.82        37.58        37.41        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ 
       31.96        36.85        26.99        78.28        50.50        86.30 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ 
       64.21       101.23        21.30        34.49       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BR TCGA-DX-A8BT 
       48.20        20.05         9.34        45.14       150.35        40.44 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
       19.43         6.58        17.79        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       66.74         9.21        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3YV TCGA-IE-A4EI 
       21.70        19.89        15.48         8.05         4.57        19.53 
TCGA-IE-A4EK TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
        1.38       171.09        85.97         5.92         1.05         3.91 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QU 
       53.33       123.78        17.36        23.38         5.19        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
       30.31        25.41         0.49        21.73        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       38.63        13.08         1.84        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT 
       16.77         3.88        25.35        32.75        19.63        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD 
       13.41        11.93         4.80        35.90        45.34        30.84 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        20.65        50.86        29.46        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.72              0.49 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           106.55            188.15 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            30.43             31.53 
[1] "0.7 - 106.5 (30.4)" "0.5 - 188.2 (31.5)"
[1] "hr=" "1.4"
D44V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  2P LOSS MUTATED                0                  3                   0
  2P LOSS WILD-TYPE              1                  4                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  2P LOSS MUTATED                     0                             0
  2P LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  2P LOSS MUTATED                       0                     13
  2P LOSS WILD-TYPE                     1                     15
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  2P LOSS MUTATED                      0                    0
  2P LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  2P LOSS MUTATED                                       0
  2P LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  2P LOSS MUTATED                                  0
  2P LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  2P LOSS MUTATED                                                2
  2P LOSS WILD-TYPE                                              0
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  2P LOSS MUTATED                                 2
  2P LOSS WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  2P LOSS MUTATED                                         0
  2P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  2P LOSS MUTATED                              0                       0
  2P LOSS WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  2P LOSS MUTATED                                  5
  2P LOSS WILD-TYPE                               12
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  2P LOSS MUTATED                                         3
  2P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  2P LOSS MUTATED                             21
  2P LOSS WILD-TYPE                           23
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  2P LOSS MUTATED                                         0
  2P LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  2P LOSS MUTATED                                           1
  2P LOSS WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  2P LOSS MUTATED                                                  0
  2P LOSS WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  2P LOSS MUTATED                                          2
  2P LOSS WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  2P LOSS MUTATED                                                         0
  2P LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  2P LOSS MUTATED                                            1
  2P LOSS WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  2P LOSS MUTATED                                                  28
  2P LOSS WILD-TYPE                                                45
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  2P LOSS MUTATED                                                    1
  2P LOSS WILD-TYPE                                                  2
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  2P LOSS MUTATED                                    2                        2
  2P LOSS WILD-TYPE                                  0                        3
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  2P LOSS MUTATED                             2                         0
  2P LOSS WILD-TYPE                           2                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  2P LOSS MUTATED                                   2
  2P LOSS WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  2P LOSS MUTATED                                   2
  2P LOSS WILD-TYPE                                 3
D44V3, multiclass
                                                         clus
vv                                                        2P LOSS MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    3
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                               13
  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                        2
  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                                      5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    28
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              2
  SUPERFICIAL TRUNK - BUTTOCK                                           2
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        2P LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      4
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 15
  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                          0
  LOWER ABDOMINAL/PELVIC - PELVIC                                         8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 2
  LOWER EXTREMITY - THIGH/KNEE                                           23
  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                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      45
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      0
  SUPERFICIAL TRUNK - BACK                                                3
  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"
D44V4, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   55 37
  2P LOSS WILD-TYPE 84 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     55   37
  2P LOSS WILD-TYPE   84   81
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              55                84
  MALE                37                81
[1] 2 2
[1] FALSE
D44V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    61  29
  2P LOSS WILD-TYPE 118  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     61   29
  2P LOSS WILD-TYPE  118   43
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               61               118
  YES              29                43
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  2P LOSS MUTATED                             13             0
  2P LOSS WILD-TYPE                           46             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  2P LOSS MUTATED                                                                          0
  2P LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  2P LOSS MUTATED                     44
  2P LOSS WILD-TYPE                   59
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  2P LOSS MUTATED                                                  1
  2P LOSS WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  2P LOSS MUTATED                 10
  2P LOSS WILD-TYPE               14
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  2P LOSS MUTATED                                                         13
  2P LOSS WILD-TYPE                                                       15
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  2P LOSS MUTATED                                          0
  2P LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  2P LOSS MUTATED                             0                             0
  2P LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  2P LOSS MUTATED                                           11
  2P LOSS WILD-TYPE                                         10
D44V6, multiclass
                                                                          clus
vv                                                                         2P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          13
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  44
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                      10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            11
                                                                          clus
vv                                                                         2P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            46
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    59
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              10
[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
  2P LOSS MUTATED   59 23  3  7
  2P LOSS WILD-TYPE 93 46  6 19
D44V7, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              59                93
  R1              23                46
  R2               3                 6
  RX               7                19
[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
  2P LOSS MUTATED       0                        10    76
  2P LOSS WILD-TYPE     6                         8   148
D44V8, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN              10                 8
  WHITE                                  76               148
[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"
D44V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  83
  2P LOSS WILD-TYPE   5 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   83
  2P LOSS WILD-TYPE    5  137
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              83               137
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    39  36
  2Q LOSS WILD-TYPE 120  62
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               75               182 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               36                62 
$`2Q LOSS MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB2H 
       34.68        16.18        67.20        15.22        14.43        15.85 
TCGA-DX-AB2P TCGA-DX-AB35 TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IF-A4AK 
       12.07        30.51        32.15        37.02        12.62        52.27 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HV TCGA-3B-A9I1 
        6.35        18.08        50.01        19.69        14.37        18.64 
TCGA-3B-A9I3 TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3M1 TCGA-DX-A3U7 
       26.56        18.54        85.02         6.28        44.68        51.02 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 
       14.99        50.43        24.26        26.47        59.84        15.95 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BK 
        3.06        41.00        16.87        62.20        30.35        61.97 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2V 
       45.14        38.17        27.95        36.69         1.15       106.55 
TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA 
       20.32        67.63        34.88         4.57         0.72         9.80 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-JV-A5VE TCGA-JV-A5VF 
        3.22        19.89        37.12        13.58        16.41         1.05 
TCGA-K1-A42W TCGA-KD-A5QS TCGA-KD-A5QT TCGA-MJ-A68H TCGA-QC-A7B5 TCGA-QC-AA9N 
       62.17        63.81        16.41        14.99        13.08        17.65 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-VT-AB3D 
       18.94         3.88        22.82         8.61        10.72        12.46 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       84.79        38.27        22.62         8.58        63.35        26.43 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
       18.08        45.34        35.18 

$`2Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BP 
       36.30        31.53        34.36        75.32        17.95        14.07 
TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       40.60       106.45        13.28        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 
       84.66        16.60        52.11        26.93        28.21       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX TCGA-QQ-A8VB 
       22.62        11.70        17.75         8.28        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        26.17        41.49        35.08        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       88.57        44.91        54.74        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       38.47        36.03         0.56        14.04        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       12.85        45.11        54.21        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA 
      136.44        33.44        31.86        35.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       73.87        68.55        34.88        85.45         9.73        45.99 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
       35.28        52.77        46.03       108.82        37.58        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       82.68        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       78.28        50.50        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       34.49       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX 
       47.87        40.77       150.35        40.44        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        6.58        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
       66.74         9.21        77.88        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        21.70        19.89        15.48         8.05 
TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 
       33.30        80.48        19.53         1.38        25.22       171.09 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       85.97         5.92         3.91       101.26        53.33       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
       17.36        23.38         5.19        35.28        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        21.73        19.73        17.98        22.39        11.57 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       10.45         7.36       122.96        37.55        38.63        81.01 
TCGA-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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
       25.35        32.75        19.63        13.22        13.41        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
        4.80        65.46        35.90        30.84        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.72              0.49 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           106.55            188.15 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           20.320            34.425 
[1] "0.7 - 106.5 (20.3)" "0.5 - 188.2 (34.4)"
[1] "hr=" "2"  
D45V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  2Q LOSS MUTATED                0                  2                   0
  2Q LOSS WILD-TYPE              1                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  2Q LOSS MUTATED                     0                             0
  2Q LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  2Q LOSS MUTATED                       0                     12
  2Q LOSS WILD-TYPE                     1                     16
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  2Q LOSS MUTATED                      1                    0
  2Q LOSS WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  2Q LOSS MUTATED                                       0
  2Q LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  2Q LOSS MUTATED                                  0
  2Q LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  2Q LOSS MUTATED                                                2
  2Q LOSS WILD-TYPE                                              0
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  2Q LOSS MUTATED                                 2
  2Q LOSS WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  2Q LOSS MUTATED                                         0
  2Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  2Q LOSS MUTATED                              0                       0
  2Q LOSS WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  2Q LOSS MUTATED                                  2
  2Q LOSS WILD-TYPE                               15
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  2Q LOSS MUTATED                                         4
  2Q LOSS WILD-TYPE                                       1
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  2Q LOSS MUTATED                             15
  2Q LOSS WILD-TYPE                           29
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  2Q LOSS MUTATED                                         0
  2Q LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  2Q LOSS MUTATED                                           1
  2Q LOSS WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  2Q LOSS MUTATED                                                  0
  2Q LOSS WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  2Q LOSS MUTATED                                          4
  2Q LOSS WILD-TYPE                                        4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  2Q LOSS MUTATED                                                         0
  2Q LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  2Q LOSS MUTATED                                            1
  2Q LOSS WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  2Q LOSS MUTATED                                                  20
  2Q LOSS WILD-TYPE                                                53
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  2Q LOSS MUTATED                                                    0
  2Q LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  2Q LOSS MUTATED                                    2                        1
  2Q LOSS WILD-TYPE                                  0                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  2Q LOSS MUTATED                             2                         0
  2Q LOSS WILD-TYPE                           2                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  2Q LOSS MUTATED                                   2
  2Q LOSS WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  2Q LOSS MUTATED                                   2
  2Q LOSS WILD-TYPE                                 3
D45V3, multiclass
                                                         clus
vv                                                        2Q LOSS 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                                               12
  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                        2
  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                                      2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               4
  LOWER EXTREMITY - THIGH/KNEE                                         15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    20
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           2
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        2Q LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 16
  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                          0
  LOWER ABDOMINAL/PELVIC - PELVIC                                         8
  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                                 1
  LOWER EXTREMITY - THIGH/KNEE                                           29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      53
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      0
  SUPERFICIAL TRUNK - BACK                                                4
  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"
D45V4, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    38  37
  2Q LOSS WILD-TYPE 101  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     38   37
  2Q LOSS WILD-TYPE  101   81
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              38               101
  MALE                37                81
[1] 2 2
[1] FALSE
D45V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    49  24
  2Q LOSS WILD-TYPE 130  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     49   24
  2Q LOSS WILD-TYPE  130   48
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               49               130
  YES              24                48
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  2Q LOSS MUTATED                             13             0
  2Q LOSS WILD-TYPE                           46             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  2Q LOSS MUTATED                                                                          0
  2Q LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  2Q LOSS MUTATED                     33
  2Q LOSS WILD-TYPE                   70
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  2Q LOSS MUTATED                                                  1
  2Q LOSS WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  2Q LOSS MUTATED                  6
  2Q LOSS WILD-TYPE               18
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  2Q LOSS MUTATED                                                         11
  2Q LOSS WILD-TYPE                                                       17
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  2Q LOSS MUTATED                                          0
  2Q LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  2Q LOSS MUTATED                             0                             0
  2Q LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  2Q LOSS MUTATED                                           11
  2Q LOSS WILD-TYPE                                         10
D45V6, multiclass
                                                                          clus
vv                                                                         2Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          13
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  33
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            11
                                                                          clus
vv                                                                         2Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            46
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    70
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              10
[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
  2Q LOSS MUTATED    41  22   3   9
  2Q LOSS WILD-TYPE 111  47   6  17
D45V7, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              41               111
  R1              22                47
  R2               3                 6
  RX               9                17
[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
  2Q LOSS MUTATED       0                         8    62
  2Q LOSS WILD-TYPE     6                        10   162
D45V8, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               8                10
  WHITE                                  62               162
[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"
D45V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  66
  2Q LOSS WILD-TYPE   5 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   66
  2Q LOSS WILD-TYPE    5  154
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              66               154
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    30  26
  3P LOSS WILD-TYPE 129  72
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               56               201 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               26                72 
$`3P LOSS MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2J TCGA-DX-AB2X 
       34.68        34.36        17.95        14.43        40.60        13.28 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-LI-A9QH TCGA-PC-A5DM 
      101.98        30.51        16.60        37.02        17.75         6.35 
TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-3B-A9HL TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
      188.15        41.49        19.69        32.71        68.61        18.54 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 
       74.66         6.28         9.04        49.05        33.44        44.68 
TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YR 
       10.68        35.28        26.47        15.95         3.06        41.00 
TCGA-DX-A7EF TCGA-DX-A7EO TCGA-DX-A8BM TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AATS 
       21.30       152.12        47.87        40.44         6.58         1.15 
TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB3C TCGA-HB-A3YV TCGA-IE-A4EJ TCGA-IE-A6BZ 
       86.10        77.88        71.31         4.57         3.22        19.89 
TCGA-IF-A3RQ TCGA-JV-A5VF TCGA-K1-A42X TCGA-K1-A6RU TCGA-MB-A8JK TCGA-MO-A47R 
       37.12         1.05       123.78        23.38        21.73        10.45 
TCGA-PC-A5DL TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-VT-AB3D TCGA-X6-A7W8 TCGA-X6-A8C4 
       37.55        16.77         3.88        12.46        26.43        20.65 
TCGA-X6-A8C7 TCGA-X9-A971 
       29.46        27.32 

$`3P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        75.32        15.22 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB36 
       14.07        15.85        12.07       106.45        22.85        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       84.66        32.15        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP 
       28.21       159.29        22.62        11.70         8.28        18.08 
TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HP 
       20.94        17.52        26.17        35.08        50.01        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       68.55        88.57        44.91        54.74        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        38.47        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
        0.56        14.04        12.85        45.11        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        66.94         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU 
       60.30         8.58         9.70        95.38        79.17        86.83 
TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
      136.44        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       73.87        68.55        50.43        34.88        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       45.99        24.26        52.77        46.03       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       37.58        37.41        82.68        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       36.85        26.99        78.28        50.50        16.87        86.30 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ 
       64.21       101.23        34.49        62.20        30.35        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN 
       48.20        20.05         9.34        61.97        45.14        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
       40.77       150.35        27.95        36.69        60.66        19.43 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S 
       17.79        12.00        15.72        65.98        66.74         9.21 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
      106.55        50.40        50.89        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32        19.89        15.48         8.05        67.63        34.88 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK 
       33.30         0.72         9.80        80.48        19.53         1.38 
TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       25.22       171.09        13.58        85.97         5.92        16.41 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV 
        3.91       101.26        53.33        62.17        17.36         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       63.81        16.41        35.28        30.31        25.41         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        22.39        11.57         7.36 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
      122.96        38.63        81.01        13.08        17.65         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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-A71O 
      111.98        64.77        10.52         0.72        18.94        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-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       10.72        11.93         4.80        84.79        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62         8.58        63.35        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X9-A973 TCGA-Z4-A8JB 
       30.84        35.18        19.17        50.86        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.05              0.49 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           188.15            171.09 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            26.45             32.15 
[1] "1.1 - 188.2 (26.4)" "0.5 - 171.1 (32.1)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  3P LOSS MUTATED                0                  3                   0
  3P LOSS WILD-TYPE              1                  4                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  3P LOSS MUTATED                     0                             0
  3P LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  3P LOSS MUTATED                       0                      2
  3P LOSS WILD-TYPE                     1                     26
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  3P LOSS MUTATED                      0                    0
  3P LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  3P LOSS MUTATED                                       0
  3P LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  3P LOSS MUTATED                                  0
  3P LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  3P LOSS MUTATED                                                0
  3P LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  3P LOSS MUTATED                                 3
  3P LOSS WILD-TYPE                               7
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  3P LOSS MUTATED                                         0
  3P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  3P LOSS MUTATED                              2                       0
  3P LOSS WILD-TYPE                            2                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  3P LOSS MUTATED                                  4
  3P LOSS WILD-TYPE                               13
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  3P LOSS MUTATED                                         2
  3P LOSS WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  3P LOSS MUTATED                              9
  3P LOSS WILD-TYPE                           35
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  3P LOSS MUTATED                                         0
  3P LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  3P LOSS MUTATED                                           1
  3P LOSS WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  3P LOSS MUTATED                                                  1
  3P LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  3P LOSS MUTATED                                          3
  3P LOSS WILD-TYPE                                        5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  3P LOSS MUTATED                                                         0
  3P LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  3P LOSS MUTATED                                            0
  3P LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  3P LOSS MUTATED                                                  15
  3P LOSS WILD-TYPE                                                58
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  3P LOSS MUTATED                                                    0
  3P LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  3P LOSS MUTATED                                    1                        0
  3P LOSS WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  3P LOSS MUTATED                             3                         1
  3P LOSS WILD-TYPE                           1                         0
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  3P LOSS MUTATED                                   4
  3P LOSS WILD-TYPE                                 3
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  3P LOSS MUTATED                                   2
  3P LOSS WILD-TYPE                                 3
D46V3, multiclass
                                                         clus
vv                                                        3P LOSS MUTATED
  CHEST - BREAST                                                        0
  CHEST - CHEST WALL                                                    3
  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                                       3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          2
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                          9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    15
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                     4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        3P LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      4
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 26
  HEAD AND NECK - HEAD                                                    2
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            2
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      58
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             1
  SUPERFICIAL TRUNK - FLANK                                               0
  UPPER EXTREMITY - SHOULDER/AXILLA                                       3
  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"
D46V4, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    30  26
  3P LOSS WILD-TYPE 109  92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     30   26
  3P LOSS WILD-TYPE  109   92
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              30               109
  MALE                26                92
[1] 2 2
[1] FALSE
D46V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    34  21
  3P LOSS WILD-TYPE 145  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     34   21
  3P LOSS WILD-TYPE  145   51
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               34               145
  YES              21                51
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  3P LOSS MUTATED                             16             0
  3P LOSS WILD-TYPE                           43             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  3P LOSS MUTATED                                                                          0
  3P LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  3P LOSS MUTATED                     11
  3P LOSS WILD-TYPE                   92
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  3P LOSS MUTATED                                                  2
  3P LOSS WILD-TYPE                                                7
                   vv
clus                MYXOFIBROSARCOMA
  3P LOSS MUTATED                  8
  3P LOSS WILD-TYPE               16
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  3P LOSS MUTATED                                                         10
  3P LOSS WILD-TYPE                                                       18
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  3P LOSS MUTATED                                          0
  3P LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  3P LOSS MUTATED                             2                             2
  3P LOSS WILD-TYPE                           0                             4
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  3P LOSS MUTATED                                            5
  3P LOSS WILD-TYPE                                         16
D46V6, multiclass
                                                                          clus
vv                                                                         3P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          16
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  11
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       2
  MYXOFIBROSARCOMA                                                                       8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            2
  SYNOVIAL SARCOMA - MONOPHASIC                                                          2
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             5
                                                                          clus
vv                                                                         3P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            43
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    92
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         7
  MYXOFIBROSARCOMA                                                                        16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              0
  SYNOVIAL SARCOMA - MONOPHASIC                                                            4
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              16
[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
  3P LOSS MUTATED    30  18   3   4
  3P LOSS WILD-TYPE 122  51   6  22
D46V7, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              30               122
  R1              18                51
  R2               3                 6
  RX               4                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
  3P LOSS MUTATED       1                         3    51
  3P LOSS WILD-TYPE     5                        15   173
D46V8, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  51               173
[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"
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  49
  3P LOSS WILD-TYPE   4 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   49
  3P LOSS WILD-TYPE    4  171
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              49               171
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    25  26
  3Q LOSS WILD-TYPE 134  72
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               51               206 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               26                72 
$`3Q LOSS MUTATED`
TCGA-DX-A3M2 TCGA-DX-A8BH TCGA-DX-AB2J TCGA-DX-AB35 TCGA-DX-AB36 TCGA-FX-A3NK 
       34.68        14.43        40.60        30.51        60.00        16.60 
TCGA-HB-A43Z TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-3B-A9HL TCGA-DX-A1KW 
       37.02        17.75         6.35       188.15        19.69        32.71 
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LS 
       68.61        18.54        54.21        74.66         6.28         9.04 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A48R 
       49.05        33.44        44.68        10.68        35.28        26.47 
TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A7EF TCGA-DX-A7EO TCGA-DX-AATS 
       15.95         3.06        41.00        21.30       152.12         1.15 
TCGA-DX-AB3C TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
       71.31         4.57        80.48         3.22        19.89        37.12 
TCGA-JV-A5VF TCGA-K1-A42X TCGA-K1-A6RU TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MJ-A68H 
        1.05       123.78        23.38        25.41        21.73        14.99 
TCGA-MO-A47R TCGA-PC-A5DL TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-VT-A80G TCGA-VT-AB3D 
       10.45        37.55        16.77         3.88        10.72        12.46 
TCGA-X6-A7W8 TCGA-X6-A8C4 TCGA-X9-A971 
       26.43        20.65        27.32 

$`3Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        16.18        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB2W 
       15.22        17.95        14.07        15.85        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A5W3 
       13.28        22.85       101.98        84.66        32.15        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       52.11        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
       11.70         8.28        18.08        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        35.08        50.01        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-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       12.85        45.11        85.02        33.53        66.94         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 
       95.38        79.17        86.83       136.44        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       51.02         4.54        14.99        73.87        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O 
       34.88        85.45         9.73        45.99        24.26        52.77 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       46.03       108.82        59.84        37.58        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS 
       36.33        28.96        31.96        36.85        26.99        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       50.50        16.87        86.30        64.21       101.23        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       62.20        30.35        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       61.97        45.14        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-FX-A2QS 
        9.21        77.88       106.55        50.40        50.89        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI 
       67.63        34.88        33.30         0.72         9.80        19.53 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
        1.38        25.22       171.09        13.58        85.97         5.92 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT 
       16.41         3.91       101.26        53.33        62.17        17.36 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA 
        5.19        63.81        16.41        35.28        30.31         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK 
       19.73        17.98        22.39        11.57         7.36       122.96 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        81.01        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-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P 
       64.77        10.52         0.72        18.94        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
       32.75         8.61        19.63        13.22        13.41        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
        4.80        84.79        38.27        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        35.90        18.08        45.34        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       19.17        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.05              0.49 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           188.15            171.09 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           23.380            33.025 
[1] "1.1 - 188.2 (23.4)" "0.5 - 171.1 (33.0)"
[1] "hr=" "1.8"
D47V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  3Q LOSS MUTATED                0                  2                   0
  3Q LOSS WILD-TYPE              1                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  3Q LOSS MUTATED                     0                             0
  3Q LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  3Q LOSS MUTATED                       0                      2
  3Q LOSS WILD-TYPE                     1                     26
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  3Q LOSS MUTATED                      0                    0
  3Q LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  3Q LOSS MUTATED                                       0
  3Q LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  3Q LOSS MUTATED                                  0
  3Q LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  3Q LOSS MUTATED                                                1
  3Q LOSS WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  3Q LOSS MUTATED                                 3
  3Q LOSS WILD-TYPE                               7
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  3Q LOSS MUTATED                                         0
  3Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  3Q LOSS MUTATED                              1                       0
  3Q LOSS WILD-TYPE                            3                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  3Q LOSS MUTATED                                  3
  3Q LOSS WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  3Q LOSS MUTATED                                         3
  3Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  3Q LOSS MUTATED                              7
  3Q LOSS WILD-TYPE                           37
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  3Q LOSS MUTATED                                         0
  3Q LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  3Q LOSS MUTATED                                           1
  3Q LOSS WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  3Q LOSS MUTATED                                                  1
  3Q LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  3Q LOSS MUTATED                                          2
  3Q LOSS WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  3Q LOSS MUTATED                                                         0
  3Q LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  3Q LOSS MUTATED                                            0
  3Q LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  3Q LOSS MUTATED                                                  16
  3Q LOSS WILD-TYPE                                                57
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  3Q LOSS MUTATED                                                    0
  3Q LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  3Q LOSS MUTATED                                    1                        0
  3Q LOSS WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  3Q LOSS MUTATED                             2                         1
  3Q LOSS WILD-TYPE                           2                         0
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  3Q LOSS MUTATED                                   3
  3Q LOSS WILD-TYPE                                 4
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  3Q LOSS MUTATED                                   2
  3Q LOSS WILD-TYPE                                 3
D47V3, multiclass
                                                         clus
vv                                                        3Q LOSS 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                                                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                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          1
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                          7
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           2
  SUPERFICIAL TRUNK - FLANK                                             1
  UPPER EXTREMITY - SHOULDER/AXILLA                                     3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        3Q LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 26
  HEAD AND NECK - HEAD                                                    2
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            3
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 2
  LOWER EXTREMITY - THIGH/KNEE                                           37
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      57
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             2
  SUPERFICIAL TRUNK - FLANK                                               0
  UPPER EXTREMITY - SHOULDER/AXILLA                                       4
  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"
D47V4, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    23  28
  3Q LOSS WILD-TYPE 116  90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     23   28
  3Q LOSS WILD-TYPE  116   90
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              23               116
  MALE                28                90
[1] 2 2
[1] FALSE
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    32  18
  3Q LOSS WILD-TYPE 147  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     32   18
  3Q LOSS WILD-TYPE  147   54
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               32               147
  YES              18                54
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  3Q LOSS MUTATED                             18             0
  3Q LOSS WILD-TYPE                           41             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  3Q LOSS MUTATED                                                                          0
  3Q LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  3Q LOSS MUTATED                     12
  3Q LOSS WILD-TYPE                   91
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  3Q LOSS MUTATED                                                  2
  3Q LOSS WILD-TYPE                                                7
                   vv
clus                MYXOFIBROSARCOMA
  3Q LOSS MUTATED                  4
  3Q LOSS WILD-TYPE               20
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  3Q LOSS MUTATED                                                          6
  3Q LOSS WILD-TYPE                                                       22
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  3Q LOSS MUTATED                                          0
  3Q LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  3Q LOSS MUTATED                             1                             1
  3Q LOSS WILD-TYPE                           1                             5
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  3Q LOSS MUTATED                                            7
  3Q LOSS WILD-TYPE                                         14
D47V6, multiclass
                                                                          clus
vv                                                                         3Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          18
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  12
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       2
  MYXOFIBROSARCOMA                                                                       4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            1
  SYNOVIAL SARCOMA - MONOPHASIC                                                          1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             7
                                                                          clus
vv                                                                         3Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            41
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    91
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         7
  MYXOFIBROSARCOMA                                                                        20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                22
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              1
  SYNOVIAL SARCOMA - MONOPHASIC                                                            5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              14
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    25  18   3   4
  3Q LOSS WILD-TYPE 127  51   6  22
D47V7, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              25               127
  R1              18                51
  R2               3                 6
  RX               4                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
  3Q LOSS MUTATED       1                         2    47
  3Q LOSS WILD-TYPE     5                        16   177
D47V8, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  47               177
[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"
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  45
  3Q LOSS WILD-TYPE   4 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   45
  3Q LOSS WILD-TYPE    4  175
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              45               175
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    22  19
  4P LOSS WILD-TYPE 137  79
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               41               216 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               19                79 
$`4P LOSS MUTATED`
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB32 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IW-A3M6 
       15.22        17.95       101.98        37.02        12.62        22.62 
TCGA-LI-A9QH TCGA-PC-A5DM TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9I3 
       17.75         6.35        50.01        19.69        88.57        26.56 
TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UD 
        8.58         9.04        49.05        51.02        10.68        50.43 
TCGA-DX-A3UE TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YS TCGA-DX-A7EF 
       34.88        24.26        26.47        15.95        78.28        21.30 
TCGA-DX-A7EI TCGA-DX-A8BK TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E 
       34.49        61.97       150.35        60.66         6.58        17.79 
TCGA-DX-AB2O TCGA-DX-AB2Z TCGA-IE-A4EK TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A42W 
       86.10        50.40         1.38         5.92         1.05        62.17 
TCGA-K1-A42X TCGA-MO-A47R TCGA-QQ-A5V9 TCGA-SI-AA8C TCGA-X2-A95T 
      123.78        10.45        46.82        19.63        63.35 

$`4P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       75.32        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
      106.45        13.28        22.85        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       32.15        16.60        52.11        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
      159.29        11.70         8.28        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        26.17        41.49        35.08        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-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       38.47        36.03        18.64         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        27.81        60.30         9.70        95.38        79.17 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48J 
        4.54        14.99        73.87        68.55        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       45.99        35.28        52.77        46.03       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       37.58        37.41        82.68        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX 
       36.85        26.99         3.06        41.00        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       86.30        64.21       101.23        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM 
       29.49        48.20        20.05         9.34        45.14        47.87 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX 
       38.17        40.77        27.95        40.44        36.69        19.43 
TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S 
        1.15        12.00        15.72        65.98        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       77.88       106.55        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       34.88         4.57        33.30         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
       19.53         3.22        19.89        37.12        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        85.97        16.41         3.91       101.26        53.33 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
       17.36        23.38         5.19        63.81        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       30.31        25.41         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        22.39        11.57         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       38.63        81.01        13.08        17.65         1.84        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        35.90        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       10.52         0.72        16.77        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       25.35        32.75         8.61        13.22        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       12.46        11.93         4.80        84.79        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62         8.58        26.43        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       30.84        35.18        19.17        20.65        50.86        29.46 
TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       27.32        36.43         4.37        13.38        15.95        15.98 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.05              0.49 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           150.35            188.15 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           26.470            31.695 
[1] "1.1 - 150.3 (26.5)" "0.5 - 188.2 (31.7)"
[1] "hr=" "1.3"
D48V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  4P LOSS MUTATED                0                  1                   0
  4P LOSS WILD-TYPE              1                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  4P LOSS MUTATED                     0                             0
  4P LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  4P LOSS MUTATED                       0                      5
  4P LOSS WILD-TYPE                     1                     23
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  4P LOSS MUTATED                      0                    0
  4P LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  4P LOSS MUTATED                                       0
  4P LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  4P LOSS MUTATED                                  0
  4P LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  4P LOSS MUTATED                                                0
  4P LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  4P LOSS MUTATED                                 1
  4P LOSS WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  4P LOSS MUTATED                                         0
  4P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  4P LOSS MUTATED                              1                       0
  4P LOSS WILD-TYPE                            3                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  4P LOSS MUTATED                                  3
  4P LOSS WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  4P LOSS MUTATED                                         2
  4P LOSS WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  4P LOSS MUTATED                              8
  4P LOSS WILD-TYPE                           36
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  4P LOSS MUTATED                                         0
  4P LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  4P LOSS MUTATED                                           0
  4P LOSS WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  4P LOSS MUTATED                                                  1
  4P LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  4P LOSS MUTATED                                          3
  4P LOSS WILD-TYPE                                        5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  4P LOSS MUTATED                                                         0
  4P LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  4P LOSS MUTATED                                            1
  4P LOSS WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  4P LOSS MUTATED                                                   8
  4P LOSS WILD-TYPE                                                65
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  4P LOSS MUTATED                                                    0
  4P LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  4P LOSS MUTATED                                    1                        1
  4P LOSS WILD-TYPE                                  1                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  4P LOSS MUTATED                             1                         0
  4P LOSS WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  4P LOSS MUTATED                                   2
  4P LOSS WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  4P LOSS MUTATED                                   2
  4P LOSS WILD-TYPE                                 3
D48V3, multiclass
                                                         clus
vv                                                        4P LOSS 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                                       1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          1
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                          8
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     8
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        4P LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      6
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  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                                         9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            3
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           36
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      65
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  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"
D48V4, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    24  17
  4P LOSS WILD-TYPE 115 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     24   17
  4P LOSS WILD-TYPE  115  101
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              24               115
  MALE                17               101
[1] 2 2
[1] FALSE
D48V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    23  17
  4P LOSS WILD-TYPE 156  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     23   17
  4P LOSS WILD-TYPE  156   55
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               23               156
  YES              17                55
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  4P LOSS MUTATED                              6             0
  4P LOSS WILD-TYPE                           53             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  4P LOSS MUTATED                                                                          0
  4P LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  4P LOSS MUTATED                     21
  4P LOSS WILD-TYPE                   82
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  4P LOSS MUTATED                                                  1
  4P LOSS WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  4P LOSS MUTATED                  5
  4P LOSS WILD-TYPE               19
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  4P LOSS MUTATED                                                          7
  4P LOSS WILD-TYPE                                                       21
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  4P LOSS MUTATED                                          0
  4P LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  4P LOSS MUTATED                             0                             0
  4P LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  4P LOSS MUTATED                                            1
  4P LOSS WILD-TYPE                                         20
D48V6, multiclass
                                                                          clus
vv                                                                         4P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           6
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  21
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             1
                                                                          clus
vv                                                                         4P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            53
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    82
  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)                                              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
  4P LOSS MUTATED    30   9   2   0
  4P LOSS WILD-TYPE 122  60   7  26
D48V7, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              30               122
  R1               9                60
  R2               2                 7
  RX               0                26
[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
  4P LOSS MUTATED       2                         4    35
  4P LOSS WILD-TYPE     4                        14   189
D48V8, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  35               189
[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"
D48V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     0  33
  4P LOSS WILD-TYPE   5 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0   33
  4P LOSS WILD-TYPE    5  187
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              33               187
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    30  20
  4Q LOSS WILD-TYPE 129  78
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               50               207 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               20                78 
$`4Q LOSS MUTATED`
TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB32 TCGA-HB-A43Z TCGA-IE-A4EH TCGA-IW-A3M6 
       34.36        17.95       101.98        37.02        26.93        22.62 
TCGA-KF-A41W TCGA-PC-A5DM TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9I3 
       11.70         6.35        50.01        19.69        88.57        26.56 
TCGA-3R-A8YX TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U7 
        0.56        74.66         8.58         9.04        49.05        51.02 
TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6YQ 
       10.68        50.43        24.26        26.47        82.68         3.06 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BK TCGA-DX-A8BM 
       78.28        16.87        21.30        34.49        61.97        47.87 
TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2O 
       38.17       150.35        60.66         6.58        17.79        86.10 
TCGA-DX-AB2Z TCGA-HS-A5N8 TCGA-IE-A4EK TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A42W 
       50.40         0.72         1.38         5.92         1.05        62.17 
TCGA-K1-A6RV TCGA-MO-A47R TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-SI-AA8C TCGA-WK-A8XS 
        5.19        10.45        17.65        46.82        19.63        84.79 
TCGA-X6-A7WD TCGA-X6-A8C4 
       30.84        20.65 

$`4Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
      106.45        13.28        22.85        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K6 
       32.15        16.60        12.62        52.11        52.27        28.21 
TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
      159.29        17.75         8.28        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        26.17        41.49        35.08        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-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       38.47        36.03        18.64        14.04        32.71        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        45.11        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       66.94         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW 
       60.30         9.70        95.38        79.17        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       33.44        44.68        31.86        35.77         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       73.87        68.55        34.88        85.45         9.73        45.99 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       35.28        52.77        46.03       108.82        59.84        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       15.95        37.41        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       26.99        41.00        50.50        86.30        64.21       101.23 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
        9.34        45.14        40.77        27.95        40.44        36.69 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q 
       19.43         1.15        12.00        15.72        65.98        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21        77.88       106.55        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV 
       67.63        34.88         4.57        33.30         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
       19.53         3.22        19.89        37.12        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        85.97        16.41         3.91       101.26        53.33 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
      123.78        17.36        23.38        63.81        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       30.31        25.41         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        22.39        11.57         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       38.63        81.01        13.08         1.84        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90        37.12       130.32       111.98        64.77        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        16.77        18.94         3.88        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D 
       32.75         8.61        13.22        13.41        10.72        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       11.93         4.80        38.27        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
       63.35        26.43        35.90        18.08        45.34        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.56              0.49 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           150.35            188.15 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           26.515            31.960 
[1] "0.6 - 150.3 (26.5)" "0.5 - 188.2 (32.0)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  4Q LOSS MUTATED                0                  2                   0
  4Q LOSS WILD-TYPE              1                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  4Q LOSS MUTATED                     0                             0
  4Q LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  4Q LOSS MUTATED                       0                      6
  4Q LOSS WILD-TYPE                     1                     22
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  4Q LOSS MUTATED                      0                    0
  4Q LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  4Q LOSS MUTATED                                       0
  4Q LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  4Q LOSS MUTATED                                  0
  4Q LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  4Q LOSS MUTATED                                                0
  4Q LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  4Q LOSS MUTATED                                 2
  4Q LOSS WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  4Q LOSS MUTATED                                         0
  4Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  4Q LOSS MUTATED                              1                       0
  4Q LOSS WILD-TYPE                            3                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  4Q LOSS MUTATED                                  4
  4Q LOSS WILD-TYPE                               13
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  4Q LOSS MUTATED                                         3
  4Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  4Q LOSS MUTATED                             12
  4Q LOSS WILD-TYPE                           32
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  4Q LOSS MUTATED                                         0
  4Q LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  4Q LOSS MUTATED                                           1
  4Q LOSS WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  4Q LOSS MUTATED                                                  1
  4Q LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  4Q LOSS MUTATED                                          2
  4Q LOSS WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  4Q LOSS MUTATED                                                         0
  4Q LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  4Q LOSS MUTATED                                            1
  4Q LOSS WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  4Q LOSS MUTATED                                                  10
  4Q LOSS WILD-TYPE                                                63
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  4Q LOSS MUTATED                                                    0
  4Q LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  4Q LOSS MUTATED                                    0                        0
  4Q LOSS WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  4Q LOSS MUTATED                             2                         0
  4Q LOSS WILD-TYPE                           2                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  4Q LOSS MUTATED                                   1
  4Q LOSS WILD-TYPE                                 6
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  4Q LOSS MUTATED                                   2
  4Q LOSS WILD-TYPE                                 3
D49V3, multiclass
                                                         clus
vv                                                        4Q LOSS 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                                                6
  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                                          1
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    10
  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                                     1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        4Q LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 22
  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                                         8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            3
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 2
  LOWER EXTREMITY - THIGH/KNEE                                           32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      63
  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                                       6
  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"
D49V4, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    32  18
  4Q LOSS WILD-TYPE 107 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     32   18
  4Q LOSS WILD-TYPE  107  100
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              32               107
  MALE                18               100
[1] 2 2
[1] FALSE
D49V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    30  19
  4Q LOSS WILD-TYPE 149  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     30   19
  4Q LOSS WILD-TYPE  149   53
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               30               149
  YES              19                53
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  4Q LOSS MUTATED                              8             0
  4Q LOSS WILD-TYPE                           51             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  4Q LOSS MUTATED                                                                          0
  4Q LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  4Q LOSS MUTATED                     23
  4Q LOSS WILD-TYPE                   80
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  4Q LOSS MUTATED                                                  1
  4Q LOSS WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  4Q LOSS MUTATED                  8
  4Q LOSS WILD-TYPE               16
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  4Q LOSS MUTATED                                                          7
  4Q LOSS WILD-TYPE                                                       21
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  4Q LOSS MUTATED                                          0
  4Q LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  4Q LOSS MUTATED                             0                             0
  4Q LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  4Q LOSS MUTATED                                            3
  4Q LOSS WILD-TYPE                                         18
D49V6, multiclass
                                                                          clus
vv                                                                         4Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           8
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  23
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             3
                                                                          clus
vv                                                                         4Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            51
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    80
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                21
  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
  4Q LOSS MUTATED    32  13   3   2
  4Q LOSS WILD-TYPE 120  56   6  24
D49V7, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              32               120
  R1              13                56
  R2               3                 6
  RX               2                24
[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
  4Q LOSS MUTATED       2                         4    40
  4Q LOSS WILD-TYPE     4                        14   184
D49V8, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  40               184
[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"
D49V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     0  42
  4Q LOSS WILD-TYPE   5 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      0   42
  4Q LOSS WILD-TYPE    5  178
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              42               178
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    11  12
  5P LOSS WILD-TYPE 148  86
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               23               234 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12                86 
$`5P LOSS MUTATED`
TCGA-DX-A8BG TCGA-X6-A8C6 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A23R 
       17.95        35.08         0.56        32.71        45.11        74.66 
TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A6YQ TCGA-DX-A6Z0 TCGA-DX-A8BJ 
       49.05        44.68        10.68         3.06        64.21         9.34 
TCGA-DX-A8BO TCGA-IS-A3K7 TCGA-K1-A42X TCGA-K1-A6RU TCGA-KD-A5QU TCGA-MB-A8JL 
       40.77       171.09       123.78        23.38        35.28        19.73 
TCGA-QQ-A5VB TCGA-WK-A8Y0 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-Z4-AAPF 
       48.59        22.62        19.17        20.65        15.95 

$`5P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J 
       75.32        15.22        14.43        14.07        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       12.07       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       52.11        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX 
       11.70        17.75         8.28         6.35        18.08        20.94 
TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL 
      188.15        17.52        26.17        41.49        50.01        19.69 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       53.49        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       14.37        42.84        10.32        38.47        36.03        18.64 
TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       26.56        14.04        68.61        12.85        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       85.02        33.53        66.94         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 
       79.17         9.04        86.83       136.44        33.44        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77        51.02         4.54        14.99        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       50.43        34.88        85.45         9.73        45.99        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       35.28        52.77        46.03        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       37.58        15.95        37.41        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       31.96        36.85        26.99        41.00        78.28        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM 
       16.87        86.30       101.23        21.30        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       30.35       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       45.14        47.87        38.17       150.35        27.95        40.44 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       36.69        60.66        19.43         6.58         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.00        15.72        65.98        86.10        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       77.88       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       67.63        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
       25.22        13.58        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV 
        3.91       101.26        53.33        62.17        17.36         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       63.81        16.41        30.31        25.41         0.49        21.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
      122.96        37.55        38.63        81.01        13.08        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
        1.84        46.82        18.08        35.90        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      111.98        64.77        10.52         0.72        16.77        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        3.88        22.82        25.35        32.75         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22        13.41        10.72        12.46        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       84.79        38.27        65.46         8.58        63.35        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 
       35.90        18.08        45.34        30.84        35.18        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPG 
       29.46        27.32        36.43         4.37        13.38        15.98 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.56              0.49 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           171.09            188.15 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           32.710            30.985 
[1] "0.6 - 171.1 (32.7)" "0.5 - 188.2 (31.0)"
[1] "hr=" "1.5"
D50V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  5P LOSS MUTATED                1                  2                   0
  5P LOSS WILD-TYPE              0                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  5P LOSS MUTATED                     0                             0
  5P LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  5P LOSS MUTATED                       0                      3
  5P LOSS WILD-TYPE                     1                     25
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  5P LOSS MUTATED                      0                    0
  5P LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  5P LOSS MUTATED                                       0
  5P LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  5P LOSS MUTATED                                  0
  5P LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  5P LOSS MUTATED                                                0
  5P LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  5P LOSS MUTATED                                 0
  5P LOSS WILD-TYPE                              10
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  5P LOSS MUTATED                                         0
  5P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  5P LOSS MUTATED                              1                       1
  5P LOSS WILD-TYPE                            3                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  5P LOSS MUTATED                                  3
  5P LOSS WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  5P LOSS MUTATED                                         1
  5P LOSS WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  5P LOSS MUTATED                              4
  5P LOSS WILD-TYPE                           40
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  5P LOSS MUTATED                                         0
  5P LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  5P LOSS MUTATED                                           0
  5P LOSS WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  5P LOSS MUTATED                                                  0
  5P LOSS WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  5P LOSS MUTATED                                          0
  5P LOSS WILD-TYPE                                        8
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  5P LOSS MUTATED                                                         0
  5P LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  5P LOSS MUTATED                                            0
  5P LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  5P LOSS MUTATED                                                   5
  5P LOSS WILD-TYPE                                                68
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  5P LOSS MUTATED                                                    0
  5P LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  5P LOSS MUTATED                                    0                        0
  5P LOSS WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  5P LOSS MUTATED                             0                         0
  5P LOSS WILD-TYPE                           4                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  5P LOSS MUTATED                                   0
  5P LOSS WILD-TYPE                                 7
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  5P LOSS MUTATED                                   2
  5P LOSS WILD-TYPE                                 3
D50V3, multiclass
                                                         clus
vv                                                        5P LOSS MUTATED
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    2
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                3
  HEAD AND NECK - HEAD                                                  0
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                       0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          1
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  LOWER EXTREMITY - THIGH/KNEE                                          4
  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                     5
  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                                     2
                                                         clus
vv                                                        5P LOSS WILD-TYPE
  CHEST - BREAST                                                          0
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 25
  HEAD AND NECK - HEAD                                                    2
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            3
  LOWER EXTREMITY - GROIN                                                 1
  LOWER EXTREMITY - LOWER LEG/CALF                                       14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           40
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                8
  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                                             4
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       7
  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"
D50V4, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    16   7
  5P LOSS WILD-TYPE 123 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     16    7
  5P LOSS WILD-TYPE  123  111
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              16               123
  MALE                 7               111
[1] 2 2
[1] FALSE
D50V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    14   9
  5P LOSS WILD-TYPE 165  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     14    9
  5P LOSS WILD-TYPE  165   63
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               14               165
  YES               9                63
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  5P LOSS MUTATED                              6             0
  5P LOSS WILD-TYPE                           53             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  5P LOSS MUTATED                                                                          0
  5P LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  5P LOSS MUTATED                      6
  5P LOSS WILD-TYPE                   97
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  5P LOSS MUTATED                                                  0
  5P LOSS WILD-TYPE                                                9
                   vv
clus                MYXOFIBROSARCOMA
  5P LOSS MUTATED                  6
  5P LOSS WILD-TYPE               18
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  5P LOSS MUTATED                                                          2
  5P LOSS WILD-TYPE                                                       26
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  5P LOSS MUTATED                                          1
  5P LOSS WILD-TYPE                                        1
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  5P LOSS MUTATED                             0                             0
  5P LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  5P LOSS MUTATED                                            2
  5P LOSS WILD-TYPE                                         19
D50V6, multiclass
                                                                          clus
vv                                                                         5P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           6
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                   6
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       0
  MYXOFIBROSARCOMA                                                                       6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               2
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               1
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             2
                                                                          clus
vv                                                                         5P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            53
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    97
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         9
  MYXOFIBROSARCOMA                                                                        18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                26
  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
  5P LOSS MUTATED    11  10   2   0
  5P LOSS WILD-TYPE 141  59   7  26
D50V7, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              11               141
  R1              10                59
  R2               2                 7
  RX               0                26
[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
  5P LOSS MUTATED       1                         0    20
  5P LOSS WILD-TYPE     5                        18   204
D50V8, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                18
  WHITE                                  20               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"
D50V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  17
  5P LOSS WILD-TYPE   5 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   17
  5P LOSS WILD-TYPE    5  203
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              17               203
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    19  15
  5Q LOSS WILD-TYPE 140  83
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               34               223 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               15                83 
$`5Q LOSS MUTATED`
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-IE-A4EH TCGA-LI-A9QH TCGA-X6-A8C6 TCGA-3R-A8YX 
       15.22        17.95        26.93        17.75        35.08         0.56 
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UA 
       32.71        45.11        74.66        49.05        44.68        10.68 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-AATS TCGA-DX-AB2E 
       64.21        21.30         9.34        40.77         1.15        17.79 
TCGA-DX-AB2F TCGA-DX-AB2Z TCGA-FX-A2QS TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-K1-A42X 
       12.00        50.40        49.15        19.89        25.22       123.78 
TCGA-K1-A6RU TCGA-KD-A5QU TCGA-MB-A8JL TCGA-QQ-A5VB TCGA-SG-A6Z4 TCGA-VT-A80G 
       23.38        35.28        19.73        48.59        18.94        10.72 
TCGA-WK-A8Y0 TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       22.62        30.84        19.17        20.65 

$`5Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       75.32        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       84.66        32.15        16.60        37.02        12.62        52.11 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 
       52.27        28.21       159.29        22.62        11.70         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
        6.35        18.08        20.94       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY 
       44.91        54.74        25.25        14.37        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KX 
       38.47        36.03        18.64        26.56        14.04        68.61 
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       12.85        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
        8.58         9.70        95.38        79.17         9.04        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
      136.44        33.44        31.86        35.77        51.02         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        45.99        24.26        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       82.68        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
        3.06        41.00        78.28        50.50        16.87        86.30 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
      101.23        34.49        62.20        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       48.20        20.05        61.97        45.14        47.87        38.17 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      150.35        27.95        40.44        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
        6.58        15.72        65.98        86.10        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE 
       77.88       106.55        50.89        71.31        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32        19.89        15.48         8.05        67.63        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
        4.57        33.30         0.72         9.80        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        3.22         1.38        37.12       171.09        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        16.41         1.05         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I 
       62.17        17.36         5.19        63.81        16.41        30.31 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       25.41         0.49        21.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       81.01        13.08        17.65         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90        37.12       130.32       111.98        64.77        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
        0.72        16.77         3.88        22.82        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO 
        8.61        19.63        13.22        13.41        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
        4.80        84.79        38.27        65.46         8.58        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C5 
       26.43        35.90        18.08        45.34        35.18        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.56              0.49 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           123.78            188.15 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            23.00             32.15 
[1] "0.6 - 123.8 (23.0)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1.5"
D51V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  5Q LOSS MUTATED                1                  2                   0
  5Q LOSS WILD-TYPE              0                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  5Q LOSS MUTATED                     0                             0
  5Q LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  5Q LOSS MUTATED                       0                      3
  5Q LOSS WILD-TYPE                     1                     25
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  5Q LOSS MUTATED                      0                    0
  5Q LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  5Q LOSS MUTATED                                       0
  5Q LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  5Q LOSS MUTATED                                  0
  5Q LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  5Q LOSS MUTATED                                                0
  5Q LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  5Q LOSS MUTATED                                 0
  5Q LOSS WILD-TYPE                              10
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  5Q LOSS MUTATED                                         0
  5Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  5Q LOSS MUTATED                              1                       1
  5Q LOSS WILD-TYPE                            3                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  5Q LOSS MUTATED                                  6
  5Q LOSS WILD-TYPE                               11
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  5Q LOSS MUTATED                                         1
  5Q LOSS WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  5Q LOSS MUTATED                              7
  5Q LOSS WILD-TYPE                           37
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  5Q LOSS MUTATED                                         0
  5Q LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  5Q LOSS MUTATED                                           0
  5Q LOSS WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  5Q LOSS MUTATED                                                  0
  5Q LOSS WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  5Q LOSS MUTATED                                          0
  5Q LOSS WILD-TYPE                                        8
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  5Q LOSS MUTATED                                                         1
  5Q LOSS WILD-TYPE                                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  5Q LOSS MUTATED                                            0
  5Q LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  5Q LOSS MUTATED                                                   7
  5Q LOSS WILD-TYPE                                                66
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  5Q LOSS MUTATED                                                    0
  5Q LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  5Q LOSS MUTATED                                    1                        0
  5Q LOSS WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  5Q LOSS MUTATED                             1                         0
  5Q LOSS WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  5Q LOSS MUTATED                                   1
  5Q LOSS WILD-TYPE                                 6
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  5Q LOSS MUTATED                                   1
  5Q LOSS WILD-TYPE                                 4
D51V3, multiclass
                                                         clus
vv                                                        5Q LOSS MUTATED
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    2
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                3
  HEAD AND NECK - HEAD                                                  0
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                       0
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          1
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  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               1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     7
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        5Q LOSS WILD-TYPE
  CHEST - BREAST                                                          0
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 25
  HEAD AND NECK - HEAD                                                    2
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            3
  LOWER EXTREMITY - GROIN                                                 1
  LOWER EXTREMITY - LOWER LEG/CALF                                       11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           37
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      66
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       6
  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"
D51V4, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    21  13
  5Q LOSS WILD-TYPE 118 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     21   13
  5Q LOSS WILD-TYPE  118  105
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              21               118
  MALE                13               105
[1] 2 2
[1] FALSE
D51V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    21  13
  5Q LOSS WILD-TYPE 158  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     21   13
  5Q LOSS WILD-TYPE  158   59
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               21               158
  YES              13                59
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  5Q LOSS MUTATED                              8             0
  5Q LOSS WILD-TYPE                           51             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  5Q LOSS MUTATED                                                                          0
  5Q LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  5Q LOSS MUTATED                      8
  5Q LOSS WILD-TYPE                   95
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  5Q LOSS MUTATED                                                  0
  5Q LOSS WILD-TYPE                                                9
                   vv
clus                MYXOFIBROSARCOMA
  5Q LOSS MUTATED                  6
  5Q LOSS WILD-TYPE               18
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  5Q LOSS MUTATED                                                          8
  5Q LOSS WILD-TYPE                                                       20
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  5Q LOSS MUTATED                                          0
  5Q LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  5Q LOSS MUTATED                             0                             0
  5Q LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  5Q LOSS MUTATED                                            4
  5Q LOSS WILD-TYPE                                         17
D51V6, multiclass
                                                                          clus
vv                                                                         5Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           8
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                   8
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       0
  MYXOFIBROSARCOMA                                                                       6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             4
                                                                          clus
vv                                                                         5Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            51
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    95
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         9
  MYXOFIBROSARCOMA                                                                        18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                20
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              17
[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
  5Q LOSS MUTATED    19  12   3   0
  5Q LOSS WILD-TYPE 133  57   6  26
D51V7, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              19               133
  R1              12                57
  R2               3                 6
  RX               0                26
[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
  5Q LOSS MUTATED       1                         1    31
  5Q LOSS WILD-TYPE     5                        17   193
D51V8, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               1                17
  WHITE                                  31               193
[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"
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  29
  5Q LOSS WILD-TYPE   5 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   29
  5Q LOSS WILD-TYPE    5  191
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              29               191
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    46  14
  6P LOSS WILD-TYPE 113  84
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               60               197 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               14                84 
$`6P LOSS MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IW-A3M6 TCGA-QQ-A8VB 
       16.18        67.20        37.02        12.62        22.62       188.15 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I3 TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT 
       42.84        10.32        26.56        45.11        74.66        49.05 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48K 
       33.44        44.68        10.68        68.55        85.45        45.99 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB 
       24.26        52.77        46.03        59.84        82.68        36.33 
TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM 
       31.96        78.28        16.87       101.23        34.49        62.20 
TCGA-DX-A8BL TCGA-DX-A8BR TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V 
       45.14       150.35        12.00        66.74        77.88       106.55 
TCGA-FX-A48G TCGA-IE-A3OV TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KD-A5QT TCGA-MB-A8JL 
       19.89        80.48       101.26        53.33        16.41        19.73 
TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A5VD TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P 
       37.55        13.08        37.12        16.77        18.94        25.35 
TCGA-SI-A71Q TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-X6-A7W8 
       32.75        10.72        11.93        84.79        65.46        26.43 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-Z4-A8JB TCGA-Z4-AAPG 
       45.34        19.17        20.65        50.86         4.37        15.98 

$`6P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        34.68        34.36        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       17.95        14.43        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       84.66        32.15        16.60        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
       28.21       159.29        11.70        17.75         8.28         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       18.08        20.94        17.52        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       50.01        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       54.74        25.25        14.37        38.47        36.03        18.64 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 
        0.56        14.04        32.71        68.61        12.85        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       54.21        85.02        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
       95.38        79.17         9.04        86.83       136.44        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UD 
       35.77        51.02         4.54        14.99        73.87        50.43 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 
       34.88         9.73        35.28        26.47       108.82        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       15.95        37.41        28.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EN 
       41.00        50.50        86.30        64.21        21.30        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      152.12        29.49        48.20        20.05         9.34        61.97 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       47.87        38.17        40.77        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G 
       60.66        19.43         6.58         1.15        17.79        15.72 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        86.10         9.21        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        21.70        20.32        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       67.63        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       19.53         3.22         1.38        19.89        37.12        25.22 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
      171.09        13.58        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
        3.91        62.17       123.78        17.36        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       63.81        35.28        30.31        25.41         0.49        21.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
      122.96        38.63        81.01        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       18.08        48.59        35.90       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C 
       10.52         0.72         3.88        22.82         8.61        19.63 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8Y0 
       13.22        13.41        12.46         4.80        38.27        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
        8.58        63.35        35.90        18.08        30.84        35.18 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43        13.38        15.95 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             4.37              0.49 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           188.15            171.09 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           37.335            28.960 
[1] "4.4 - 188.2 (37.3)" "0.5 - 171.1 (29.0)"
[1] "hr=" "2.3"
D52V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  6P LOSS MUTATED                1                  1                   0
  6P LOSS WILD-TYPE              0                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  6P LOSS MUTATED                     0                             0
  6P LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  6P LOSS MUTATED                       0                      5
  6P LOSS WILD-TYPE                     1                     23
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  6P LOSS MUTATED                      1                    0
  6P LOSS WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  6P LOSS MUTATED                                       0
  6P LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  6P LOSS MUTATED                                  1
  6P LOSS WILD-TYPE                                0
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  6P LOSS MUTATED                                                0
  6P LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  6P LOSS MUTATED                                 2
  6P LOSS WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  6P LOSS MUTATED                                         0
  6P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  6P LOSS MUTATED                              2                       0
  6P LOSS WILD-TYPE                            2                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  6P LOSS MUTATED                                  5
  6P LOSS WILD-TYPE                               12
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  6P LOSS MUTATED                                         2
  6P LOSS WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  6P LOSS MUTATED                              9
  6P LOSS WILD-TYPE                           35
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  6P LOSS MUTATED                                         1
  6P LOSS WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  6P LOSS MUTATED                                           1
  6P LOSS WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  6P LOSS MUTATED                                                  0
  6P LOSS WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  6P LOSS MUTATED                                          1
  6P LOSS WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  6P LOSS MUTATED                                                         0
  6P LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  6P LOSS MUTATED                                            0
  6P LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  6P LOSS MUTATED                                                  20
  6P LOSS WILD-TYPE                                                53
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  6P LOSS MUTATED                                                    2
  6P LOSS WILD-TYPE                                                  1
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  6P LOSS MUTATED                                    0                        1
  6P LOSS WILD-TYPE                                  2                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  6P LOSS MUTATED                             1                         0
  6P LOSS WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  6P LOSS MUTATED                                   2
  6P LOSS WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  6P LOSS MUTATED                                   1
  6P LOSS WILD-TYPE                                 4
D52V3, multiclass
                                                         clus
vv                                                        6P LOSS MUTATED
  CHEST - BREAST                                                        1
  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                                                  1
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                       2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          2
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                          9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  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                    20
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        6P LOSS WILD-TYPE
  CHEST - BREAST                                                          0
  CHEST - CHEST WALL                                                      6
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 23
  HEAD AND NECK - HEAD                                                    1
  HEAD AND NECK - NECK                                                    1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                   2
  LOWER ABDOMINAL/PELVIC - BLADDER                                        0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                          2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            2
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  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                      53
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    36  24
  6P LOSS WILD-TYPE 103  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     36   24
  6P LOSS WILD-TYPE  103   94
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              36               103
  MALE                24                94
[1] 2 2
[1] FALSE
D52V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    41  18
  6P LOSS WILD-TYPE 138  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     41   18
  6P LOSS WILD-TYPE  138   54
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               41               138
  YES              18                54
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  6P LOSS MUTATED                             10             1
  6P LOSS WILD-TYPE                           49             1
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  6P LOSS MUTATED                                                                          0
  6P LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  6P LOSS MUTATED                     30
  6P LOSS WILD-TYPE                   73
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  6P LOSS MUTATED                                                  4
  6P LOSS WILD-TYPE                                                5
                   vv
clus                MYXOFIBROSARCOMA
  6P LOSS MUTATED                  7
  6P LOSS WILD-TYPE               17
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  6P LOSS MUTATED                                                          5
  6P LOSS WILD-TYPE                                                       23
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  6P LOSS MUTATED                                          0
  6P LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  6P LOSS MUTATED                             0                             0
  6P LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  6P LOSS MUTATED                                            3
  6P LOSS WILD-TYPE                                         18
D52V6, multiclass
                                                                          clus
vv                                                                         6P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          10
  DESMOID TUMOR                                                                          1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  30
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       4
  MYXOFIBROSARCOMA                                                                       7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             3
                                                                          clus
vv                                                                         6P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            49
  DESMOID TUMOR                                                                            1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    73
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         5
  MYXOFIBROSARCOMA                                                                        17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                23
  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
  6P LOSS MUTATED    40  13   1   5
  6P LOSS WILD-TYPE 112  56   8  21
D52V7, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              40               112
  R1              13                56
  R2               1                 8
  RX               5                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
  6P LOSS MUTATED       2                         3    53
  6P LOSS WILD-TYPE     4                        15   171
D52V8, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  53               171
[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"
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  52
  6P LOSS WILD-TYPE   4 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   52
  6P LOSS WILD-TYPE    4  168
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              52               168
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    34  18
  6Q LOSS WILD-TYPE 125  80
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               52               205 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               18                80 
$`6Q LOSS MUTATED`
TCGA-DX-A6YT TCGA-DX-A8BP TCGA-HB-A43Z TCGA-QQ-A8VB TCGA-3B-A9HR TCGA-3B-A9HU 
       67.20        14.07        37.02       188.15        88.57        25.25 
TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-DX-A23R TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UF 
       42.84        26.56        74.66        51.02        10.68        85.45 
TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6YS TCGA-DX-A6YX 
       24.26        46.03        59.84        82.68        78.28        16.87 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BL TCGA-DX-A8BR TCGA-DX-AB2F 
       21.30        34.49        62.20        45.14       150.35        12.00 
TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-FX-A3TO TCGA-FX-A48G TCGA-HS-A5N8 TCGA-IE-A3OV 
       66.74       106.55        20.32        19.89         0.72        80.48 
TCGA-K1-A6RV TCGA-MB-A8JL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5VD TCGA-QQ-A8VF 
        5.19        19.73        81.01        13.08        37.12       111.98 
TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-VT-A80G 
       10.52        16.77        18.94         3.88        25.35        10.72 
TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC 
       11.93        84.79        65.46        22.62        26.43        45.34 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-Z4-A8JB TCGA-Z4-AAPG 
       19.17        50.86         4.37        15.98 

$`6Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        17.95        14.43        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       84.66        32.15        16.60        12.62        52.11        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH 
       52.27        28.21       159.29        22.62        11.70        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J 
        8.28         6.35        18.08        20.94        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       41.49        35.08        50.01        19.69        53.49        68.55 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       44.91        54.74        14.37        10.32        38.47        36.03 
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        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       45.11        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        14.99        73.87        68.55        50.43        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U 
        9.73        45.99        35.28        52.77        26.47       108.82 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       37.58        15.95        37.41        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YZ 
       36.85        26.99         3.06        41.00        50.50        86.30 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       64.21       101.23        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       20.05         9.34        61.97        47.87        38.17        40.77 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S 
        1.15        17.79        15.72        65.98        86.10         9.21 
TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       77.88        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       21.70        15.48         8.05        67.63        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       33.30         9.80        19.53         3.22         1.38        19.89 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       37.12        25.22       171.09        13.58        85.97         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       16.41         1.05         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
      123.78        17.36        23.38        63.81        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J 
       30.31        25.41         0.49        21.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       38.63        17.65         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SI-A71O TCGA-SI-A71Q 
       35.90       130.32        64.77         0.72        22.82        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XQ 
        8.61        19.63        13.22        13.41        12.46         4.80 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       38.27         8.58        63.35        35.90        18.08        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A9VC 
       35.18        20.65        29.46        27.32        36.43        13.38 
TCGA-Z4-AAPF 
       15.95 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.72              0.49 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           188.15            171.09 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           30.525            31.130 
[1] "0.7 - 188.2 (30.5)" "0.5 - 171.1 (31.1)"
[1] "hr=" "1.3"
D53V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  6Q LOSS MUTATED                1                  1                   0
  6Q LOSS WILD-TYPE              0                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  6Q LOSS MUTATED                     0                             1
  6Q LOSS WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  6Q LOSS MUTATED                       0                      3
  6Q LOSS WILD-TYPE                     1                     25
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  6Q LOSS MUTATED                      1                    0
  6Q LOSS WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  6Q LOSS MUTATED                                       0
  6Q LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  6Q LOSS MUTATED                                  0
  6Q LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  6Q LOSS MUTATED                                                0
  6Q LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  6Q LOSS MUTATED                                 1
  6Q LOSS WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  6Q LOSS MUTATED                                         0
  6Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  6Q LOSS MUTATED                              2                       0
  6Q LOSS WILD-TYPE                            2                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  6Q LOSS MUTATED                                  4
  6Q LOSS WILD-TYPE                               13
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  6Q LOSS MUTATED                                         2
  6Q LOSS WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  6Q LOSS MUTATED                             12
  6Q LOSS WILD-TYPE                           32
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  6Q LOSS MUTATED                                         1
  6Q LOSS WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  6Q LOSS MUTATED                                           1
  6Q LOSS WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  6Q LOSS MUTATED                                                  0
  6Q LOSS WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  6Q LOSS MUTATED                                          1
  6Q LOSS WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  6Q LOSS MUTATED                                                         0
  6Q LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  6Q LOSS MUTATED                                            0
  6Q LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  6Q LOSS MUTATED                                                  14
  6Q LOSS WILD-TYPE                                                59
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  6Q LOSS MUTATED                                                    2
  6Q LOSS WILD-TYPE                                                  1
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  6Q LOSS MUTATED                                    0                        1
  6Q LOSS WILD-TYPE                                  2                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  6Q LOSS MUTATED                             1                         0
  6Q LOSS WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  6Q LOSS MUTATED                                   2
  6Q LOSS WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  6Q LOSS MUTATED                                   0
  6Q LOSS WILD-TYPE                                 5
D53V3, multiclass
                                                         clus
vv                                                        6Q LOSS MUTATED
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    1
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                3
  HEAD AND NECK - HEAD                                                  1
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                       1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          2
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                         12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  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                    14
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     0
                                                         clus
vv                                                        6Q LOSS WILD-TYPE
  CHEST - BREAST                                                          0
  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                                         9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            2
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  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                      59
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  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"
D53V4, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    32  20
  6Q LOSS WILD-TYPE 107  98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     32   20
  6Q LOSS WILD-TYPE  107   98
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              32               107
  MALE                20                98
[1] 2 2
[1] FALSE
D53V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    33  19
  6Q LOSS WILD-TYPE 146  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     33   19
  6Q LOSS WILD-TYPE  146   53
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               33               146
  YES              19                53
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  6Q LOSS MUTATED                              5             1
  6Q LOSS WILD-TYPE                           54             1
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  6Q LOSS MUTATED                                                                          0
  6Q LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  6Q LOSS MUTATED                     25
  6Q LOSS WILD-TYPE                   78
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  6Q LOSS MUTATED                                                  4
  6Q LOSS WILD-TYPE                                                5
                   vv
clus                MYXOFIBROSARCOMA
  6Q LOSS MUTATED                  6
  6Q LOSS WILD-TYPE               18
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  6Q LOSS MUTATED                                                          7
  6Q LOSS WILD-TYPE                                                       21
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  6Q LOSS MUTATED                                          0
  6Q LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  6Q LOSS MUTATED                             0                             0
  6Q LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  6Q LOSS MUTATED                                            4
  6Q LOSS WILD-TYPE                                         17
D53V6, multiclass
                                                                          clus
vv                                                                         6Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           5
  DESMOID TUMOR                                                                          1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  25
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       4
  MYXOFIBROSARCOMA                                                                       6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             4
                                                                          clus
vv                                                                         6Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            54
  DESMOID TUMOR                                                                            1
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    78
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         5
  MYXOFIBROSARCOMA                                                                        18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              17
[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
  6Q LOSS MUTATED    31  12   1   7
  6Q LOSS WILD-TYPE 121  57   8  19
D53V7, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              31               121
  R1              12                57
  R2               1                 8
  RX               7                19
[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
  6Q LOSS MUTATED       1                         3    46
  6Q LOSS WILD-TYPE     5                        15   178
D53V8, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  46               178
[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"
D53V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  45
  6Q LOSS WILD-TYPE   4 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   45
  6Q LOSS WILD-TYPE    4  175
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              45               175
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    21  11
  7P LOSS WILD-TYPE 138  87
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               32               225 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               11                87 
$`7P LOSS MUTATED`
TCGA-DX-A8BP TCGA-DX-AB2P TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DM TCGA-X6-A8C6 
       14.07        12.07        22.62        11.70         6.35        35.08 
TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48P TCGA-DX-A48U 
        6.28        33.44        51.02        50.43        46.03       108.82 
TCGA-DX-A48V TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A8BV 
       59.84        31.96        26.99        21.30        30.35        60.66 
TCGA-FX-A3TO TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-K1-A42W TCGA-K1-A6RV TCGA-KD-A5QS 
       20.32        33.30        80.48        62.17         5.19        63.81 
TCGA-MB-A5YA TCGA-PC-A5DO TCGA-SG-A6Z4 TCGA-SI-AA8C TCGA-VT-AB3D TCGA-WK-A8XS 
        0.49        81.01        18.94        19.63        12.46        84.79 
TCGA-WK-A8XX TCGA-X9-A971 
       38.27        27.32 

$`7P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J 
       75.32        15.22        17.95        14.43        15.85        40.60 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       84.66        32.15        16.60        37.02        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-MB-A5Y9 
       26.93        52.27        28.21       159.29        17.75         8.28 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
       18.08        20.94       188.15        17.52        26.17        41.49 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       50.01        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        49.05        86.83       136.44        44.68        31.86 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       35.77         4.54        14.99        10.68        73.87        68.55 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        85.45         9.73        45.99        24.26        35.28 
TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       52.77        26.47        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       36.33        28.96        36.85         3.06        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       50.50        16.87        86.30        64.21       101.23        34.49 
TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       62.20       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       61.97        45.14        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       27.95        40.44        36.69        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
        9.21        77.88       106.55        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        21.70        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI 
       67.63        34.88         4.57         0.72         9.80        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
        3.22         1.38        19.89        37.12        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        85.97         5.92        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT 
      101.26        53.33       123.78        17.36        23.38        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       35.28        30.31        25.41        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55        38.63        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-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O 
       64.77        10.52         0.72        16.77         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       25.35        32.75         8.61        13.22        13.41        10.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       11.93         4.80        65.46        22.62         8.58        63.35 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       26.43        35.90        18.08        45.34        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        20.65        50.86        29.46        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.49              0.56 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           108.82            188.15 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           31.155            31.130 
[1] "0.5 - 108.8 (31.2)" "0.6 - 188.2 (31.1)"
[1] "hr=" "1.1"
D54V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  7P LOSS MUTATED                0                  0                   0
  7P LOSS WILD-TYPE              1                  7                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  7P LOSS MUTATED                     0                             0
  7P LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  7P LOSS MUTATED                       0                      3
  7P LOSS WILD-TYPE                     1                     25
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  7P LOSS MUTATED                      0                    0
  7P LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  7P LOSS MUTATED                                       0
  7P LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  7P LOSS MUTATED                                  0
  7P LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  7P LOSS MUTATED                                                0
  7P LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  7P LOSS MUTATED                                 1
  7P LOSS WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  7P LOSS MUTATED                                         0
  7P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  7P LOSS MUTATED                              0                       0
  7P LOSS WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  7P LOSS MUTATED                                  0
  7P LOSS WILD-TYPE                               17
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  7P LOSS MUTATED                                         1
  7P LOSS WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  7P LOSS MUTATED                              9
  7P LOSS WILD-TYPE                           35
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  7P LOSS MUTATED                                         1
  7P LOSS WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  7P LOSS MUTATED                                           1
  7P LOSS WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  7P LOSS MUTATED                                                  0
  7P LOSS WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  7P LOSS MUTATED                                          1
  7P LOSS WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  7P LOSS MUTATED                                                         0
  7P LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  7P LOSS MUTATED                                            1
  7P LOSS WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  7P LOSS MUTATED                                                  12
  7P LOSS WILD-TYPE                                                61
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  7P LOSS MUTATED                                                    0
  7P LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  7P LOSS MUTATED                                    0                        0
  7P LOSS WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  7P LOSS MUTATED                             0                         0
  7P LOSS WILD-TYPE                           4                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  7P LOSS MUTATED                                   1
  7P LOSS WILD-TYPE                                 6
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  7P LOSS MUTATED                                   1
  7P LOSS WILD-TYPE                                 4
D54V3, multiclass
                                                         clus
vv                                                        7P LOSS 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                                                3
  HEAD AND NECK - HEAD                                                  0
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                       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                               1
  LOWER EXTREMITY - THIGH/KNEE                                          9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  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                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    12
  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                                     1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        7P LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      7
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  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                                         9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       17
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  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                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      61
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             4
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       6
  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"
D54V4, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    13  19
  7P LOSS WILD-TYPE 126  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     13   19
  7P LOSS WILD-TYPE  126   99
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE              13               126
  MALE                19                99
[1] 2 2
[1] FALSE
D54V5, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    22  10
  7P LOSS WILD-TYPE 157  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     22   10
  7P LOSS WILD-TYPE  157   62
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               22               157
  YES              10                62
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  7P LOSS MUTATED                              4             0
  7P LOSS WILD-TYPE                           55             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  7P LOSS MUTATED                                                                          0
  7P LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  7P LOSS MUTATED                     19
  7P LOSS WILD-TYPE                   84
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  7P LOSS MUTATED                                                  1
  7P LOSS WILD-TYPE                                                8
                   vv
clus                MYXOFIBROSARCOMA
  7P LOSS MUTATED                  2
  7P LOSS WILD-TYPE               22
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  7P LOSS MUTATED                                                          4
  7P LOSS WILD-TYPE                                                       24
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  7P LOSS MUTATED                                          0
  7P LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  7P LOSS MUTATED                             0                             0
  7P LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  7P LOSS MUTATED                                            2
  7P LOSS WILD-TYPE                                         19
D54V6, multiclass
                                                                          clus
vv                                                                         7P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           4
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  19
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       1
  MYXOFIBROSARCOMA                                                                       2
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             2
                                                                          clus
vv                                                                         7P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            55
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    84
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         8
  MYXOFIBROSARCOMA                                                                        22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                24
  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
  7P LOSS MUTATED    19  11   0   2
  7P LOSS WILD-TYPE 133  58   9  24
D54V7, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              19               133
  R1              11                58
  R2               0                 9
  RX               2                24
[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
  7P LOSS MUTATED       1                         0    30
  7P LOSS WILD-TYPE     5                        18   194
D54V8, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                18
  WHITE                                  30               194
[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"
D54V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  30
  7P LOSS WILD-TYPE   5 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   30
  7P LOSS WILD-TYPE    5  190
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              30               190
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    20  16
  7Q LOSS WILD-TYPE 139  82
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               36               221 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               16                82 
$`7Q LOSS MUTATED`
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2P TCGA-PC-A5DM 
       34.36        15.22        17.95        14.07        12.07         6.35 
TCGA-PC-A5DP TCGA-3B-A9HQ TCGA-3B-A9HY TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3UD 
       18.08        68.55        10.32        33.44        51.02        50.43 
TCGA-DX-A48J TCGA-DX-A48P TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A7EN TCGA-DX-A8BV 
        9.73        46.03        31.96        26.99        30.35        60.66 
TCGA-DX-AB2E TCGA-FX-A3TO TCGA-HB-A3L4 TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IW-A3M5 
       17.79        20.32        34.88        37.12        25.22         5.92 
TCGA-K1-A42W TCGA-KD-A5QS TCGA-MB-A5YA TCGA-QQ-A5VA TCGA-QQ-A8VH TCGA-SG-A6Z4 
       62.17        63.81         0.49        18.08        10.52        18.94 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A7W8 
        8.61        19.63        12.46        84.79        38.27        26.43 

$`7Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       14.43        15.85        40.60       106.45        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
      101.98        30.51        60.00        84.66        32.15        16.60 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       37.02        12.62        52.11        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX 
      159.29        22.62        11.70        17.75         8.28        20.94 
TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI 
      188.15        17.52        26.17        41.49        35.08        50.01 
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       19.69        53.49        88.57        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       14.37        42.84        38.47        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
        0.56        14.04        32.71        68.61        12.85        45.11 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       18.54        54.21        85.02        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       86.83       136.44        44.68        31.86        35.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        10.68        73.87        68.55        34.88        85.45 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U 
       45.99        24.26        35.28        52.77        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       28.96        36.85         3.06        41.00        78.28        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        86.30        64.21       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       62.20       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       61.97        45.14        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       27.95        40.44        36.69        19.43         6.58         1.15 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.00        15.72        65.98        86.10        66.74         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       77.88       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       31.13        21.70        19.89        15.48         8.05        67.63 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
        4.57        33.30         0.72         9.80        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        3.22         1.38        19.89       171.09        13.58        85.97 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       16.41         1.05         3.91       101.26        53.33       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I 
       17.36        23.38         5.19        16.41        35.28        30.31 
TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       25.41        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       81.01        13.08        17.65         1.84        46.82        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       35.90        37.12       130.32       111.98        64.77         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT 
       16.77         3.88        22.82        25.35        32.75        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-WK-A8Y0 
       13.41        10.72        11.93         4.80        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        8.58        63.35        35.90        18.08        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       35.18        19.17        20.65        50.86        29.46        27.32 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.49              0.56 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            84.79            188.15 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            22.77             32.71 
[1] "0.5 - 84.8 (22.8)"  "0.6 - 188.2 (32.7)"
[1] "hr=" "1.6"
D55V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  7Q LOSS MUTATED                0                  1                   0
  7Q LOSS WILD-TYPE              1                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  7Q LOSS MUTATED                     0                             1
  7Q LOSS WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  7Q LOSS MUTATED                       0                      3
  7Q LOSS WILD-TYPE                     1                     25
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  7Q LOSS MUTATED                      0                    0
  7Q LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  7Q LOSS MUTATED                                       0
  7Q LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  7Q LOSS MUTATED                                  0
  7Q LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  7Q LOSS MUTATED                                                0
  7Q LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  7Q LOSS MUTATED                                 1
  7Q LOSS WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  7Q LOSS MUTATED                                         0
  7Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  7Q LOSS MUTATED                              0                       0
  7Q LOSS WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  7Q LOSS MUTATED                                  1
  7Q LOSS WILD-TYPE                               16
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  7Q LOSS MUTATED                                         1
  7Q LOSS WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  7Q LOSS MUTATED                              9
  7Q LOSS WILD-TYPE                           35
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  7Q LOSS MUTATED                                         1
  7Q LOSS WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  7Q LOSS MUTATED                                           1
  7Q LOSS WILD-TYPE                                         1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  7Q LOSS MUTATED                                                  0
  7Q LOSS WILD-TYPE                                                5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  7Q LOSS MUTATED                                          1
  7Q LOSS WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  7Q LOSS MUTATED                                                         0
  7Q LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  7Q LOSS MUTATED                                            1
  7Q LOSS WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  7Q LOSS MUTATED                                                  12
  7Q LOSS WILD-TYPE                                                61
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  7Q LOSS MUTATED                                                    0
  7Q LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  7Q LOSS MUTATED                                    1                        0
  7Q LOSS WILD-TYPE                                  1                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  7Q LOSS MUTATED                             0                         0
  7Q LOSS WILD-TYPE                           4                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  7Q LOSS MUTATED                                   1
  7Q LOSS WILD-TYPE                                 6
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  7Q LOSS MUTATED                                   1
  7Q LOSS WILD-TYPE                                 4
D55V3, multiclass
                                                         clus
vv                                                        7Q LOSS 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                                                3
  HEAD AND NECK - HEAD                                                  0
  HEAD AND NECK - NECK                                                  0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                 0
  LOWER ABDOMINAL/PELVIC - BLADDER                                      0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                        0
  LOWER ABDOMINAL/PELVIC - PELVIC                                       1
  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                               1
  LOWER EXTREMITY - THIGH/KNEE                                          9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  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                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           0
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        7Q LOSS 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                                         9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  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                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      61
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             4
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       6
  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"
D55V4, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    17  19
  7Q LOSS WILD-TYPE 122  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     17   19
  7Q LOSS WILD-TYPE  122   99
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              17               122
  MALE                19                99
[1] 2 2
[1] FALSE
D55V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    27   9
  7Q LOSS WILD-TYPE 152  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     27    9
  7Q LOSS WILD-TYPE  152   63
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               27               152
  YES               9                63
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  7Q LOSS MUTATED                              5             0
  7Q LOSS WILD-TYPE                           54             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  7Q LOSS MUTATED                                                                          0
  7Q LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  7Q LOSS MUTATED                     17
  7Q LOSS WILD-TYPE                   86
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  7Q LOSS MUTATED                                                  2
  7Q LOSS WILD-TYPE                                                7
                   vv
clus                MYXOFIBROSARCOMA
  7Q LOSS MUTATED                  5
  7Q LOSS WILD-TYPE               19
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  7Q LOSS MUTATED                                                          4
  7Q LOSS WILD-TYPE                                                       24
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  7Q LOSS MUTATED                                          0
  7Q LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  7Q LOSS MUTATED                             0                             0
  7Q LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  7Q LOSS MUTATED                                            3
  7Q LOSS WILD-TYPE                                         18
D55V6, multiclass
                                                                          clus
vv                                                                         7Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           5
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  17
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       2
  MYXOFIBROSARCOMA                                                                       5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             3
                                                                          clus
vv                                                                         7Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            54
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    86
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         7
  MYXOFIBROSARCOMA                                                                        19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                24
  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
  7Q LOSS MUTATED    23  10   0   3
  7Q LOSS WILD-TYPE 129  59   9  23
D55V7, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              23               129
  R1              10                59
  R2               0                 9
  RX               3                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
  7Q LOSS MUTATED       0                         2    34
  7Q LOSS WILD-TYPE     6                        16   190
D55V8, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  34               190
[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"
D55V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  35
  7Q LOSS WILD-TYPE   5 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   35
  7Q LOSS WILD-TYPE    5  185
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              35               185
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    34  28
  8P LOSS WILD-TYPE 125  70
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               62               195 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               28                70 
$`8P LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       31.53        16.18        67.20        15.22        17.95        14.43 
TCGA-DX-AB2X TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-KF-A41W TCGA-LI-A9QH 
       13.28        16.60        37.02        52.11        11.70        17.75 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9I1 
       50.01        19.69        88.57        44.91        14.37        18.64 
TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y 
        0.56        32.71        68.61        45.11        85.02         6.28 
TCGA-DX-A3LS TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48K 
        9.04        51.02        10.68        73.87         9.73        45.99 
TCGA-DX-A48R TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BL TCGA-DX-A8BV 
       26.47        16.87        21.30        34.49        45.14        60.66 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V 
        1.15        17.79        12.00        86.10        77.88       106.55 
TCGA-FX-A3RE TCGA-HB-A3L4 TCGA-HS-A5N8 TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-JV-A5VE 
       21.70        34.88         0.72        19.89       171.09        16.41 
TCGA-K1-A6RV TCGA-MB-A8JK TCGA-MB-A8JL TCGA-QQ-A5VB TCGA-QQ-A8VH TCGA-SG-A6Z7 
        5.19        21.73        19.73        48.59        10.52         3.88 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-VT-A80G TCGA-WK-A8XS TCGA-X6-A8C2 TCGA-X6-A8C4 
       22.82        32.75        10.72        84.79        35.18        20.65 
TCGA-X9-A971 TCGA-Z4-AAPG 
       27.32        15.98 

$`8P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        34.68        34.36        75.32        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       40.60        12.07       106.45        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK 
       60.00        84.66        32.15        12.62        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP 
       28.21       159.29        22.62         8.28         6.35        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       20.94       188.15        17.52        26.17        41.49        35.08 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       53.49        68.55        54.74        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 
       38.47        36.03        26.56        14.04        12.85        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       54.21        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       79.17        49.05        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD 
       31.86        35.77         4.54        14.99        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88        85.45        24.26        35.28        52.77        46.03 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
      108.82        59.84        37.58        15.95        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       36.33        28.96        31.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       41.00        78.28        50.50        86.30        64.21       101.23 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
        9.34        61.97        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2G 
       27.95        40.44        36.69        19.43         6.58        15.72 
TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
       65.98        66.74         9.21        50.40        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       67.63         4.57        33.30         9.80        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 
        3.22         1.38        37.12        25.22        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        5.92         1.05         3.91       101.26        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
      123.78        17.36        23.38        63.81        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       30.31        25.41         0.49        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       81.01        13.08        17.65         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       35.90        37.12       130.32       111.98        64.77         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       16.77        18.94        25.35         8.61        19.63        13.22 
TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY 
       13.41        12.46        11.93         4.80        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       22.62         8.58        63.35        26.43        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       45.34        30.84        19.17        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.56              0.49 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           171.09            188.15 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            21.50             33.44 
[1] "0.6 - 171.1 (21.5)" "0.5 - 188.2 (33.4)"
[1] "hr=" "1.5"
D56V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  8P LOSS MUTATED                1                  1                   0
  8P LOSS WILD-TYPE              0                  6                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  8P LOSS MUTATED                     0                             1
  8P LOSS WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  8P LOSS MUTATED                       1                      8
  8P LOSS WILD-TYPE                     0                     20
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  8P LOSS MUTATED                      0                    0
  8P LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  8P LOSS MUTATED                                       0
  8P LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  8P LOSS MUTATED                                  0
  8P LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  8P LOSS MUTATED                                                0
  8P LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  8P LOSS MUTATED                                 2
  8P LOSS WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  8P LOSS MUTATED                                         0
  8P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  8P LOSS MUTATED                              1                       1
  8P LOSS WILD-TYPE                            3                       1
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  8P LOSS MUTATED                                  6
  8P LOSS WILD-TYPE                               11
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  8P LOSS MUTATED                                         2
  8P LOSS WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  8P LOSS MUTATED                              9
  8P LOSS WILD-TYPE                           35
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  8P LOSS MUTATED                                         0
  8P LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  8P LOSS MUTATED                                           2
  8P LOSS WILD-TYPE                                         0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  8P LOSS MUTATED                                                  1
  8P LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  8P LOSS MUTATED                                          1
  8P LOSS WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  8P LOSS MUTATED                                                         0
  8P LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  8P LOSS MUTATED                                            0
  8P LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  8P LOSS MUTATED                                                  16
  8P LOSS WILD-TYPE                                                57
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  8P LOSS MUTATED                                                    1
  8P LOSS WILD-TYPE                                                  2
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  8P LOSS MUTATED                                    2                        1
  8P LOSS WILD-TYPE                                  0                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  8P LOSS MUTATED                             1                         0
  8P LOSS WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  8P LOSS MUTATED                                   3
  8P LOSS WILD-TYPE                                 4
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  8P LOSS MUTATED                                   1
  8P LOSS WILD-TYPE                                 4
D56V3, multiclass
                                                         clus
vv                                                        8P LOSS MUTATED
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    1
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                                8
  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                                          1
  LOWER EXTREMITY - GROIN                                               1
  LOWER EXTREMITY - LOWER LEG/CALF                                      6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                          9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    16
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    2
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           1
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        8P LOSS WILD-TYPE
  CHEST - BREAST                                                          0
  CHEST - CHEST WALL                                                      6
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           1
  GYNECOLOGICAL - OVARY                                                   0
  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                                         8
  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                                           35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               0
  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                      57
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      0
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             3
  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"
D56V4, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    35  27
  8P LOSS WILD-TYPE 104  91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     35   27
  8P LOSS WILD-TYPE  104   91
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              35               104
  MALE                27                91
[1] 2 2
[1] FALSE
D56V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    44  18
  8P LOSS WILD-TYPE 135  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     44   18
  8P LOSS WILD-TYPE  135   54
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               44               135
  YES              18                54
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  8P LOSS MUTATED                             15             0
  8P LOSS WILD-TYPE                           44             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  8P LOSS MUTATED                                                                          0
  8P LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  8P LOSS MUTATED                     23
  8P LOSS WILD-TYPE                   80
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  8P LOSS MUTATED                                                  3
  8P LOSS WILD-TYPE                                                6
                   vv
clus                MYXOFIBROSARCOMA
  8P LOSS MUTATED                  7
  8P LOSS WILD-TYPE               17
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  8P LOSS MUTATED                                                          9
  8P LOSS WILD-TYPE                                                       19
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  8P LOSS MUTATED                                          0
  8P LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  8P LOSS MUTATED                             0                             0
  8P LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  8P LOSS MUTATED                                            5
  8P LOSS WILD-TYPE                                         16
D56V6, multiclass
                                                                          clus
vv                                                                         8P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          15
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  23
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       3
  MYXOFIBROSARCOMA                                                                       7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             5
                                                                          clus
vv                                                                         8P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            44
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    80
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         6
  MYXOFIBROSARCOMA                                                                        17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              16
[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
  8P LOSS MUTATED    36  15   3   8
  8P LOSS WILD-TYPE 116  54   6  18
D56V7, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              36               116
  R1              15                54
  R2               3                 6
  RX               8                18
[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
  8P LOSS MUTATED       0                         7    51
  8P LOSS WILD-TYPE     6                        11   173
D56V8, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               7                11
  WHITE                                  51               173
[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"
D56V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0  51
  8P LOSS WILD-TYPE   5 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   51
  8P LOSS WILD-TYPE    5  169
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              51               169
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    28  17
  8Q LOSS WILD-TYPE 131  81
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               45               212 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               17                81 
$`8Q LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BG TCGA-FX-A3NK TCGA-HB-A43Z 
       31.53        67.20        15.22        17.95        16.60        37.02 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS 
       11.70        17.75        50.01        19.69        88.57        44.91 
TCGA-3B-A9I1 TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LS 
       18.64        68.61        45.11        85.02         6.28         9.04 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF 
        9.73        24.26         3.06        16.87        86.30        21.30 
TCGA-DX-A7EI TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2F 
       34.49        45.14        38.17        60.66         1.15        12.00 
TCGA-DX-AB2V TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-K1-A6RV 
      106.55         3.22        19.89       171.09        16.41         5.19 
TCGA-MB-A8JK TCGA-PC-A5DO TCGA-QC-AA9N TCGA-SI-AA8B TCGA-WK-A8XS TCGA-X2-A95T 
       21.73        81.01        17.65         8.61        84.79        63.35 
TCGA-X6-A8C2 TCGA-X9-A971 TCGA-Z4-AAPG 
       35.18        27.32        15.98 

$`8Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BH 
       36.30        34.68        16.18        34.36        75.32        14.43 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X 
       14.07        15.85        40.60        12.07       106.45        13.28 
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-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       12.62        52.11        26.93        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       22.62         8.28         6.35        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        26.17        41.49        35.08        53.49        68.55 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY 
       36.03        26.56         0.56        14.04        32.71        12.85 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       18.54        54.21        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       95.38        79.17        49.05        86.83       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        73.87        68.55        50.43        34.88        85.45 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       45.99        35.28        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       59.84        37.58        15.95        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS 
       28.96        31.96        36.85        26.99        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       50.50        64.21       101.23        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM 
       29.49        48.20        20.05         9.34        61.97        47.87 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX 
       40.77       150.35        27.95        40.44        36.69        19.43 
TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
        6.58        17.79        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21        77.88        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       67.63        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA 
       80.48        19.53         1.38        37.12        25.22        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       85.97         5.92         1.05         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT 
       62.17       123.78        17.36        23.38        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       35.28        30.31        25.41         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       37.55        38.63        13.08         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        35.90        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       10.52         0.72        16.77        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       25.35        32.75        19.63        13.22        13.41        10.72 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       12.46        11.93         4.80        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        8.58        26.43        35.90        18.08        45.34        30.84 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB 
       19.17        20.65        50.86        29.46        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF 
       13.38        15.95 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.15              0.49 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           171.09            188.15 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           21.730            32.055 
[1] "1.1 - 171.1 (21.7)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1"  
D57V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  8Q LOSS MUTATED                0                  0                   0
  8Q LOSS WILD-TYPE              1                  7                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  8Q LOSS MUTATED                     0                             0
  8Q LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  8Q LOSS MUTATED                       0                      5
  8Q LOSS WILD-TYPE                     1                     23
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  8Q LOSS MUTATED                      0                    0
  8Q LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  8Q LOSS MUTATED                                       0
  8Q LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  8Q LOSS MUTATED                                  0
  8Q LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  8Q LOSS MUTATED                                                0
  8Q LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  8Q LOSS MUTATED                                 2
  8Q LOSS WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  8Q LOSS MUTATED                                         0
  8Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  8Q LOSS MUTATED                              0                       0
  8Q LOSS WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  8Q LOSS MUTATED                                  3
  8Q LOSS WILD-TYPE                               14
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  8Q LOSS MUTATED                                         1
  8Q LOSS WILD-TYPE                                       4
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  8Q LOSS MUTATED                             11
  8Q LOSS WILD-TYPE                           33
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  8Q LOSS MUTATED                                         0
  8Q LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  8Q LOSS MUTATED                                           2
  8Q LOSS WILD-TYPE                                         0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  8Q LOSS MUTATED                                                  1
  8Q LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  8Q LOSS MUTATED                                          0
  8Q LOSS WILD-TYPE                                        8
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  8Q LOSS MUTATED                                                         0
  8Q LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  8Q LOSS MUTATED                                            0
  8Q LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  8Q LOSS MUTATED                                                  13
  8Q LOSS WILD-TYPE                                                60
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  8Q LOSS MUTATED                                                    0
  8Q LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  8Q LOSS MUTATED                                    1                        1
  8Q LOSS WILD-TYPE                                  1                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  8Q LOSS MUTATED                             2                         0
  8Q LOSS WILD-TYPE                           2                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  8Q LOSS MUTATED                                   2
  8Q LOSS WILD-TYPE                                 5
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  8Q LOSS MUTATED                                   1
  8Q LOSS WILD-TYPE                                 4
D57V3, multiclass
                                                         clus
vv                                                        8Q LOSS 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                                                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                                      3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               1
  LOWER EXTREMITY - THIGH/KNEE                                         11
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             2
  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                    13
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    1
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           2
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        8Q LOSS WILD-TYPE
  CHEST - BREAST                                                          1
  CHEST - CHEST WALL                                                      7
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  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                                         8
  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                                 4
  LOWER EXTREMITY - THIGH/KNEE                                           33
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      60
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      1
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             2
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                       4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    27  18
  8Q LOSS WILD-TYPE 112 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     27   18
  8Q LOSS WILD-TYPE  112  100
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              27               112
  MALE                18               100
[1] 2 2
[1] FALSE
D57V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    28  16
  8Q LOSS WILD-TYPE 151  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     28   16
  8Q LOSS WILD-TYPE  151   56
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               28               151
  YES              16                56
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  8Q LOSS MUTATED                             11             0
  8Q LOSS WILD-TYPE                           48             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  8Q LOSS MUTATED                                                                          0
  8Q LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  8Q LOSS MUTATED                     14
  8Q LOSS WILD-TYPE                   89
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  8Q LOSS MUTATED                                                  0
  8Q LOSS WILD-TYPE                                                9
                   vv
clus                MYXOFIBROSARCOMA
  8Q LOSS MUTATED                  7
  8Q LOSS WILD-TYPE               17
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  8Q LOSS MUTATED                                                          7
  8Q LOSS WILD-TYPE                                                       21
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  8Q LOSS MUTATED                                          0
  8Q LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  8Q LOSS MUTATED                             0                             0
  8Q LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  8Q LOSS MUTATED                                            6
  8Q LOSS WILD-TYPE                                         15
D57V6, multiclass
                                                                          clus
vv                                                                         8Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          11
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  14
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       0
  MYXOFIBROSARCOMA                                                                       7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               7
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             6
                                                                          clus
vv                                                                         8Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            48
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    89
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         9
  MYXOFIBROSARCOMA                                                                        17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                21
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              15
[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
  8Q LOSS MUTATED    26  14   1   4
  8Q LOSS WILD-TYPE 126  55   8  22
D57V7, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              26               126
  R1              14                55
  R2               1                 8
  RX               4                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
  8Q LOSS MUTATED       0                         6    37
  8Q LOSS WILD-TYPE     6                        12   187
D57V8, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  37               187
[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"
D57V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  41
  8Q LOSS WILD-TYPE   5 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   41
  8Q LOSS WILD-TYPE    5  179
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              41               179
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    43  39
  9P LOSS WILD-TYPE 116  59
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               82               175 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               39                59 
$`9P LOSS MUTATED`
TCGA-DX-A3M2 TCGA-DX-A7EL TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB32 
       34.68        75.32        14.07        40.60        12.07       101.98 
TCGA-DX-AB3A TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QQ-A8VB TCGA-VT-A80J TCGA-3B-A9HR 
       32.15        17.75         8.28       188.15        26.17        88.57 
TCGA-3B-A9HS TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       44.91        38.47        18.64        26.56         0.56        14.04 
TCGA-DX-A1KY TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3LY 
       12.85        66.87         6.28         9.04       136.44        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48R 
       44.68        51.02        50.43        85.45         9.73        26.47 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR 
       59.84        37.58        82.68        31.96         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI 
       78.28        16.87        86.30        64.21        21.30        34.49 
TCGA-DX-A7EQ TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BZ 
       29.49         9.34        38.17        40.77       150.35         6.58 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HS-A5N8 
       17.79        12.00        49.15        21.70        67.63         0.72 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A75J 
       80.48        19.53         3.22       171.09         5.92         3.91 
TCGA-K1-A42W TCGA-K1-A6RU TCGA-KD-A5QS TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MO-A47R 
       62.17        23.38        63.81        25.41        19.73        10.45 
TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A8VH TCGA-RN-AAAQ 
        7.36        38.63        81.01        13.08        10.52        16.77 
TCGA-SI-A71Q TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       32.75        13.41        10.72        38.27        65.46        22.62 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A971 TCGA-Z4-AAPG 
       19.17        20.65        27.32        15.98 

$`9P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        34.36        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       17.95        14.43        15.85       106.45        13.28        22.85 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       30.51        60.00        84.66        16.60        37.02        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       52.11        26.93        52.27        28.21       159.29        22.62 
TCGA-KF-A41W TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-WK-A8XT 
       11.70         6.35        18.08        20.94        17.52        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT 
       35.08        50.01        19.69        53.49        68.55        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-DX-A1KW 
       25.25        14.37        42.84        10.32        36.03        32.71 
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       68.61        45.11        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z TCGA-DX-A240 
       66.94        74.66         5.26        76.41        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU 
        8.58         9.70        95.38        79.17        49.05        86.83 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       31.86        35.77         4.54        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       68.55        34.88        45.99        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       46.03       108.82        15.95        37.41        36.33        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN 
       36.85        26.99        50.50       101.23        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
      152.12        48.20        20.05        61.97        45.14        47.87 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       27.95        40.44        36.69        60.66        19.43         1.15 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       15.72        65.98        86.10        66.74         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3TO 
      106.55        50.40        50.89        71.31        31.13        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       19.89        15.48         8.05        34.88         4.57        33.30 
TCGA-HS-A5NA TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA 
        9.80         1.38        19.89        37.12        25.22        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       85.97        16.41         1.05       101.26        53.33       123.78 
TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA 
       17.36         5.19        16.41        35.28        30.31         0.49 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK 
       21.73        14.99        17.98        22.39        11.57       122.96 
TCGA-PC-A5DL TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       37.55        17.65         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       35.90        37.12       130.32       111.98        64.77         0.72 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C 
       18.94         3.88        22.82        25.35         8.61        19.63 
TCGA-UE-A6QT TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WP-A9GB 
       13.22        12.46        11.93         4.80        84.79         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       63.35        26.43        35.90        18.08        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       35.18        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF 
       15.95 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.56              0.49 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           188.15            159.29 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            26.94             31.86 
[1] "0.6 - 188.2 (26.9)" "0.5 - 159.3 (31.9)"
[1] "hr=" "1.5"
D58V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  9P LOSS MUTATED                1                  5                   0
  9P LOSS WILD-TYPE              0                  2                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  9P LOSS MUTATED                     1                             1
  9P LOSS WILD-TYPE                   0                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  9P LOSS MUTATED                       1                      7
  9P LOSS WILD-TYPE                     0                     21
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  9P LOSS MUTATED                      1                    0
  9P LOSS WILD-TYPE                    1                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  9P LOSS MUTATED                                       0
  9P LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  9P LOSS MUTATED                                  0
  9P LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  9P LOSS MUTATED                                                0
  9P LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  9P LOSS MUTATED                                 2
  9P LOSS WILD-TYPE                               8
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  9P LOSS MUTATED                                         0
  9P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  9P LOSS MUTATED                              0                       0
  9P LOSS WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  9P LOSS MUTATED                                  7
  9P LOSS WILD-TYPE                               10
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  9P LOSS MUTATED                                         3
  9P LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  9P LOSS MUTATED                             16
  9P LOSS WILD-TYPE                           28
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  9P LOSS MUTATED                                         1
  9P LOSS WILD-TYPE                                       3
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  9P LOSS MUTATED                                           0
  9P LOSS WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  9P LOSS MUTATED                                                  1
  9P LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  9P LOSS MUTATED                                          1
  9P LOSS WILD-TYPE                                        7
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  9P LOSS MUTATED                                                         2
  9P LOSS WILD-TYPE                                                       0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  9P LOSS MUTATED                                            1
  9P LOSS WILD-TYPE                                          0
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  9P LOSS MUTATED                                                  24
  9P LOSS WILD-TYPE                                                49
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  9P LOSS MUTATED                                                    1
  9P LOSS WILD-TYPE                                                  2
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  9P LOSS MUTATED                                    0                        0
  9P LOSS WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  9P LOSS MUTATED                             2                         0
  9P LOSS WILD-TYPE                           2                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  9P LOSS MUTATED                                   4
  9P LOSS WILD-TYPE                                 3
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  9P LOSS MUTATED                                   0
  9P LOSS WILD-TYPE                                 5
D58V3, multiclass
                                                         clus
vv                                                        9P LOSS MUTATED
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    5
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 1
  GYNECOLOGICAL - UTERUS                                                7
  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                                       2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          0
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               3
  LOWER EXTREMITY - THIGH/KNEE                                         16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    24
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           2
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     0
                                                         clus
vv                                                        9P LOSS WILD-TYPE
  CHEST - BREAST                                                          0
  CHEST - CHEST WALL                                                      2
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     0
  CHEST - OTHER (PLEASE SPECIFY                                           1
  GYNECOLOGICAL - OVARY                                                   0
  GYNECOLOGICAL - UTERUS                                                 21
  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                                         8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            4
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                       10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 2
  LOWER EXTREMITY - THIGH/KNEE                                           28
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                7
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      49
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             2
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       3
  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"
D58V4, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   49 33
  9P LOSS WILD-TYPE 90 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     49   33
  9P LOSS WILD-TYPE   90   85
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              49                90
  MALE                33                85
[1] 2 2
[1] FALSE
D58V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    55  26
  9P LOSS WILD-TYPE 124  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     55   26
  9P LOSS WILD-TYPE  124   46
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               55               124
  YES              26                46
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  9P LOSS MUTATED                             15             0
  9P LOSS WILD-TYPE                           44             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  9P LOSS MUTATED                                                                          0
  9P LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  9P LOSS MUTATED                     32
  9P LOSS WILD-TYPE                   71
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  9P LOSS MUTATED                                                  4
  9P LOSS WILD-TYPE                                                5
                   vv
clus                MYXOFIBROSARCOMA
  9P LOSS MUTATED                 10
  9P LOSS WILD-TYPE               14
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  9P LOSS MUTATED                                                         10
  9P LOSS WILD-TYPE                                                       18
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  9P LOSS MUTATED                                          0
  9P LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  9P LOSS MUTATED                             0                             1
  9P LOSS WILD-TYPE                           2                             5
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  9P LOSS MUTATED                                           10
  9P LOSS WILD-TYPE                                         11
D58V6, multiclass
                                                                          clus
vv                                                                         9P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          15
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  32
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       4
  MYXOFIBROSARCOMA                                                                      10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            10
                                                                          clus
vv                                                                         9P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            44
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    71
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         5
  MYXOFIBROSARCOMA                                                                        14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              11
[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
  9P LOSS MUTATED    43  25   6   7
  9P LOSS WILD-TYPE 109  44   3  19
D58V7, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              43               109
  R1              25                44
  R2               6                 3
  RX               7                19
[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
  9P LOSS MUTATED       3                         7    68
  9P LOSS WILD-TYPE     3                        11   156
D58V8, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   3                 3
  BLACK OR AFRICAN AMERICAN               7                11
  WHITE                                  68               156
[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"
D58V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     1  67
  9P LOSS WILD-TYPE   4 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   67
  9P LOSS WILD-TYPE    4  153
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              67               153
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    25  25
  9Q LOSS WILD-TYPE 134  73
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               50               207 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               25                73 
$`9Q LOSS MUTATED`
TCGA-DX-A3M2 TCGA-DX-AB3A TCGA-QQ-A8VB TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       34.68        32.15       188.15        18.64        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3UD 
       14.04        12.85         6.28         9.04       136.44        50.43 
TCGA-DX-A48J TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A6YX 
        9.73        26.47        59.84        31.96        78.28        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BR 
       86.30        64.21        34.49         9.34        38.17       150.35 
TCGA-DX-AB2E TCGA-DX-AB2T TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IS-A3K7 
       17.79        77.88        67.63         0.72        80.48       171.09 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A6RV TCGA-KD-A5QS TCGA-MB-A5Y8 
       13.58         5.92         3.91         5.19        63.81        25.41 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DO TCGA-QQ-A8VH TCGA-RN-AAAQ 
       19.73        14.99        10.45        81.01        10.52        16.77 
TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XX TCGA-WP-A9GB 
        3.88        32.75        13.41        10.72        38.27         8.58 
TCGA-X6-A8C4 TCGA-Z4-AAPG 
       20.65        15.98 

$`9Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        16.18        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J 
       15.22        17.95        14.43        14.07        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       12.07       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       60.00        84.66        16.60        37.02        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 
       17.75         8.28         6.35        18.08        20.94        17.52 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP 
       26.17        41.49        35.08        50.01        19.69        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       68.55        88.57        44.91        54.74        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KX 
       42.84        10.32        38.47        36.03        32.71        68.61 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       45.11        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU 
        8.58         9.70        95.38        79.17        49.05        86.83 
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        73.87        68.55        34.88        85.45 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       45.99        24.26        35.28        52.77        46.03       108.82 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       37.58        15.95        37.41        82.68        36.33        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6Z2 
       36.85        26.99         3.06        41.00        50.50       101.23 
TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS 
       20.05        61.97        45.14        47.87        40.77        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       40.44        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.00        15.72        65.98        86.10        66.74         9.21 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      106.55        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       21.70        20.32        19.89        15.48         8.05        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        4.57        33.30         9.80        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF 
       19.89        37.12        25.22        85.97        16.41         1.05 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
      101.26        53.33        62.17       123.78        17.36        23.38 
TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J 
       16.41        35.28        30.31         0.49        21.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       22.39        11.57         7.36       122.96        37.55        38.63 
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-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       35.90        37.12       130.32       111.98        64.77         0.72 
TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       18.94        22.82        25.35         8.61        19.63        13.22 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 
       12.46        11.93         4.80        84.79        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       63.35        26.43        35.90        18.08        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       35.18        19.17        50.86        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.56              0.49 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           188.15            159.29 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            20.19             33.30 
[1] "0.6 - 188.2 (20.2)" "0.5 - 159.3 (33.3)"
[1] "hr=" "1.6"
D59V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  9Q LOSS MUTATED                1                  2                   0
  9Q LOSS WILD-TYPE              0                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  9Q LOSS MUTATED                     0                             1
  9Q LOSS WILD-TYPE                   1                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  9Q LOSS MUTATED                       0                      8
  9Q LOSS WILD-TYPE                     1                     20
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  9Q LOSS MUTATED                      0                    0
  9Q LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  9Q LOSS MUTATED                                       0
  9Q LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  9Q LOSS MUTATED                                  0
  9Q LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  9Q LOSS MUTATED                                                1
  9Q LOSS WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  9Q LOSS MUTATED                                 0
  9Q LOSS WILD-TYPE                              10
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  9Q LOSS MUTATED                                         0
  9Q LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  9Q LOSS MUTATED                              0                       0
  9Q LOSS WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  9Q LOSS MUTATED                                  2
  9Q LOSS WILD-TYPE                               15
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  9Q LOSS MUTATED                                         2
  9Q LOSS WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  9Q LOSS MUTATED                              9
  9Q LOSS WILD-TYPE                           35
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  9Q LOSS MUTATED                                         0
  9Q LOSS WILD-TYPE                                       4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  9Q LOSS MUTATED                                           0
  9Q LOSS WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  9Q LOSS MUTATED                                                  1
  9Q LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  9Q LOSS MUTATED                                          2
  9Q LOSS WILD-TYPE                                        6
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  9Q LOSS MUTATED                                                         0
  9Q LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  9Q LOSS MUTATED                                            0
  9Q LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  9Q LOSS MUTATED                                                  17
  9Q LOSS WILD-TYPE                                                56
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  9Q LOSS MUTATED                                                    0
  9Q LOSS WILD-TYPE                                                  3
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  9Q LOSS MUTATED                                    0                        0
  9Q LOSS WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  9Q LOSS MUTATED                             1                         0
  9Q LOSS WILD-TYPE                           3                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  9Q LOSS MUTATED                                   3
  9Q LOSS WILD-TYPE                                 4
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  9Q LOSS MUTATED                                   0
  9Q LOSS WILD-TYPE                                 5
D59V3, multiclass
                                                         clus
vv                                                        9Q LOSS MUTATED
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    2
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                                8
  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                        1
  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                                      2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                          9
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    17
  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                                     3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     0
                                                         clus
vv                                                        9Q LOSS WILD-TYPE
  CHEST - BREAST                                                          0
  CHEST - CHEST WALL                                                      5
  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                          1
  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                                           35
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      56
  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                                       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"
D59V4, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    29  21
  9Q LOSS WILD-TYPE 110  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     29   21
  9Q LOSS WILD-TYPE  110   97
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              29               110
  MALE                21                97
[1] 2 2
[1] FALSE
D59V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    35  15
  9Q LOSS WILD-TYPE 144  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     35   15
  9Q LOSS WILD-TYPE  144   57
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               35               144
  YES              15                57
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  9Q LOSS MUTATED                             11             0
  9Q LOSS WILD-TYPE                           48             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  9Q LOSS MUTATED                                                                          0
  9Q LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  9Q LOSS MUTATED                     20
  9Q LOSS WILD-TYPE                   83
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  9Q LOSS MUTATED                                                  4
  9Q LOSS WILD-TYPE                                                5
                   vv
clus                MYXOFIBROSARCOMA
  9Q LOSS MUTATED                  6
  9Q LOSS WILD-TYPE               18
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  9Q LOSS MUTATED                                                          3
  9Q LOSS WILD-TYPE                                                       25
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  9Q LOSS MUTATED                                          0
  9Q LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  9Q LOSS MUTATED                             0                             0
  9Q LOSS WILD-TYPE                           2                             6
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  9Q LOSS MUTATED                                            6
  9Q LOSS WILD-TYPE                                         15
D59V6, multiclass
                                                                          clus
vv                                                                         9Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          11
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  20
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       4
  MYXOFIBROSARCOMA                                                                       6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             6
                                                                          clus
vv                                                                         9Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            48
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    83
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         5
  MYXOFIBROSARCOMA                                                                        18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                25
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              15
[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
  9Q LOSS MUTATED    25  14   4   6
  9Q LOSS WILD-TYPE 127  55   5  20
D59V7, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              25               127
  R1              14                55
  R2               4                 5
  RX               6                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
  9Q LOSS MUTATED       2                         6    39
  9Q LOSS WILD-TYPE     4                        12   185
D59V8, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  39               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  38
  9Q LOSS WILD-TYPE   4 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   38
  9Q LOSS WILD-TYPE    4  182
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              38               182
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   74 47
  10P LOSS WILD-TYPE 85 51
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               121                136 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                47                 51 
$`10P LOSS MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       16.18        34.36        75.32        15.22        17.95        14.43 
TCGA-DX-AB2P TCGA-DX-AB30 TCGA-DX-AB32 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IF-A4AK 
       12.07        22.85       101.98        37.02        12.62        52.27 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 
       22.62        11.70        17.75        20.94       188.15        17.52 
TCGA-VT-A80J TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       26.17        50.01        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KW 
       44.91        14.37        10.32        36.03        26.56        32.71 
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3U9 TCGA-DX-A3UA 
       68.61        18.54        74.66         6.28        14.99        10.68 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B7 
       34.88        85.45        45.99        46.03        26.47        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YQ 
       15.95        37.41        82.68        36.33        31.96         3.06 
TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A8BJ 
       41.00        16.87        64.21       101.23        62.20         9.34 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV 
       47.87        40.77       150.35        27.95        40.44        60.66 
TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB3C TCGA-FX-A2QS 
        6.58        12.00        86.10       106.55        71.31        49.15 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
       21.70        20.32        19.89        15.48        67.63         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AJ 
       33.30         0.72        80.48        19.53         3.22        25.22 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
      171.09         5.92        16.41         1.05         3.91       101.26 
TCGA-K1-A42W TCGA-K1-A6RU TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       62.17        23.38        35.28        25.41         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       19.73        14.99        10.45         7.36       122.96        37.55 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC 
       81.01        13.08        17.65        46.82        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       37.12        10.52        16.77        22.82        25.35        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XS 
        8.61        19.63        13.41        12.46        11.93        84.79 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X9-A971 
       26.43        35.90        30.84        19.17        50.86        27.32 
TCGA-Z4-AAPG 
       15.98 

$`10P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        31.53        34.68        67.20        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       40.60       106.45        13.28        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 
       32.15        16.60        52.11        26.93        28.21       159.29 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HT 
        8.28         6.35        18.08        41.49        35.08        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU 
       25.25        42.84        38.47        18.64         0.56        14.04 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       12.85        45.11        54.21        85.02        33.53        66.94 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        95.38        79.17         9.04        49.05        86.83 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      136.44        33.44        44.68        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48L 
        4.54        73.87        68.55        50.43         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BE TCGA-DX-A6BG 
       35.28        52.77       108.82        59.84        28.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI 
       26.99        78.28        50.50        86.30        21.30        34.49 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK 
       30.35       152.12        29.49        48.20        20.05        61.97 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E 
       45.14        38.17        36.69        19.43         1.15        17.79 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z 
       15.72        65.98        66.74         9.21        77.88        50.40 
TCGA-DX-AB3B TCGA-FX-A3NJ TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5NA TCGA-IE-A4EK 
       50.89        31.13         8.05        34.88         9.80         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-K1-A3PO TCGA-K1-A42X 
       19.89        37.12        13.58        85.97        53.33       123.78 
TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-MJ-A68J 
       17.36         5.19        63.81        16.41        30.31        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD 
       22.39        11.57        38.63         1.84        18.08       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-UE-A6QT 
      111.98        64.77         0.72        18.94         3.88        13.22 
TCGA-VT-A80G TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       10.72         4.80        38.27        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C7 
       63.35        18.08        45.34        35.18        20.65        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       36.43         4.37        13.38        15.95 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.49               0.56 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            188.15             159.29 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             26.43              34.01 
[1] "0.5 - 188.2 (26.4)" "0.6 - 159.3 (34.0)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  10P LOSS MUTATED                1                  5                   0
  10P LOSS WILD-TYPE              0                  2                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  10P LOSS MUTATED                     0                             2
  10P LOSS WILD-TYPE                   1                             0
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  10P LOSS MUTATED                       1                     13
  10P LOSS WILD-TYPE                     0                     15
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  10P LOSS MUTATED                      1                    0
  10P LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  10P LOSS MUTATED                                       0
  10P LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  10P LOSS MUTATED                                  0
  10P LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  10P LOSS MUTATED                                                2
  10P LOSS WILD-TYPE                                              0
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  10P LOSS MUTATED                                 5
  10P LOSS WILD-TYPE                               5
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  10P LOSS MUTATED                                         0
  10P LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  10P LOSS MUTATED                              2                       1
  10P LOSS WILD-TYPE                            2                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  10P LOSS MUTATED                                  9
  10P LOSS WILD-TYPE                                8
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  10P LOSS MUTATED                                         2
  10P LOSS WILD-TYPE                                       3
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  10P LOSS MUTATED                             22
  10P LOSS WILD-TYPE                           22
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  10P LOSS MUTATED                                         3
  10P LOSS WILD-TYPE                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  10P LOSS MUTATED                                           1
  10P LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  10P LOSS MUTATED                                                  1
  10P LOSS WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  10P LOSS MUTATED                                          2
  10P LOSS WILD-TYPE                                        6
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  10P LOSS MUTATED                                                         2
  10P LOSS WILD-TYPE                                                       0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  10P LOSS MUTATED                                            1
  10P LOSS WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  10P LOSS MUTATED                                                  27
  10P LOSS WILD-TYPE                                                46
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  10P LOSS MUTATED                                                    1
  10P LOSS WILD-TYPE                                                  2
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  10P LOSS MUTATED                                    2
  10P LOSS WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  10P LOSS MUTATED                          3                           3
  10P LOSS WILD-TYPE                        2                           1
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  10P LOSS MUTATED                           0
  10P LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  10P LOSS MUTATED                                   5
  10P LOSS WILD-TYPE                                 2
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  10P LOSS MUTATED                                   3
  10P LOSS WILD-TYPE                                 2
D60V3, multiclass
                                                         clus
vv                                                        10P LOSS MUTATED
  CHEST - BREAST                                                         1
  CHEST - CHEST WALL                                                     5
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          2
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                13
  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                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           2
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                       9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                2
  LOWER EXTREMITY - THIGH/KNEE                                          22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     27
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               3
  SUPERFICIAL TRUNK - BUTTOCK                                            3
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      3
                                                         clus
vv                                                        10P LOSS WILD-TYPE
  CHEST - BREAST                                                           0
  CHEST - CHEST WALL                                                       2
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            0
  GYNECOLOGICAL - OVARY                                                    0
  GYNECOLOGICAL - UTERUS                                                  15
  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                           0
  LOWER ABDOMINAL/PELVIC - PELVIC                                          5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             2
  LOWER EXTREMITY - GROIN                                                  1
  LOWER EXTREMITY - LOWER LEG/CALF                                         8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  3
  LOWER EXTREMITY - THIGH/KNEE                                            22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 6
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       46
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 2
  SUPERFICIAL TRUNK - BUTTOCK                                              1
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        2
[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"
D60V4, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   77 44
  10P LOSS WILD-TYPE 62 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     77   44
  10P LOSS WILD-TYPE   62   74
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               77                 62
  MALE                 44                 74
[1] 2 2
[1] FALSE
D60V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    79  41
  10P LOSS WILD-TYPE 100  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     79   41
  10P LOSS WILD-TYPE  100   31
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                79                100
  YES               41                 31
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  10P LOSS MUTATED                             12             0
  10P LOSS WILD-TYPE                           47             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  10P LOSS MUTATED                                                                          0
  10P LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  10P LOSS MUTATED                     61
  10P LOSS WILD-TYPE                   42
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  10P LOSS MUTATED                                                  7
  10P LOSS WILD-TYPE                                                2
                    vv
clus                 MYXOFIBROSARCOMA
  10P LOSS MUTATED                 13
  10P LOSS WILD-TYPE               11
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  10P LOSS MUTATED                                                         14
  10P LOSS WILD-TYPE                                                       14
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  10P LOSS MUTATED                                          0
  10P LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  10P LOSS MUTATED                             0                             1
  10P LOSS WILD-TYPE                           2                             5
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  10P LOSS MUTATED                                           13
  10P LOSS WILD-TYPE                                          8
D60V6, multiclass
                                                                          clus
vv                                                                         10P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           12
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   61
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        7
  MYXOFIBROSARCOMA                                                                       13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             13
                                                                          clus
vv                                                                         10P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             47
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     42
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          2
  MYXOFIBROSARCOMA                                                                         11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                8
[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
  10P LOSS MUTATED   74 29  4 13
  10P LOSS WILD-TYPE 78 40  5 13
D60V7, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               74                 78
  R1               29                 40
  R2                4                  5
  RX               13                 13
[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
  10P LOSS MUTATED       4                        13   100
  10P LOSS WILD-TYPE     2                         5   124
D60V8, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    4                  2
  BLACK OR AFRICAN AMERICAN               13                  5
  WHITE                                  100                124
[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"
D60V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1 107
  10P LOSS WILD-TYPE   4 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1  107
  10P LOSS WILD-TYPE    4  113
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO              107                113
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   78 53
  10Q LOSS WILD-TYPE 81 45
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               131                126 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                53                 45 
$`10Q LOSS MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       16.18        34.36        75.32        15.22        17.95        14.43 
TCGA-DX-AB2P TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       12.07        37.02        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-PC-A5DP 
       28.21        22.62        11.70        17.75         6.35        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ 
       20.94       188.15        17.52        50.01        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ 
       88.57        44.91        25.25        14.37        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A3U7 
       36.03        26.56        68.61        18.54         6.28        51.02 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K 
       14.99        10.68        68.55        34.88        85.45        45.99 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 
       24.26        52.77        46.03        26.47       108.82        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YQ 
       15.95        37.41        82.68        36.33        31.96         3.06 
TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM 
       41.00        16.87        86.30        64.21       101.23        62.20 
TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV 
        9.34        40.77       150.35        27.95        40.44        60.66 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2T 
        6.58         1.15        17.79        12.00        86.10        77.88 
TCGA-DX-AB2V TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
      106.55        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV 
       15.48        67.63         4.57        33.30         0.72        80.48 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA 
        3.22         1.38        19.89        25.22       171.09        13.58 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU 
       16.41         1.05         3.91       101.26        62.17        23.38 
TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H 
       63.81        35.28        25.41         0.49        21.73        14.99 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V9 
       10.45         7.36        37.55        81.01        13.08        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 
       48.59        35.90        37.12        10.52        16.77        18.94 
TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS 
       22.82         8.61        13.41        10.72        12.46        84.79 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       65.46        22.62        26.43        35.90        18.08        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X9-A971 TCGA-Z4-AAPG 
       35.18        19.17        50.86        27.32        15.98 

$`10Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        31.53        34.68        67.20        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       40.60       106.45        13.28        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-IS-A3K8 TCGA-MB-A5Y9 
       60.00        84.66        32.15        16.60       159.29         8.28 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HT TCGA-3B-A9HX 
       26.17        41.49        35.08        19.69        54.74        42.84 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ 
       18.64         0.56        14.04        32.71        12.85        45.11 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB 
       33.44        44.68        31.86        35.77         4.54        73.87 
TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48V TCGA-DX-A6BE TCGA-DX-A6BG 
       50.43         9.73        35.28        59.84        28.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN 
       26.99        78.28        50.50        21.30        34.49        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL 
      152.12        29.49        48.20        20.05        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AB2G TCGA-DX-AB2L 
       47.87        38.17        36.69        19.43        15.72        65.98 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A8OO 
       66.74         9.21        50.40        50.89        71.31         8.05 
TCGA-HB-A3L4 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IF-A3RQ TCGA-IW-A3M4 TCGA-IW-A3M5 
       34.88         9.80        19.53        37.12        85.97         5.92 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I 
       53.33       123.78        17.36         5.19        16.41        30.31 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN 
       19.73        17.98        22.39        11.57       122.96        38.63 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       17.65         1.84        18.08       130.32       111.98        64.77 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT 
        0.72         3.88        25.35        32.75        19.63        13.22 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WC 
       11.93         4.80        38.27         8.58        63.35        45.34 
TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       20.65        29.46        36.43         4.37        13.38        15.95 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.49               0.56 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            188.15             159.29 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            26.560             33.485 
[1] "0.5 - 188.2 (26.6)" "0.6 - 159.3 (33.5)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  10Q LOSS MUTATED                0                  4                   0
  10Q LOSS WILD-TYPE              1                  3                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  10Q LOSS MUTATED                     1                             2
  10Q LOSS WILD-TYPE                   0                             0
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  10Q LOSS MUTATED                       1                     18
  10Q LOSS WILD-TYPE                     0                     10
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  10Q LOSS MUTATED                      1                    0
  10Q LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  10Q LOSS MUTATED                                       0
  10Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  10Q LOSS MUTATED                                  0
  10Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  10Q LOSS MUTATED                                                2
  10Q LOSS WILD-TYPE                                              0
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  10Q LOSS MUTATED                                 5
  10Q LOSS WILD-TYPE                               5
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  10Q LOSS MUTATED                                         0
  10Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  10Q LOSS MUTATED                              2                       1
  10Q LOSS WILD-TYPE                            2                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  10Q LOSS MUTATED                                 10
  10Q LOSS WILD-TYPE                                7
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  10Q LOSS MUTATED                                         4
  10Q LOSS WILD-TYPE                                       1
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  10Q LOSS MUTATED                             21
  10Q LOSS WILD-TYPE                           23
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  10Q LOSS MUTATED                                         3
  10Q LOSS WILD-TYPE                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  10Q LOSS MUTATED                                           1
  10Q LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  10Q LOSS MUTATED                                                  1
  10Q LOSS WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  10Q LOSS MUTATED                                          4
  10Q LOSS WILD-TYPE                                        4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  10Q LOSS MUTATED                                                         2
  10Q LOSS WILD-TYPE                                                       0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  10Q LOSS MUTATED                                            1
  10Q LOSS WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  10Q LOSS MUTATED                                                  28
  10Q LOSS WILD-TYPE                                                45
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  10Q LOSS MUTATED                                                    2
  10Q LOSS WILD-TYPE                                                  1
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  10Q LOSS MUTATED                                    2
  10Q LOSS WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  10Q LOSS MUTATED                          3                           3
  10Q LOSS WILD-TYPE                        2                           1
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  10Q LOSS MUTATED                           0
  10Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  10Q LOSS MUTATED                                   6
  10Q LOSS WILD-TYPE                                 1
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  10Q LOSS MUTATED                                   3
  10Q LOSS WILD-TYPE                                 2
D61V3, multiclass
                                                         clus
vv                                                        10Q LOSS MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     4
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    1
  CHEST - OTHER (PLEASE SPECIFY                                          2
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                18
  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                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           2
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                      10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                4
  LOWER EXTREMITY - THIGH/KNEE                                          21
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     28
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               3
  SUPERFICIAL TRUNK - BUTTOCK                                            3
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      3
                                                         clus
vv                                                        10Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       3
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      0
  CHEST - OTHER (PLEASE SPECIFY                                            0
  GYNECOLOGICAL - OVARY                                                    0
  GYNECOLOGICAL - UTERUS                                                  10
  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                           0
  LOWER ABDOMINAL/PELVIC - PELVIC                                          5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             2
  LOWER EXTREMITY - GROIN                                                  1
  LOWER EXTREMITY - LOWER LEG/CALF                                         7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  1
  LOWER EXTREMITY - THIGH/KNEE                                            23
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       45
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 2
  SUPERFICIAL TRUNK - BUTTOCK                                              1
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        2
[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"
D61V4, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   82 49
  10Q LOSS WILD-TYPE 57 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     82   49
  10Q LOSS WILD-TYPE   57   69
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               82                 57
  MALE                 49                 69
[1] 2 2
[1] FALSE
D61V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   85 42
  10Q LOSS WILD-TYPE 94 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     85   42
  10Q LOSS WILD-TYPE   94   30
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                85                 94
  YES               42                 30
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  10Q LOSS MUTATED                              8             0
  10Q LOSS WILD-TYPE                           51             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  10Q LOSS MUTATED                                                                          0
  10Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  10Q LOSS MUTATED                     75
  10Q LOSS WILD-TYPE                   28
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  10Q LOSS MUTATED                                                  4
  10Q LOSS WILD-TYPE                                                5
                    vv
clus                 MYXOFIBROSARCOMA
  10Q LOSS MUTATED                 14
  10Q LOSS WILD-TYPE               10
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  10Q LOSS MUTATED                                                         15
  10Q LOSS WILD-TYPE                                                       13
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  10Q LOSS MUTATED                                          0
  10Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  10Q LOSS MUTATED                             0                             0
  10Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  10Q LOSS MUTATED                                           15
  10Q LOSS WILD-TYPE                                          6
D61V6, multiclass
                                                                          clus
vv                                                                         10Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            8
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   75
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        4
  MYXOFIBROSARCOMA                                                                       14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               15
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             15
                                                                          clus
vv                                                                         10Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             51
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     28
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          5
  MYXOFIBROSARCOMA                                                                         10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 13
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                6
[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
  10Q LOSS MUTATED   79 34  5 12
  10Q LOSS WILD-TYPE 73 35  4 14
D61V7, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               79                 73
  R1               34                 35
  R2                5                  4
  RX               12                 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
  10Q LOSS MUTATED       4                        13   109
  10Q LOSS WILD-TYPE     2                         5   115
D61V8, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    4                  2
  BLACK OR AFRICAN AMERICAN               13                  5
  WHITE                                  109                115
[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"
D61V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1 117
  10Q LOSS WILD-TYPE   4 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1  117
  10Q LOSS WILD-TYPE    4  103
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO              117                103
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    53  43
  11P LOSS WILD-TYPE 106  55
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                96                161 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                43                 55 
$`11P LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB35 
       31.53        67.20        34.36        15.22        17.95        30.51 
TCGA-DX-AB37 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IW-A3M6 
       84.66        37.02        12.62        52.11        52.27        22.62 
TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-X6-A8C6 TCGA-3B-A9HR TCGA-3B-A9HS 
       17.75         6.35       188.15        35.08        88.57        44.91 
TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX 
       14.37        42.84        18.64         0.56        32.71        68.61 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23Y 
       45.11        18.54        85.02        74.66         5.26         6.28 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.70        95.38        49.05       136.44        33.44        44.68 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       14.99        50.43        85.45        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YZ 
       46.03        15.95        31.96         3.06        78.28        86.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS 
       34.49        62.20        61.97        47.87        40.77        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2G TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B 
       36.69        60.66        15.72        77.88       106.55        50.89 
TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A6BZ 
       21.70        67.63         4.57        33.30         0.72        19.89 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42W 
       37.12        25.22         5.92         1.05       101.26        62.17 
TCGA-KD-A5QS TCGA-MB-A8JK TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DO TCGA-RN-AAAQ 
       63.81        21.73        10.45        37.55        81.01        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       19.63        10.72        12.46        84.79        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X9-A971 
       22.62         8.58        18.08        45.34        20.65        27.32 

$`11P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-A8BP 
       36.30        34.68        16.18        75.32        14.43        14.07 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       15.85        40.60        12.07       106.45        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-IE-A4EH TCGA-IS-A3K6 
      101.98        60.00        32.15        16.60        26.93        28.21 
TCGA-IS-A3K8 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 
      159.29        11.70         8.28        18.08        20.94        17.52 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       26.17        41.49        50.01        19.69        53.49        68.55 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 
       54.74        25.25        10.32        38.47        36.03        26.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23U 
       14.04        12.85        54.21        33.53        66.94        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 TCGA-DX-A3LS 
       66.87        27.81        60.30         8.58        79.17         9.04 
TCGA-DX-A3LU TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       86.83        31.86        35.77        51.02         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48R 
       73.87        68.55        34.88         9.73        45.99        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
      108.82        59.84        37.58        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX 
       28.96        36.85        26.99        41.00        50.50        16.87 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       64.21       101.23        21.30        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BR 
       48.20        20.05         9.34        45.14        38.17       150.35 
TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       40.44        19.43         6.58         1.15        17.79        12.00 
TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB3C 
       65.98        86.10        66.74         9.21        50.40        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        20.32        19.89        15.48         8.05 
TCGA-HB-A3L4 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       34.88         9.80        80.48        19.53         3.22         1.38 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO 
      171.09        13.58        85.97        16.41         3.91        53.33 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT TCGA-KD-A5QU 
      123.78        17.36        23.38         5.19        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       30.31        25.41         0.49        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QC-A7B5 
       22.39        11.57         7.36       122.96        38.63        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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-X2-A95T TCGA-X6-A7W8 
       13.22        13.41        11.93         4.80        63.35        26.43 
TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
       35.90        30.84        35.18        19.17        50.86        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       36.43         4.37        13.38        15.95        15.98 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.56               0.49 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            188.15             171.09 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             33.37              29.46 
[1] "0.6 - 188.2 (33.4)" "0.5 - 171.1 (29.5)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  11P LOSS MUTATED                0                  3                   0
  11P LOSS WILD-TYPE              1                  4                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  11P LOSS MUTATED                     0                             0
  11P LOSS WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  11P LOSS MUTATED                       1                     11
  11P LOSS WILD-TYPE                     0                     17
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  11P LOSS MUTATED                      0                    0
  11P LOSS WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  11P LOSS MUTATED                                       0
  11P LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  11P LOSS MUTATED                                  0
  11P LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  11P LOSS MUTATED                                                1
  11P LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  11P LOSS MUTATED                                 2
  11P LOSS WILD-TYPE                               8
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  11P LOSS MUTATED                                         0
  11P LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  11P LOSS MUTATED                              1                       0
  11P LOSS WILD-TYPE                            3                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  11P LOSS MUTATED                                  5
  11P LOSS WILD-TYPE                               12
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  11P LOSS MUTATED                                         5
  11P LOSS WILD-TYPE                                       0
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  11P LOSS MUTATED                             18
  11P LOSS WILD-TYPE                           26
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  11P LOSS MUTATED                                         1
  11P LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  11P LOSS MUTATED                                           1
  11P LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  11P LOSS MUTATED                                                  2
  11P LOSS WILD-TYPE                                                3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  11P LOSS MUTATED                                          4
  11P LOSS WILD-TYPE                                        4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  11P LOSS MUTATED                                                         0
  11P LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  11P LOSS MUTATED                                            1
  11P LOSS WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  11P LOSS MUTATED                                                  29
  11P LOSS WILD-TYPE                                                44
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  11P LOSS MUTATED                                                    1
  11P LOSS WILD-TYPE                                                  2
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  11P LOSS MUTATED                                    1
  11P LOSS WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  11P LOSS MUTATED                          1                           2
  11P LOSS WILD-TYPE                        4                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  11P LOSS MUTATED                           0
  11P LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  11P LOSS MUTATED                                   3
  11P LOSS WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  11P LOSS MUTATED                                   2
  11P LOSS WILD-TYPE                                 3
D62V3, multiclass
                                                         clus
vv                                                        11P LOSS MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     3
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          0
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                11
  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                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                5
  LOWER EXTREMITY - THIGH/KNEE                                          18
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     29
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        11P LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       4
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    0
  GYNECOLOGICAL - UTERUS                                                  17
  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                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  0
  LOWER EXTREMITY - THIGH/KNEE                                            26
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       44
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        4
  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"
D62V4, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   54 42
  11P LOSS WILD-TYPE 85 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     54   42
  11P LOSS WILD-TYPE   85   76
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               54                 85
  MALE                 42                 76
[1] 2 2
[1] FALSE
D62V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    62  34
  11P LOSS WILD-TYPE 117  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     62   34
  11P LOSS WILD-TYPE  117   38
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                62                117
  YES               34                 38
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  11P LOSS MUTATED                             24             0
  11P LOSS WILD-TYPE                           35             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  11P LOSS MUTATED                                                                          0
  11P LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  11P LOSS MUTATED                     38
  11P LOSS WILD-TYPE                   65
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  11P LOSS MUTATED                                                  6
  11P LOSS WILD-TYPE                                                3
                    vv
clus                 MYXOFIBROSARCOMA
  11P LOSS MUTATED                 10
  11P LOSS WILD-TYPE               14
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  11P LOSS MUTATED                                                          9
  11P LOSS WILD-TYPE                                                       19
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  11P LOSS MUTATED                                          0
  11P LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  11P LOSS MUTATED                             0                             1
  11P LOSS WILD-TYPE                           2                             5
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  11P LOSS MUTATED                                            8
  11P LOSS WILD-TYPE                                         13
D62V6, multiclass
                                                                          clus
vv                                                                         11P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           24
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   38
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        6
  MYXOFIBROSARCOMA                                                                       10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              8
                                                                          clus
vv                                                                         11P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             35
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     65
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          3
  MYXOFIBROSARCOMA                                                                         14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             5
  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
  11P LOSS MUTATED    52  27   5  11
  11P LOSS WILD-TYPE 100  42   4  15
D62V7, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               52                100
  R1               27                 42
  R2                5                  4
  RX               11                 15
[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
  11P LOSS MUTATED       2                         8    81
  11P LOSS WILD-TYPE     4                        10   143
D62V8, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                8                 10
  WHITE                                   81                143
[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"
D62V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  86
  11P LOSS WILD-TYPE   5 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   86
  11P LOSS WILD-TYPE    5  134
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               86                134
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    57  36
  11Q LOSS WILD-TYPE 102  62
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                93                164 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                36                 62 
$`11Q LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-A8BG 
       31.53        16.18        67.20        34.36        15.22        17.95 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK 
      101.98        30.51        84.66        12.62        52.11        52.27 
TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-QQ-A8VB TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HV 
       22.62        17.75       188.15        88.57        44.91        14.37 
TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ 
       42.84        38.47         0.56        32.71        68.61        45.11 
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23Y TCGA-DX-A2J0 
       18.54        85.02        74.66         5.26         6.28         9.70 
TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48L 
       95.38        49.05        44.68        14.99        50.43        24.26 
TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF 
       35.28        26.47       108.82        15.95        82.68        31.96 
TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BK TCGA-DX-A8BM 
       78.28        86.30        34.49        62.20        61.97        47.87 
TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2G 
       40.77        27.95        40.44        36.69        60.66        15.72 
TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB3B TCGA-FX-A2QS TCGA-HB-A2OT 
       86.10        77.88       106.55        50.89        49.15        67.63 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IW-A3M5 
        4.57         0.72        80.48        19.89        37.12         5.92 
TCGA-JV-A5VF TCGA-K1-A42W TCGA-KD-A5QS TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 
        1.05        62.17        63.81        35.28        30.31        25.41 
TCGA-MB-A8JK TCGA-QC-AA9N TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       21.73        17.65        16.77        18.94         3.88        22.82 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-AB3D 
       25.35        32.75         8.61        19.63        10.72        12.46 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WC 
       84.79        38.27        65.46        22.62         8.58        45.34 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A971 
       19.17        20.65        27.32 

$`11Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A7EL TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       36.30        34.68        75.32        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 
       40.60        12.07       106.45        13.28        22.85        60.00 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IS-A3K8 
       32.15        16.60        37.02        26.93        28.21       159.29 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 
       11.70         8.28         6.35        18.08        20.94        17.52 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP 
       26.17        41.49        35.08        50.01        19.69        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 
       68.55        54.74        25.25        10.32        36.03        18.64 
TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       26.56        14.04        12.85        54.21        33.53        66.94 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 
       76.41        66.87        27.81        60.30         8.58        79.17 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        86.83       136.44        33.44        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       51.02         4.54        10.68        73.87        68.55        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V 
       85.45         9.73        45.99        52.77        46.03        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       37.58        37.41        36.33        28.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
        3.06        41.00        50.50        16.87        64.21       101.23 
TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       21.30        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BX TCGA-DX-A8BZ 
        9.34        45.14        38.17       150.35        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S 
        1.15        17.79        12.00        65.98        66.74         9.21 
TCGA-DX-AB2Z TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       50.40        71.31        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EI 
       15.48         8.05        34.88        33.30         9.80        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        3.22         1.38        25.22       171.09        13.58        85.97 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
       16.41         3.91       101.26        53.33       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       23.38         5.19        16.41         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55        38.63        81.01        13.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
       64.77        10.52         0.72        13.22        13.41        11.93 
TCGA-WK-A8XQ TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
        4.80        63.35        26.43        35.90        18.08        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       35.18        50.86        29.46        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.56               0.49 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            188.15             171.09 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             34.36              29.21 
[1] "0.6 - 188.2 (34.4)" "0.5 - 171.1 (29.2)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  11Q LOSS MUTATED                0                  4                   0
  11Q LOSS WILD-TYPE              1                  3                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  11Q LOSS MUTATED                     1                             0
  11Q LOSS WILD-TYPE                   0                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  11Q LOSS MUTATED                       0                      8
  11Q LOSS WILD-TYPE                     1                     20
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  11Q LOSS MUTATED                      0                    0
  11Q LOSS WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  11Q LOSS MUTATED                                       0
  11Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  11Q LOSS MUTATED                                  0
  11Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  11Q LOSS MUTATED                                                1
  11Q LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  11Q LOSS MUTATED                                 3
  11Q LOSS WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  11Q LOSS MUTATED                                         0
  11Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  11Q LOSS MUTATED                              1                       0
  11Q LOSS WILD-TYPE                            3                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  11Q LOSS MUTATED                                  7
  11Q LOSS WILD-TYPE                               10
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  11Q LOSS MUTATED                                         3
  11Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  11Q LOSS MUTATED                             19
  11Q LOSS WILD-TYPE                           25
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  11Q LOSS MUTATED                                         1
  11Q LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  11Q LOSS MUTATED                                           1
  11Q LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  11Q LOSS MUTATED                                                  1
  11Q LOSS WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  11Q LOSS MUTATED                                          4
  11Q LOSS WILD-TYPE                                        4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  11Q LOSS MUTATED                                                         1
  11Q LOSS WILD-TYPE                                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  11Q LOSS MUTATED                                            1
  11Q LOSS WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  11Q LOSS MUTATED                                                  24
  11Q LOSS WILD-TYPE                                                49
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  11Q LOSS MUTATED                                                    1
  11Q LOSS WILD-TYPE                                                  2
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  11Q LOSS MUTATED                                    1
  11Q LOSS WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  11Q LOSS MUTATED                          1                           3
  11Q LOSS WILD-TYPE                        4                           1
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  11Q LOSS MUTATED                           0
  11Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  11Q LOSS MUTATED                                   4
  11Q LOSS WILD-TYPE                                 3
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  11Q LOSS MUTATED                                   2
  11Q LOSS WILD-TYPE                                 3
D63V3, multiclass
                                                         clus
vv                                                        11Q LOSS MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     4
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    1
  CHEST - OTHER (PLEASE SPECIFY                                          0
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 8
  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                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                3
  LOWER EXTREMITY - THIGH/KNEE                                          19
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     24
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            3
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        11Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       3
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      0
  CHEST - OTHER (PLEASE SPECIFY                                            2
  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                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  2
  LOWER EXTREMITY - THIGH/KNEE                                            25
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       49
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              1
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        3
  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"
D63V4, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   52 41
  11Q LOSS WILD-TYPE 87 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     52   41
  11Q LOSS WILD-TYPE   87   77
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               52                 87
  MALE                 41                 77
[1] 2 2
[1] FALSE
D63V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    58  35
  11Q LOSS WILD-TYPE 121  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     58   35
  11Q LOSS WILD-TYPE  121   37
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                58                121
  YES               35                 37
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  11Q LOSS MUTATED                             24             0
  11Q LOSS WILD-TYPE                           35             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  11Q LOSS MUTATED                                                                          0
  11Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  11Q LOSS MUTATED                     30
  11Q LOSS WILD-TYPE                   73
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  11Q LOSS MUTATED                                                  6
  11Q LOSS WILD-TYPE                                                3
                    vv
clus                 MYXOFIBROSARCOMA
  11Q LOSS MUTATED                 11
  11Q LOSS WILD-TYPE               13
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  11Q LOSS MUTATED                                                         11
  11Q LOSS WILD-TYPE                                                       17
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  11Q LOSS MUTATED                                          0
  11Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  11Q LOSS MUTATED                             0                             1
  11Q LOSS WILD-TYPE                           2                             5
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  11Q LOSS MUTATED                                           10
  11Q LOSS WILD-TYPE                                         11
D63V6, multiclass
                                                                          clus
vv                                                                         11Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           24
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   30
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        6
  MYXOFIBROSARCOMA                                                                       11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             10
                                                                          clus
vv                                                                         11Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             35
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     73
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          3
  MYXOFIBROSARCOMA                                                                         13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               11
[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
  11Q LOSS MUTATED    51  26   5  10
  11Q LOSS WILD-TYPE 101  43   4  16
D63V7, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               51                101
  R1               26                 43
  R2                5                  4
  RX               10                 16
[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
  11Q LOSS MUTATED       2                         8    80
  11Q LOSS WILD-TYPE     4                        10   144
D63V8, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                8                 10
  WHITE                                   80                144
[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"
D63V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  80
  11Q LOSS WILD-TYPE   5 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   80
  11Q LOSS WILD-TYPE    5  140
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               80                140
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    44  23
  12P LOSS WILD-TYPE 115  75
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                67                190 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                23                 75 
$`12P LOSS MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-AB2H TCGA-DX-AB35 
       34.68        67.20        34.36        15.22        15.85        30.51 
TCGA-IE-A4EH TCGA-KF-A41W TCGA-LI-A9QH TCGA-PC-A5DM TCGA-QC-A6FX TCGA-3B-A9HI 
       26.93        11.70        17.75         6.35        20.94        50.01 
TCGA-3B-A9HL TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A23R 
       19.69        18.64        26.56        32.71        54.21        74.66 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LY TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF 
        8.58         9.70        33.44        14.99        50.43        85.45 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6BF 
       24.26        26.47        59.84        37.58        15.95        31.96 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF 
        3.06        41.00        50.50        86.30       101.23        21.30 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       62.20        30.35        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2F 
       40.77       150.35        27.95        36.69        60.66        12.00 
TCGA-DX-AB2T TCGA-FX-A3NJ TCGA-HS-A5N7 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-JV-A5VE 
       77.88        31.13        33.30         3.22        19.89        16.41 
TCGA-JV-A5VF TCGA-K1-A6RV TCGA-KD-A5QU TCGA-MJ-A68H TCGA-QC-A7B5 TCGA-QQ-A5VB 
        1.05         5.19        35.28        14.99        13.08        48.59 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X2-A95T 
       18.94         3.88        22.82        84.79        38.27        63.35 
TCGA-X6-A7WD 
       30.84 

$`12P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BH 
       36.30        31.53        16.18        75.32        17.95        14.43 
TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       14.07        40.60        12.07       106.45        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z 
      101.98        60.00        84.66        32.15        16.60        37.02 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 
       12.62        52.11        52.27        28.21       159.29        22.62 
TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
        8.28        18.08       188.15        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       35.08        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        14.04        68.61        12.85        45.11        18.54 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       85.02        33.53        66.94         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
        6.28        27.81        60.30        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       49.05        86.83       136.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       51.02         4.54        10.68        73.87        68.55        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
        9.73        45.99        35.28        52.77        46.03       108.82 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       37.41        82.68        36.33        28.96        36.85        26.99 
TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ 
       78.28        16.87        64.21        34.49       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ 
       48.20        20.05         9.34        40.44        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
        1.15        17.79        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       34.88         4.57         0.72         9.80        80.48        19.53 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        37.12        25.22       171.09        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        5.92         3.91       101.26        53.33        62.17       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 
       17.36        23.38        63.81        16.41        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        21.73        19.73        17.98        22.39        11.57 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       10.45         7.36       122.96        37.55        38.63        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
       17.65         1.84        46.82        18.08        35.90        37.12 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
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-A8XY TCGA-WK-A8Y0 
       10.72        12.46        11.93         4.80        65.46        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
        8.58        26.43        35.90        18.08        45.34        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       19.17        20.65        50.86        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.05               0.49 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            150.35             188.15 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             31.13              30.92 
[1] "1.1 - 150.3 (31.1)" "0.5 - 188.2 (30.9)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  12P LOSS MUTATED                0                  2                   0
  12P LOSS WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  12P LOSS MUTATED                     0                             0
  12P LOSS WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  12P LOSS MUTATED                       0                      5
  12P LOSS WILD-TYPE                     1                     23
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  12P LOSS MUTATED                      1                    0
  12P LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  12P LOSS MUTATED                                       0
  12P LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  12P LOSS MUTATED                                  0
  12P LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  12P LOSS MUTATED                                                2
  12P LOSS WILD-TYPE                                              0
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  12P LOSS MUTATED                                 2
  12P LOSS WILD-TYPE                               8
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  12P LOSS MUTATED                                         0
  12P LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  12P LOSS MUTATED                              0                       1
  12P LOSS WILD-TYPE                            4                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  12P LOSS MUTATED                                  4
  12P LOSS WILD-TYPE                               13
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  12P LOSS MUTATED                                         3
  12P LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  12P LOSS MUTATED                             14
  12P LOSS WILD-TYPE                           30
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  12P LOSS MUTATED                                         1
  12P LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  12P LOSS MUTATED                                           1
  12P LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  12P LOSS MUTATED                                                  0
  12P LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  12P LOSS MUTATED                                          3
  12P LOSS WILD-TYPE                                        5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  12P LOSS MUTATED                                                         0
  12P LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  12P LOSS MUTATED                                            0
  12P LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  12P LOSS MUTATED                                                  22
  12P LOSS WILD-TYPE                                                51
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  12P LOSS MUTATED                                                    0
  12P LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  12P LOSS MUTATED                                    1
  12P LOSS WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  12P LOSS MUTATED                          1                           1
  12P LOSS WILD-TYPE                        4                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  12P LOSS MUTATED                           0
  12P LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  12P LOSS MUTATED                                   2
  12P LOSS WILD-TYPE                                 5
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  12P LOSS MUTATED                                   1
  12P LOSS WILD-TYPE                                 4
D64V3, multiclass
                                                         clus
vv                                                        12P LOSS 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                                                 5
  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                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        2
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                       4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                3
  LOWER EXTREMITY - THIGH/KNEE                                          14
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     22
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            1
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        12P LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  23
  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                           0
  LOWER ABDOMINAL/PELVIC - PELVIC                                          8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  1
  LOWER EXTREMITY - LOWER LEG/CALF                                        13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  2
  LOWER EXTREMITY - THIGH/KNEE                                            30
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       51
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              3
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    34  33
  12P LOSS WILD-TYPE 105  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     34   33
  12P LOSS WILD-TYPE  105   85
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               34                105
  MALE                 33                 85
[1] 2 2
[1] FALSE
D64V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    45  20
  12P LOSS WILD-TYPE 134  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     45   20
  12P LOSS WILD-TYPE  134   52
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                45                134
  YES               20                 52
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  12P LOSS MUTATED                             14             0
  12P LOSS WILD-TYPE                           45             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  12P LOSS MUTATED                                                                          0
  12P LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  12P LOSS MUTATED                     28
  12P LOSS WILD-TYPE                   75
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  12P LOSS MUTATED                                                  1
  12P LOSS WILD-TYPE                                                8
                    vv
clus                 MYXOFIBROSARCOMA
  12P LOSS MUTATED                  8
  12P LOSS WILD-TYPE               16
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  12P LOSS MUTATED                                                         14
  12P LOSS WILD-TYPE                                                       14
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  12P LOSS MUTATED                                          0
  12P LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  12P LOSS MUTATED                             0                             0
  12P LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  12P LOSS MUTATED                                            2
  12P LOSS WILD-TYPE                                         19
D64V6, multiclass
                                                                          clus
vv                                                                         12P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           14
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   28
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                        8
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               14
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              2
                                                                          clus
vv                                                                         12P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             45
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     75
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          8
  MYXOFIBROSARCOMA                                                                         16
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 14
  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
  12P LOSS MUTATED    41  19   2   5
  12P LOSS WILD-TYPE 111  50   7  21
D64V7, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               41                111
  R1               19                 50
  R2                2                  7
  RX                5                 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
  12P LOSS MUTATED       0                         7    58
  12P LOSS WILD-TYPE     6                        11   166
D64V8, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                7                 11
  WHITE                                   58                166
[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"
D64V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  61
  12P LOSS WILD-TYPE   5 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   61
  12P LOSS WILD-TYPE    5  159
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               61                159
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    38  21
  12Q LOSS WILD-TYPE 121  77
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                59                198 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                21                 77 
$`12Q LOSS MUTATED`
TCGA-DX-A6YU TCGA-DX-A7ET TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB35 TCGA-IE-A4EH 
       34.36        15.22        15.85        12.07        30.51        26.93 
TCGA-KF-A41W TCGA-PC-A5DM TCGA-QC-A6FX TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HU 
       11.70         6.35        20.94        50.01        19.69        25.25 
TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y 
       38.47        26.56        32.71        54.21        74.66         6.28 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LY TCGA-DX-A3UF TCGA-DX-A48L 
        8.58         9.70         9.04        33.44        85.45        24.26 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YV TCGA-DX-A6YX 
       26.47        15.95        82.68        31.96        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BN 
       86.30        21.30        62.20        30.35        61.97        38.17 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2T TCGA-FX-A3NJ 
      150.35        27.95        17.79        12.00        77.88        31.13 
TCGA-HS-A5N7 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KD-A5QU 
       33.30         3.22        19.89        16.41         1.05        35.28 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z7 
       21.73        14.99        81.01        13.08        48.59         3.88 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X2-A95T TCGA-X6-A7WD TCGA-X9-A971 
       84.79        38.27        63.35        30.84        27.32 

$`12Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        67.20        75.32 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X 
       17.95        14.43        14.07        40.60       106.45        13.28 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
       22.85       101.98        60.00        84.66        32.15        16.60 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       37.02        12.62        52.11        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-SG-A849 
       22.62        17.75         8.28        18.08       188.15        17.52 
TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       26.17        41.49        35.08        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I0 
       44.91        54.74        14.37        42.84        10.32        36.03 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       18.64         0.56        14.04        68.61        12.85        45.11 
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       18.54        85.02        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       66.87        27.81        60.30        95.38        79.17        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       86.83       136.44        44.68        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        73.87        68.55        50.43 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        45.99        35.28        52.77        46.03 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
      108.82        59.84        37.58        37.41        36.33        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6Z0 
       36.85        26.99         3.06        41.00        78.28        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
      101.23        34.49       152.12        29.49        48.20        20.05 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BT TCGA-DX-A8BU 
        9.34        45.14        47.87        40.77        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2G TCGA-DX-AB2L 
       60.66        19.43         6.58         1.15        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       86.10        66.74         9.21       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       71.31        49.15        21.70        20.32        19.89        15.48 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA 
        8.05        67.63        34.88         4.57         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
       80.48        19.53         1.38        37.12        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        85.97         5.92         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS 
       62.17       123.78        17.36        23.38         5.19        63.81 
TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       16.41        30.31        25.41         0.49        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       38.63        17.65         1.84        46.82        18.08        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       16.77        18.94        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-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA 
        4.80        65.46        22.62         8.58        26.43        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08        45.34        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       29.46        36.43         4.37        13.38        15.95        15.98 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              1.05               0.49 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            150.35             188.15 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             27.32              34.01 
[1] "1.1 - 150.3 (27.3)" "0.5 - 188.2 (34.0)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  12Q LOSS MUTATED                0                  1                   0
  12Q LOSS WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  12Q LOSS MUTATED                     1                             0
  12Q LOSS WILD-TYPE                   0                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  12Q LOSS MUTATED                       0                      4
  12Q LOSS WILD-TYPE                     1                     24
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  12Q LOSS MUTATED                      1                    0
  12Q LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  12Q LOSS MUTATED                                       0
  12Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  12Q LOSS MUTATED                                  0
  12Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  12Q LOSS MUTATED                                                1
  12Q LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  12Q LOSS MUTATED                                 3
  12Q LOSS WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  12Q LOSS MUTATED                                         0
  12Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  12Q LOSS MUTATED                              0                       1
  12Q LOSS WILD-TYPE                            4                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  12Q LOSS MUTATED                                  2
  12Q LOSS WILD-TYPE                               15
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  12Q LOSS MUTATED                                         1
  12Q LOSS WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  12Q LOSS MUTATED                             12
  12Q LOSS WILD-TYPE                           32
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  12Q LOSS MUTATED                                         0
  12Q LOSS WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  12Q LOSS MUTATED                                           1
  12Q LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  12Q LOSS MUTATED                                                  0
  12Q LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  12Q LOSS MUTATED                                          2
  12Q LOSS WILD-TYPE                                        6
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  12Q LOSS MUTATED                                                         0
  12Q LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  12Q LOSS MUTATED                                            0
  12Q LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  12Q LOSS MUTATED                                                  22
  12Q LOSS WILD-TYPE                                                51
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  12Q LOSS MUTATED                                                    0
  12Q LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  12Q LOSS MUTATED                                    1
  12Q LOSS WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  12Q LOSS MUTATED                          1                           1
  12Q LOSS WILD-TYPE                        4                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  12Q LOSS MUTATED                           0
  12Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  12Q LOSS MUTATED                                   3
  12Q LOSS WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  12Q LOSS MUTATED                                   1
  12Q LOSS WILD-TYPE                                 4
D65V3, multiclass
                                                         clus
vv                                                        12Q LOSS 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                                                 4
  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                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                       2
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     22
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            1
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        12Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      0
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  24
  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                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  1
  LOWER EXTREMITY - LOWER LEG/CALF                                        15
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            32
  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                       51
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              3
  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"
D65V4, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    34  25
  12Q LOSS WILD-TYPE 105  93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     34   25
  12Q LOSS WILD-TYPE  105   93
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               34                105
  MALE                 25                 93
[1] 2 2
[1] FALSE
D65V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    41  16
  12Q LOSS WILD-TYPE 138  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     41   16
  12Q LOSS WILD-TYPE  138   56
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                41                138
  YES               16                 56
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  12Q LOSS MUTATED                             15             0
  12Q LOSS WILD-TYPE                           44             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  12Q LOSS MUTATED                                                                          0
  12Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  12Q LOSS MUTATED                     26
  12Q LOSS WILD-TYPE                   77
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  12Q LOSS MUTATED                                                  0
  12Q LOSS WILD-TYPE                                                9
                    vv
clus                 MYXOFIBROSARCOMA
  12Q LOSS MUTATED                  6
  12Q LOSS WILD-TYPE               18
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  12Q LOSS MUTATED                                                         10
  12Q LOSS WILD-TYPE                                                       18
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  12Q LOSS MUTATED                                          0
  12Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  12Q LOSS MUTATED                             0                             0
  12Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  12Q LOSS MUTATED                                            2
  12Q LOSS WILD-TYPE                                         19
D65V6, multiclass
                                                                          clus
vv                                                                         12Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           15
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   26
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        0
  MYXOFIBROSARCOMA                                                                        6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              2
                                                                          clus
vv                                                                         12Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             44
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     77
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          9
  MYXOFIBROSARCOMA                                                                         18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 18
  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
  12Q LOSS MUTATED    37  17   1   4
  12Q LOSS WILD-TYPE 115  52   8  22
D65V7, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               37                115
  R1               17                 52
  R2                1                  8
  RX                4                 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
  12Q LOSS MUTATED       0                         7    50
  12Q LOSS WILD-TYPE     6                        11   174
D65V8, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                7                 11
  WHITE                                   50                174
[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"
D65V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  53
  12Q LOSS WILD-TYPE   5 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   53
  12Q LOSS WILD-TYPE    5  167
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               53                167
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   78 54
  13Q LOSS WILD-TYPE 81 44
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               132                125 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                54                 44 
$`13Q LOSS MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH 
       16.18        67.20        34.36        75.32        15.22        14.43 
TCGA-DX-A8BP TCGA-DX-AB2W TCGA-DX-AB35 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IW-A3M6 
       14.07       106.45        30.51        37.02        12.62        22.62 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 
       11.70         8.28         6.35        20.94       188.15        17.52 
TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       26.17        35.08        19.69        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 
       25.25        42.84        10.32        38.47        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        0.56        14.04        68.61        45.11        18.54        54.21 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY 
       74.66         6.28         9.70         9.04        49.05        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J 
       44.68        14.99        68.55        50.43        85.45         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6B8 
       45.99        24.26        52.77        46.03        59.84        15.95 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YX 
       82.68        36.33        31.96         3.06        78.28        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN 
       86.30        64.21       101.23        21.30        62.20        30.35 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BT TCGA-DX-A8BU 
        9.34        61.97        45.14        40.77        40.44        36.69 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V 
        1.15        17.79        12.00        86.10        66.74       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT 
       50.40        50.89        21.70        20.32        19.89        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ 
       34.88         4.57        33.30         0.72         9.80         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-JV-A75J 
       19.89        37.12       171.09        85.97         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 
      101.26        62.17        23.38        63.81        35.28        25.41 
TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 
       19.73        10.45         7.36        37.55        81.01        13.08 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-RN-AAAQ 
       46.82        18.08        48.59        35.90        10.52        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C 
       18.94         3.88        22.82        25.35         8.61        19.63 
TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       10.72        11.93        84.79        38.27        65.46        22.62 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       26.43        35.90        45.34        19.17        20.65        50.86 

$`13Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A8BG TCGA-DX-AB2H TCGA-DX-AB2J 
       36.30        31.53        34.68        17.95        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 
       12.07        13.28        22.85       101.98        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       32.15        16.60        52.11        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-PC-A5DP TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HP 
      159.29        17.75        18.08        41.49        50.01        53.49 
TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L2 
       44.91        14.37        36.03        32.71        12.85        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        66.94         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW 
       60.30         8.58        95.38        79.17        86.83       136.44 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       31.86        35.77        51.02         4.54        10.68        73.87 
TCGA-DX-A3UE TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
       34.88        35.28        26.47       108.82        37.58        37.41 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A7EI 
       28.96        36.85        26.99        41.00        50.50        34.49 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BM TCGA-DX-A8BN 
      152.12        29.49        48.20        20.05        47.87        38.17 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2G 
      150.35        27.95        60.66        19.43         6.58        15.72 
TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       65.98         9.21        77.88        71.31        49.15        31.13 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
       15.48         8.05        80.48        19.53         1.38        25.22 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
       13.58         5.92        16.41        53.33       123.78        17.36 
TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H 
        5.19        16.41        30.31         0.49        21.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QC-AA9N 
       17.98        22.39        11.57       122.96        38.63        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
        1.84        37.12       130.32       111.98        64.77         0.72 
TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XQ TCGA-WP-A9GB 
       32.75        13.22        13.41        12.46         4.80         8.58 
TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C7 TCGA-X9-A971 
       63.35        18.08        30.84        35.18        29.46        27.32 
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 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.56               0.49 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            188.15             159.29 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             30.43              31.53 
[1] "0.6 - 188.2 (30.4)" "0.5 - 159.3 (31.5)"
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  13Q LOSS MUTATED                1                  3                   0
  13Q LOSS WILD-TYPE              0                  4                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  13Q LOSS MUTATED                     1                             2
  13Q LOSS WILD-TYPE                   0                             0
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  13Q LOSS MUTATED                       1                     15
  13Q LOSS WILD-TYPE                     0                     13
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  13Q LOSS MUTATED                      1                    0
  13Q LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  13Q LOSS MUTATED                                       1
  13Q LOSS WILD-TYPE                                     1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  13Q LOSS MUTATED                                  0
  13Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  13Q LOSS MUTATED                                                1
  13Q LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  13Q LOSS MUTATED                                 4
  13Q LOSS WILD-TYPE                               6
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  13Q LOSS MUTATED                                         0
  13Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  13Q LOSS MUTATED                              1                       1
  13Q LOSS WILD-TYPE                            3                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  13Q LOSS MUTATED                                 10
  13Q LOSS WILD-TYPE                                7
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  13Q LOSS MUTATED                                         5
  13Q LOSS WILD-TYPE                                       0
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  13Q LOSS MUTATED                             22
  13Q LOSS WILD-TYPE                           22
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  13Q LOSS MUTATED                                         1
  13Q LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  13Q LOSS MUTATED                                           1
  13Q LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  13Q LOSS MUTATED                                                  1
  13Q LOSS WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  13Q LOSS MUTATED                                          4
  13Q LOSS WILD-TYPE                                        4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  13Q LOSS MUTATED                                                         1
  13Q LOSS WILD-TYPE                                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  13Q LOSS MUTATED                                            1
  13Q LOSS WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  13Q LOSS MUTATED                                                  38
  13Q LOSS WILD-TYPE                                                35
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  13Q LOSS MUTATED                                                    2
  13Q LOSS WILD-TYPE                                                  1
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  13Q LOSS MUTATED                                    2
  13Q LOSS WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  13Q LOSS MUTATED                          2                           2
  13Q LOSS WILD-TYPE                        3                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  13Q LOSS MUTATED                           0
  13Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  13Q LOSS MUTATED                                   5
  13Q LOSS WILD-TYPE                                 2
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  13Q LOSS MUTATED                                   2
  13Q LOSS WILD-TYPE                                 3
D66V3, multiclass
                                                         clus
vv                                                        13Q LOSS MUTATED
  CHEST - BREAST                                                         1
  CHEST - CHEST WALL                                                     3
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    1
  CHEST - OTHER (PLEASE SPECIFY                                          2
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                15
  HEAD AND NECK - HEAD                                                   1
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  1
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                      10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                5
  LOWER EXTREMITY - THIGH/KNEE                                          22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     38
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        13Q LOSS WILD-TYPE
  CHEST - BREAST                                                           0
  CHEST - CHEST WALL                                                       4
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      0
  CHEST - OTHER (PLEASE SPECIFY                                            0
  GYNECOLOGICAL - OVARY                                                    0
  GYNECOLOGICAL - UTERUS                                                  13
  HEAD AND NECK - HEAD                                                     1
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    1
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           1
  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                                         7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  0
  LOWER EXTREMITY - THIGH/KNEE                                            22
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 4
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       35
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        2
  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"
D66V4, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   79 53
  13Q LOSS WILD-TYPE 60 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     79   53
  13Q LOSS WILD-TYPE   60   65
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               79                 60
  MALE                 53                 65
[1] 2 2
[1] FALSE
D66V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   89 42
  13Q LOSS WILD-TYPE 90 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     89   42
  13Q LOSS WILD-TYPE   90   30
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                89                 90
  YES               42                 30
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  13Q LOSS MUTATED                             22             0
  13Q LOSS WILD-TYPE                           37             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  13Q LOSS MUTATED                                                                          0
  13Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  13Q LOSS MUTATED                     58
  13Q LOSS WILD-TYPE                   45
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  13Q LOSS MUTATED                                                  6
  13Q LOSS WILD-TYPE                                                3
                    vv
clus                 MYXOFIBROSARCOMA
  13Q LOSS MUTATED                 13
  13Q LOSS WILD-TYPE               11
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  13Q LOSS MUTATED                                                         18
  13Q LOSS WILD-TYPE                                                       10
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  13Q LOSS MUTATED                                          0
  13Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  13Q LOSS MUTATED                             0                             1
  13Q LOSS WILD-TYPE                           2                             5
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  13Q LOSS MUTATED                                           14
  13Q LOSS WILD-TYPE                                          7
D66V6, multiclass
                                                                          clus
vv                                                                         13Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           22
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   58
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        6
  MYXOFIBROSARCOMA                                                                       13
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             14
                                                                          clus
vv                                                                         13Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             37
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     45
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          3
  MYXOFIBROSARCOMA                                                                         11
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                7
[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
  13Q LOSS MUTATED   72 38  6 15
  13Q LOSS WILD-TYPE 80 31  3 11
D66V7, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               72                 80
  R1               38                 31
  R2                6                  3
  RX               15                 11
[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
  13Q LOSS MUTATED       3                         9   114
  13Q LOSS WILD-TYPE     3                         9   110
D66V8, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    3                  3
  BLACK OR AFRICAN AMERICAN                9                  9
  WHITE                                  114                110
[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"
D66V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     2 116
  13Q LOSS WILD-TYPE   3 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2  116
  13Q LOSS WILD-TYPE    3  104
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              116                104
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    43  19
  14Q LOSS WILD-TYPE 116  79
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                62                195 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                 79 
$`14Q LOSS MUTATED`
TCGA-DX-A3M2 TCGA-DX-A6YU TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB35 TCGA-IS-A3K6 
       34.68        34.36        12.07       101.98        30.51        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-3B-A9HL TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-DX-A1KU 
      159.29        22.62        19.69        42.84        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A3LT 
       32.71        68.61        45.11        85.02        74.66        49.05 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       86.83        33.44        31.86        35.28        52.77        46.03 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A8BM 
      108.82        37.58        15.95        86.30       101.23        47.87 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2O 
       38.17        40.77        40.44        36.69         6.58        86.10 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HS-A5N8 
       49.15        31.13        19.89        15.48        34.88         0.72 
TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VE 
        9.80         3.22        37.12       171.09        85.97        16.41 
TCGA-JV-A5VF TCGA-K1-A42X TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-QC-A7B5 
        1.05       123.78        63.81        35.28        25.41        13.08 
TCGA-QQ-A5V9 TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-AA8B TCGA-VT-A80G TCGA-WP-A9GB 
       46.82        16.77        25.35         8.61        10.72         8.58 
TCGA-X6-A7WB TCGA-X6-A8C2 
       18.08        35.18 

$`14Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A7EL TCGA-DX-A7ET 
       36.30        31.53        16.18        67.20        75.32        15.22 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W 
       17.95        14.43        14.07        15.85        40.60       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
       13.28        22.85        60.00        84.66        32.15        16.60 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-KF-A41W 
       37.02        12.62        52.11        26.93        52.27        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB 
       17.75         8.28         6.35        18.08        20.94       188.15 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HP 
       17.52        26.17        41.49        35.08        50.01        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       68.55        88.57        44.91        54.74        25.25        14.37 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KY 
       10.32        38.47        36.03        18.64         0.56        12.85 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       18.54        54.21        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 
       95.38        79.17         9.04       136.44        44.68        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       51.02         4.54        14.99        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       50.43        34.88        85.45         9.73        45.99        24.26 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       26.47        59.84        37.41        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       31.96        36.85        26.99         3.06        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM 
       50.50        16.87        64.21        21.30        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-A8BX 
       61.97        45.14       150.35        27.95        60.66        19.43 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q 
        1.15        17.79        12.00        15.72        65.98        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
        9.21        77.88       106.55        50.40        50.89        71.31 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 
       21.70        20.32         8.05        67.63         4.57        33.30 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3KA 
       80.48        19.53         1.38        19.89        25.22        13.58 
TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT 
        5.92         3.91       101.26        53.33        62.17        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK 
       23.38         5.19        16.41        30.31         0.49        21.73 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N 
        7.36       122.96        37.55        38.63        81.01        17.65 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
        1.84        18.08        48.59        35.90        37.12       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 
      111.98        64.77        10.52         0.72        18.94         3.88 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D 
       22.82        32.75        19.63        13.22        13.41        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        84.79        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 
       63.35        26.43        35.90        45.34        30.84        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       20.65        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       13.38        15.95        15.98 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.72               0.49 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            171.09             188.15 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             35.03              27.95 
[1] "0.7 - 171.1 (35.0)" "0.5 - 188.2 (27.9)"
[1] "hr=" "1.5"
D67V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  14Q LOSS MUTATED                0                  2                   0
  14Q LOSS WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  14Q LOSS MUTATED                     0                             0
  14Q LOSS WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  14Q LOSS MUTATED                       0                     15
  14Q LOSS WILD-TYPE                     1                     13
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  14Q LOSS MUTATED                      1                    0
  14Q LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  14Q LOSS MUTATED                                       0
  14Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  14Q LOSS MUTATED                                  0
  14Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  14Q LOSS MUTATED                                                0
  14Q LOSS WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  14Q LOSS MUTATED                                 3
  14Q LOSS WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  14Q LOSS MUTATED                                         0
  14Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  14Q LOSS MUTATED                              0                       0
  14Q LOSS WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  14Q LOSS MUTATED                                  4
  14Q LOSS WILD-TYPE                               13
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  14Q LOSS MUTATED                                         1
  14Q LOSS WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  14Q LOSS MUTATED                              7
  14Q LOSS WILD-TYPE                           37
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  14Q LOSS MUTATED                                         2
  14Q LOSS WILD-TYPE                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  14Q LOSS MUTATED                                           0
  14Q LOSS WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  14Q LOSS MUTATED                                                  0
  14Q LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  14Q LOSS MUTATED                                          1
  14Q LOSS WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  14Q LOSS MUTATED                                                         1
  14Q LOSS WILD-TYPE                                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  14Q LOSS MUTATED                                            0
  14Q LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  14Q LOSS MUTATED                                                  19
  14Q LOSS WILD-TYPE                                                54
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  14Q LOSS MUTATED                                                    0
  14Q LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  14Q LOSS MUTATED                                    0
  14Q LOSS WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  14Q LOSS MUTATED                          0                           1
  14Q LOSS WILD-TYPE                        5                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  14Q LOSS MUTATED                           0
  14Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  14Q LOSS MUTATED                                   3
  14Q LOSS WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  14Q LOSS MUTATED                                   1
  14Q LOSS WILD-TYPE                                 4
D67V3, multiclass
                                                         clus
vv                                                        14Q LOSS 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                                                15
  HEAD AND NECK - HEAD                                                   1
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  0
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         0
  LOWER ABDOMINAL/PELVIC - PELVIC                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       4
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                           7
  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                1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     19
  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                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        14Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  13
  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                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            37
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  2
  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                       54
  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                                        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"
D67V4, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    34  28
  14Q LOSS WILD-TYPE 105  90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     34   28
  14Q LOSS WILD-TYPE  105   90
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               34                105
  MALE                 28                 90
[1] 2 2
[1] FALSE
D67V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    43  16
  14Q LOSS WILD-TYPE 136  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     43   16
  14Q LOSS WILD-TYPE  136   56
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                43                136
  YES               16                 56
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  14Q LOSS MUTATED                             16             0
  14Q LOSS WILD-TYPE                           43             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  14Q LOSS MUTATED                                                                          0
  14Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  14Q LOSS MUTATED                     27
  14Q LOSS WILD-TYPE                   76
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  14Q LOSS MUTATED                                                  2
  14Q LOSS WILD-TYPE                                                7
                    vv
clus                 MYXOFIBROSARCOMA
  14Q LOSS MUTATED                  3
  14Q LOSS WILD-TYPE               21
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  14Q LOSS MUTATED                                                          8
  14Q LOSS WILD-TYPE                                                       20
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  14Q LOSS MUTATED                                          0
  14Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  14Q LOSS MUTATED                             0                             0
  14Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  14Q LOSS MUTATED                                            6
  14Q LOSS WILD-TYPE                                         15
D67V6, multiclass
                                                                          clus
vv                                                                         14Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           16
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   27
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        2
  MYXOFIBROSARCOMA                                                                        3
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                8
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              6
                                                                          clus
vv                                                                         14Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             43
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     76
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          7
  MYXOFIBROSARCOMA                                                                         21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 20
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               15
[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
  14Q LOSS MUTATED    34  17   4   6
  14Q LOSS WILD-TYPE 118  52   5  20
D67V7, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               34                118
  R1               17                 52
  R2                4                  5
  RX                6                 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
  14Q LOSS MUTATED       1                         3    56
  14Q LOSS WILD-TYPE     5                        15   168
D67V8, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                3                 15
  WHITE                                   56                168
[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"
D67V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     0  52
  14Q LOSS WILD-TYPE   5 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   52
  14Q LOSS WILD-TYPE    5  168
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               52                168
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    20  26
  15Q LOSS WILD-TYPE 139  72
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                46                211 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                26                 72 
$`15Q LOSS MUTATED`
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-KF-A41W 
       15.22        14.43        84.66        32.15        16.60        11.70 
TCGA-PC-A5DM TCGA-X6-A8C6 TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HV TCGA-DX-A1KU 
        6.35        35.08        50.01        19.69        14.37        14.04 
TCGA-DX-A1KW TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48R 
       32.71         9.04        49.05        10.68        73.87        26.47 
TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A8BK 
       15.95        31.96         3.06        86.30        21.30        61.97 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ 
       45.14        47.87        27.95        40.44        60.66         6.58 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-IS-A3K7 
       49.15        20.32        19.89         4.57        37.12       171.09 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-KD-A5QU TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A8VH 
        5.92        16.41        35.28        13.08        17.65        10.52 
TCGA-VT-AB3D TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X6-A7WB 
       12.46        38.27        22.62        18.08 

$`15Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       75.32        17.95        14.07        15.85        40.60        12.07 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        22.85       101.98        30.51        60.00 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 
       37.02        12.62        52.11        26.93        52.27        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QC-A6FX 
      159.29        22.62        17.75         8.28        18.08        20.94 
TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-3B-A9HP TCGA-3B-A9HQ 
      188.15        17.52        26.17        41.49        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       88.57        44.91        54.74        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KX 
       38.47        36.03        18.64        26.56         0.56        68.61 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        45.11        18.54        54.21        85.02        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       66.94        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        95.38        79.17 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       51.02         4.54        14.99        68.55        50.43        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       85.45         9.73        45.99        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       46.03       108.82        59.84        37.58        37.41        82.68 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS 
       36.33        28.96        36.85        26.99        41.00        78.28 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM 
       50.50        16.87        64.21       101.23        34.49        62.20 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       30.35       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS 
       38.17        40.77       150.35        36.69        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2Q 
       17.79        12.00        15.72        65.98        86.10        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C 
        9.21        77.88       106.55        50.40        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       31.13        21.70        15.48         8.05        67.63        34.88 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       33.30         0.72         9.80        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VF 
        1.38        19.89        25.22        13.58        85.97         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91       101.26        53.33        62.17       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 
       23.38         5.19        63.81        16.41        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       81.01         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
       37.12       130.32       111.98        64.77         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88        22.82        25.35        32.75         8.61 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.63        13.22        13.41        10.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       84.79        65.46         8.58        63.35        26.43        35.90 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       45.34        30.84        35.18        19.17        20.65        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              3.06               0.49 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            171.09             188.15 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             20.81              33.30 
[1] "3.1 - 171.1 (20.8)" "0.5 - 188.2 (33.3)"
[1] "hr=" "2.1"
D68V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  15Q LOSS MUTATED                0                  1                   0
  15Q LOSS WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  15Q LOSS MUTATED                     0                             1
  15Q LOSS WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  15Q LOSS MUTATED                       0                      7
  15Q LOSS WILD-TYPE                     1                     21
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  15Q LOSS MUTATED                      1                    0
  15Q LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  15Q LOSS MUTATED                                       0
  15Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  15Q LOSS MUTATED                                  0
  15Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  15Q LOSS MUTATED                                                0
  15Q LOSS WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  15Q LOSS MUTATED                                 1
  15Q LOSS WILD-TYPE                               9
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  15Q LOSS MUTATED                                         0
  15Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  15Q LOSS MUTATED                              1                       0
  15Q LOSS WILD-TYPE                            3                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  15Q LOSS MUTATED                                  0
  15Q LOSS WILD-TYPE                               17
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  15Q LOSS MUTATED                                         2
  15Q LOSS WILD-TYPE                                       3
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  15Q LOSS MUTATED                              7
  15Q LOSS WILD-TYPE                           37
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  15Q LOSS MUTATED                                         0
  15Q LOSS WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  15Q LOSS MUTATED                                           1
  15Q LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  15Q LOSS MUTATED                                                  0
  15Q LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  15Q LOSS MUTATED                                          1
  15Q LOSS WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  15Q LOSS MUTATED                                                         1
  15Q LOSS WILD-TYPE                                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  15Q LOSS MUTATED                                            0
  15Q LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  15Q LOSS MUTATED                                                  11
  15Q LOSS WILD-TYPE                                                62
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  15Q LOSS MUTATED                                                    1
  15Q LOSS WILD-TYPE                                                  2
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  15Q LOSS MUTATED                                    2
  15Q LOSS WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  15Q LOSS MUTATED                          0                           2
  15Q LOSS WILD-TYPE                        5                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  15Q LOSS MUTATED                           0
  15Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  15Q LOSS MUTATED                                   3
  15Q LOSS WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  15Q LOSS MUTATED                                   3
  15Q LOSS WILD-TYPE                                 2
D68V3, multiclass
                                                         clus
vv                                                        15Q LOSS 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                                                 7
  HEAD AND NECK - HEAD                                                   1
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  0
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         0
  LOWER ABDOMINAL/PELVIC - PELVIC                                        1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       0
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                2
  LOWER EXTREMITY - THIGH/KNEE                                           7
  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                1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     11
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               0
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      3
                                                         clus
vv                                                        15Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            1
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  21
  HEAD AND NECK - HEAD                                                     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                                          9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        17
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  3
  LOWER EXTREMITY - THIGH/KNEE                                            37
  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                  1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       62
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        2
[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"
D68V4, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    23  23
  15Q LOSS WILD-TYPE 116  95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     23   23
  15Q LOSS WILD-TYPE  116   95
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               23                116
  MALE                 23                 95
[1] 2 2
[1] FALSE
D68V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    30  16
  15Q LOSS WILD-TYPE 149  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     30   16
  15Q LOSS WILD-TYPE  149   56
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                30                149
  YES               16                 56
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  15Q LOSS MUTATED                             12             0
  15Q LOSS WILD-TYPE                           47             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  15Q LOSS MUTATED                                                                          0
  15Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  15Q LOSS MUTATED                     15
  15Q LOSS WILD-TYPE                   88
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  15Q LOSS MUTATED                                                  1
  15Q LOSS WILD-TYPE                                                8
                    vv
clus                 MYXOFIBROSARCOMA
  15Q LOSS MUTATED                  4
  15Q LOSS WILD-TYPE               20
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  15Q LOSS MUTATED                                                          9
  15Q LOSS WILD-TYPE                                                       19
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  15Q LOSS MUTATED                                          0
  15Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  15Q LOSS MUTATED                             0                             0
  15Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  15Q LOSS MUTATED                                            5
  15Q LOSS WILD-TYPE                                         16
D68V6, multiclass
                                                                          clus
vv                                                                         15Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           12
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   15
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                        4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              5
                                                                          clus
vv                                                                         15Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             47
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     88
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          8
  MYXOFIBROSARCOMA                                                                         20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               16
[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
  15Q LOSS MUTATED    27  12   1   6
  15Q LOSS WILD-TYPE 125  57   8  20
D68V7, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               27                125
  R1               12                 57
  R2                1                  8
  RX                6                 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
  15Q LOSS MUTATED       0                         5    40
  15Q LOSS WILD-TYPE     6                        13   184
D68V8, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   40                184
[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"
D68V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0  41
  15Q LOSS WILD-TYPE   5 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   41
  15Q LOSS WILD-TYPE    5  179
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               41                179
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    42  33
  16P LOSS WILD-TYPE 117  65
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                75                182 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                33                 65 
$`16P LOSS MUTATED`
TCGA-DX-A6YT TCGA-DX-A8BP TCGA-DX-AB2W TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HB-A5W3 
       67.20        14.07       106.45        32.15        37.02        12.62 
TCGA-KF-A41W TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HR 
       11.70        20.94        17.52        26.17        35.08        88.57 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y 
       18.64         0.56        18.54        85.02        74.66         6.28 
TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48O 
       49.05        51.02        10.68        50.43        85.45        52.77 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YZ TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BR 
       15.95        82.68        86.30         9.34        40.77       150.35 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2Q TCGA-DX-AB2T 
       36.69        60.66         6.58         1.15        66.74        77.88 
TCGA-DX-AB2Z TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EJ 
       50.40        20.32        19.89         4.57         0.72         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN 
       19.89        37.12       171.09        16.41         1.05       101.26 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A8JL TCGA-MJ-A68H TCGA-N1-A6IA 
        5.19        63.81        35.28        19.73        14.99         7.36 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VH 
       13.08        17.65        46.82        35.90        37.12        10.52 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS 
        8.61        19.63        13.41        10.72        12.46        84.79 
TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       38.27        22.62         8.58        18.08        30.84        35.18 
TCGA-X6-A8C4 TCGA-X9-A973 TCGA-Z4-AAPG 
       20.65        36.43        15.98 

$`16P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        31.53        34.68        16.18        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       15.22        17.95        14.43        15.85        40.60        12.07 
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-FX-A3NK TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       16.60        52.11        26.93        52.27        28.21       159.29 
TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A8VB 
       22.62        17.75         8.28         6.35        18.08       188.15 
TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS 
       41.49        50.01        19.69        53.49        68.55        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       54.74        25.25        14.37        42.84        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       36.03        26.56        14.04        32.71        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       45.11        54.21        33.53        66.94         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       79.17         9.04        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       31.86        35.77         4.54        14.99        73.87        68.55 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48P 
       34.88         9.73        45.99        24.26        35.28        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB 
       26.47       108.82        59.84        37.58        37.41        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       78.28        50.50        16.87        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS 
       20.05        61.97        45.14        47.87        38.17        27.95 
TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       40.44        19.43        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       86.10         9.21       106.55        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       31.13        21.70        15.48         8.05        67.63        34.88 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
       33.30         9.80        80.48        19.53         1.38        25.22 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W 
       13.58        85.97         5.92         3.91        53.33        62.17 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 
      123.78        17.36        23.38        16.41        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        0.49        21.73        17.98        22.39        11.57        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5VA 
      122.96        37.55        38.63        81.01         1.84        18.08 
TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
       48.59       130.32       111.98        64.77         0.72        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT 
       18.94         3.88        22.82        25.35        32.75        13.22 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       11.93         4.80        65.46        63.35        26.43        35.90 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB 
       45.34        19.17        50.86        29.46        27.32         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF 
       13.38        15.95 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.56               0.49 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            171.09             188.15 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            20.940             32.335 
[1] "0.6 - 171.1 (20.9)" "0.5 - 188.2 (32.3)"
[1] "hr=" "1.4"
D69V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  16P LOSS MUTATED                1                  2                   0
  16P LOSS WILD-TYPE              0                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  16P LOSS MUTATED                     0                             1
  16P LOSS WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  16P LOSS MUTATED                       0                     12
  16P LOSS WILD-TYPE                     1                     16
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  16P LOSS MUTATED                      1                    0
  16P LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  16P LOSS MUTATED                                       0
  16P LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  16P LOSS MUTATED                                  0
  16P LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  16P LOSS MUTATED                                                1
  16P LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  16P LOSS MUTATED                                 4
  16P LOSS WILD-TYPE                               6
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  16P LOSS MUTATED                                         0
  16P LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  16P LOSS MUTATED                              2                       0
  16P LOSS WILD-TYPE                            2                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  16P LOSS MUTATED                                  6
  16P LOSS WILD-TYPE                               11
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  16P LOSS MUTATED                                         1
  16P LOSS WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  16P LOSS MUTATED                             16
  16P LOSS WILD-TYPE                           28
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  16P LOSS MUTATED                                         0
  16P LOSS WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  16P LOSS MUTATED                                           1
  16P LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  16P LOSS MUTATED                                                  0
  16P LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  16P LOSS MUTATED                                          3
  16P LOSS WILD-TYPE                                        5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  16P LOSS MUTATED                                                         0
  16P LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  16P LOSS MUTATED                                            0
  16P LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  16P LOSS MUTATED                                                  15
  16P LOSS WILD-TYPE                                                58
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  16P LOSS MUTATED                                                    0
  16P LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  16P LOSS MUTATED                                    0
  16P LOSS WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  16P LOSS MUTATED                          1                           3
  16P LOSS WILD-TYPE                        4                           1
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  16P LOSS MUTATED                           0
  16P LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  16P LOSS MUTATED                                   2
  16P LOSS WILD-TYPE                                 5
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  16P LOSS MUTATED                                   3
  16P LOSS WILD-TYPE                                 2
D69V3, multiclass
                                                         clus
vv                                                        16P LOSS MUTATED
  CHEST - BREAST                                                         1
  CHEST - CHEST WALL                                                     2
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                12
  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                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           2
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          16
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     15
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            3
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      3
                                                         clus
vv                                                        16P LOSS WILD-TYPE
  CHEST - BREAST                                                           0
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            1
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  16
  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                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             2
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            28
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       58
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       2
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              1
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        2
[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"
D69V4, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   46 29
  16P LOSS WILD-TYPE 93 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     46   29
  16P LOSS WILD-TYPE   93   89
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               46                 93
  MALE                 29                 89
[1] 2 2
[1] FALSE
D69V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    50  24
  16P LOSS WILD-TYPE 129  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     50   24
  16P LOSS WILD-TYPE  129   48
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                50                129
  YES               24                 48
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  16P LOSS MUTATED                              8             0
  16P LOSS WILD-TYPE                           51             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  16P LOSS MUTATED                                                                          0
  16P LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  16P LOSS MUTATED                     32
  16P LOSS WILD-TYPE                   71
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  16P LOSS MUTATED                                                  2
  16P LOSS WILD-TYPE                                                7
                    vv
clus                 MYXOFIBROSARCOMA
  16P LOSS MUTATED                  5
  16P LOSS WILD-TYPE               19
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  16P LOSS MUTATED                                                         11
  16P LOSS WILD-TYPE                                                       17
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  16P LOSS MUTATED                                          0
  16P LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  16P LOSS MUTATED                             0                             0
  16P LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  16P LOSS MUTATED                                           17
  16P LOSS WILD-TYPE                                          4
D69V6, multiclass
                                                                          clus
vv                                                                         16P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            8
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   32
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        2
  MYXOFIBROSARCOMA                                                                        5
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             17
                                                                          clus
vv                                                                         16P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             51
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     71
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          7
  MYXOFIBROSARCOMA                                                                         19
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                4
[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
  16P LOSS MUTATED    44  19   3   9
  16P LOSS WILD-TYPE 108  50   6  17
D69V7, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               44                108
  R1               19                 50
  R2                3                  6
  RX                9                 17
[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
  16P LOSS MUTATED       1                         9    63
  16P LOSS WILD-TYPE     5                         9   161
D69V8, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                9                  9
  WHITE                                   63                161
[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"
D69V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1  68
  16P LOSS WILD-TYPE   4 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   68
  16P LOSS WILD-TYPE    4  152
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               68                152
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   72 52
  16Q LOSS WILD-TYPE 87 46
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               124                133 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                52                 46 
$`16Q LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2P 
       31.53        67.20        15.22        14.07        40.60        12.07 
TCGA-DX-AB2X TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-KF-A41W 
       13.28        37.02        12.62        26.93        52.27        11.70 
TCGA-LI-A9QH TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-X6-A8C6 
       17.75        18.08        20.94        17.52        26.17        35.08 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ 
       50.01        19.69        88.57        25.25        10.32        38.47 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1L0 TCGA-DX-A1L2 
       18.64        26.56         0.56        14.04        18.54        85.02 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U7 
       74.66         6.28         9.70        49.05        33.44        51.02 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K 
       14.99        10.68        68.55        50.43        85.45        45.99 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 
       24.26        52.77        46.03        26.47        59.84        15.95 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM 
       82.68        36.33        16.87        86.30        64.21        62.20 
TCGA-DX-A7EO TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU 
      152.12         9.34        40.77       150.35        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2T 
       60.66         6.58         1.15        12.00        66.74        77.88 
TCGA-DX-AB2Z TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       50.40        31.13        21.70        20.32        19.89        15.48 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI 
       67.63         4.57        33.30         0.72         9.80        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA 
        3.22         1.38        19.89        37.12        25.22        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42X TCGA-K1-A6RU 
       85.97        16.41         1.05       101.26       123.78        23.38 
TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H 
        5.19        63.81        35.28        25.41        19.73        14.99 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
       10.45         7.36        37.55        81.01        13.08        17.65 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VH TCGA-SI-AA8B 
       46.82        48.59        35.90        37.12        10.52         8.61 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XS TCGA-WK-A8XX 
       19.63        13.41        10.72        12.46        84.79        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       65.46         8.58        26.43        35.90        18.08        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X9-A973 
       35.18        20.65        50.86        36.43 

$`16Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        34.68        16.18        34.36        75.32        17.95 
TCGA-DX-A8BH TCGA-DX-AB2H TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       14.43        15.85       106.45        22.85       101.98        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HS-A5N9 TCGA-IS-A3K6 
       60.00        84.66        32.15        16.60        52.11        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-WK-A8XT 
      159.29        22.62         8.28         6.35       188.15        41.49 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HV TCGA-3B-A9HX 
       53.49        68.55        44.91        54.74        14.37        42.84 
TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       36.03        32.71        68.61        12.85        45.11        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        66.94         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       60.30         8.58        95.38        79.17         9.04        86.83 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB 
      136.44        44.68        31.86        35.77         4.54        73.87 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
       34.88         9.73        35.28       108.82        37.58        37.41 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN 
       78.28        50.50       101.23        21.30        34.49        30.35 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       29.49        48.20        20.05        61.97        45.14        47.87 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L 
       38.17        27.95        19.43        17.79        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       86.10         9.21       106.55        50.89        71.31        49.15 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-IE-A3OV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A75J 
        8.05        34.88        80.48       171.09         5.92         3.91 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA 
       53.33        62.17        17.36        16.41        30.31         0.49 
TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN 
       21.73        17.98        22.39        11.57       122.96        38.63 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
        1.84        18.08       130.32       111.98        64.77         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       16.77        18.94         3.88        22.82        25.35        32.75 
TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WC 
       13.22        11.93         4.80        22.62        63.35        45.34 
TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       19.17        29.46        27.32         4.37        13.38        15.95 
TCGA-Z4-AAPG 
       15.98 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.56               0.49 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            152.12             188.15 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             26.30              33.53 
[1] "0.6 - 152.1 (26.3)" "0.5 - 188.2 (33.5)"
[1] "hr=" "1.4"
D70V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  16Q LOSS MUTATED                1                  1                   0
  16Q LOSS WILD-TYPE              0                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  16Q LOSS MUTATED                     1                             2
  16Q LOSS WILD-TYPE                   0                             0
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  16Q LOSS MUTATED                       1                     17
  16Q LOSS WILD-TYPE                     0                     11
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  16Q LOSS MUTATED                      1                    0
  16Q LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  16Q LOSS MUTATED                                       0
  16Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  16Q LOSS MUTATED                                  0
  16Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  16Q LOSS MUTATED                                                2
  16Q LOSS WILD-TYPE                                              0
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  16Q LOSS MUTATED                                 6
  16Q LOSS WILD-TYPE                               4
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  16Q LOSS MUTATED                                         0
  16Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  16Q LOSS MUTATED                              2                       1
  16Q LOSS WILD-TYPE                            2                       1
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  16Q LOSS MUTATED                                 12
  16Q LOSS WILD-TYPE                                5
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  16Q LOSS MUTATED                                         1
  16Q LOSS WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  16Q LOSS MUTATED                             24
  16Q LOSS WILD-TYPE                           20
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  16Q LOSS MUTATED                                         0
  16Q LOSS WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  16Q LOSS MUTATED                                           1
  16Q LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  16Q LOSS MUTATED                                                  2
  16Q LOSS WILD-TYPE                                                3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  16Q LOSS MUTATED                                          5
  16Q LOSS WILD-TYPE                                        3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  16Q LOSS MUTATED                                                         0
  16Q LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  16Q LOSS MUTATED                                            0
  16Q LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  16Q LOSS MUTATED                                                  29
  16Q LOSS WILD-TYPE                                                44
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  16Q LOSS MUTATED                                                    2
  16Q LOSS WILD-TYPE                                                  1
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  16Q LOSS MUTATED                                    1
  16Q LOSS WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  16Q LOSS MUTATED                          1                           3
  16Q LOSS WILD-TYPE                        4                           1
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  16Q LOSS MUTATED                           1
  16Q LOSS WILD-TYPE                         0
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  16Q LOSS MUTATED                                   3
  16Q LOSS WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  16Q LOSS MUTATED                                   4
  16Q LOSS WILD-TYPE                                 1
D70V3, multiclass
                                                         clus
vv                                                        16Q LOSS MUTATED
  CHEST - BREAST                                                         1
  CHEST - CHEST WALL                                                     1
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    1
  CHEST - OTHER (PLEASE SPECIFY                                          2
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                17
  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                         2
  LOWER ABDOMINAL/PELVIC - PELVIC                                        6
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           2
  LOWER EXTREMITY - GROIN                                                1
  LOWER EXTREMITY - LOWER LEG/CALF                                      12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          24
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       2
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     29
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            3
  SUPERFICIAL TRUNK - FLANK                                              1
  UPPER EXTREMITY - SHOULDER/AXILLA                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      4
                                                         clus
vv                                                        16Q LOSS WILD-TYPE
  CHEST - BREAST                                                           0
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      0
  CHEST - OTHER (PLEASE SPECIFY                                            0
  GYNECOLOGICAL - OVARY                                                    0
  GYNECOLOGICAL - UTERUS                                                  11
  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                           0
  LOWER ABDOMINAL/PELVIC - PELVIC                                          4
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             2
  LOWER EXTREMITY - GROIN                                                  1
  LOWER EXTREMITY - LOWER LEG/CALF                                         5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            20
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         3
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       44
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              1
  SUPERFICIAL TRUNK - FLANK                                                0
  UPPER EXTREMITY - SHOULDER/AXILLA                                        4
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        1
[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"
D70V4, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   74 50
  16Q LOSS WILD-TYPE 65 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     74   50
  16Q LOSS WILD-TYPE   65   68
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               74                 65
  MALE                 50                 68
[1] 2 2
[1] FALSE
D70V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   84 37
  16Q LOSS WILD-TYPE 95 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     84   37
  16Q LOSS WILD-TYPE   95   35
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                84                 95
  YES               37                 35
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  16Q LOSS MUTATED                             14             0
  16Q LOSS WILD-TYPE                           45             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  16Q LOSS MUTATED                                                                          0
  16Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  16Q LOSS MUTATED                     65
  16Q LOSS WILD-TYPE                   38
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  16Q LOSS MUTATED                                                  2
  16Q LOSS WILD-TYPE                                                7
                    vv
clus                 MYXOFIBROSARCOMA
  16Q LOSS MUTATED                  9
  16Q LOSS WILD-TYPE               15
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  16Q LOSS MUTATED                                                         16
  16Q LOSS WILD-TYPE                                                       12
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  16Q LOSS MUTATED                                          0
  16Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  16Q LOSS MUTATED                             1                             0
  16Q LOSS WILD-TYPE                           1                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  16Q LOSS MUTATED                                           17
  16Q LOSS WILD-TYPE                                          4
D70V6, multiclass
                                                                          clus
vv                                                                         16Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           14
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   65
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        2
  MYXOFIBROSARCOMA                                                                        9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             1
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             17
                                                                          clus
vv                                                                         16Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             45
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     38
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          7
  MYXOFIBROSARCOMA                                                                         15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               1
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                                4
[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
  16Q LOSS MUTATED   68 39  5 12
  16Q LOSS WILD-TYPE 84 30  4 14
D70V7, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               68                 84
  R1               39                 30
  R2                5                  4
  RX               12                 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
  16Q LOSS MUTATED       2                        13   104
  16Q LOSS WILD-TYPE     4                         5   120
D70V8, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN               13                  5
  WHITE                                  104                120
[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"
D70V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     2 109
  16Q LOSS WILD-TYPE   3 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2  109
  16Q LOSS WILD-TYPE    3  111
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              109                111
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    33  24
  17P LOSS WILD-TYPE 126  74
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                57                200 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                24                 74 
$`17P LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       31.53        15.22        17.95        14.43        14.07        15.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-HS-A5N9 TCGA-IS-A3K6 TCGA-KF-A41W TCGA-QC-A6FX 
      101.98        30.51        52.11        28.21        11.70        20.94 
TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9I3 TCGA-DX-A1KZ TCGA-DX-A23R 
       50.01        53.49        88.57        26.56        45.11        74.66 
TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A6BB TCGA-DX-A6YX TCGA-DX-A6Z2 
       49.05        14.99        10.68        36.33        16.87       101.23 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A8BJ TCGA-DX-A8BU TCGA-DX-A8BZ 
       21.30        34.49       152.12         9.34        36.69         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2O TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A2OT 
        1.15        17.79        86.10        31.13        15.48        67.63 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K7 
        0.72        80.48         3.22         1.38        25.22       171.09 
TCGA-K1-A42W TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-PC-A5DL TCGA-QQ-A5VC 
       62.17        25.41         0.49        21.73        37.55        35.90 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
       10.52         3.88        22.82        32.75         8.61        19.63 
TCGA-WK-A8XO TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93        38.27        65.46 

$`17P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        34.68        16.18        67.20        34.36        75.32 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 
       40.60        12.07       106.45        13.28        22.85        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EH 
       84.66        32.15        16.60        37.02        12.62        26.93 
TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
       52.27       159.29        22.62        17.75         8.28         6.35 
TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       18.08       188.15        17.52        26.17        41.49        35.08 
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV 
       19.69        68.55        44.91        54.74        25.25        14.37 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       42.84        10.32        38.47        36.03        18.64         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        32.71        68.61        12.85        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       85.02        33.53        66.94         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       79.17         9.04        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       31.86        35.77        51.02         4.54        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       50.43        34.88        85.45         9.73        45.99        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       35.28        52.77        46.03        26.47       108.82        59.84 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF 
       37.58        15.95        37.41        82.68        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       36.85        26.99         3.06        41.00        78.28        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER 
       86.30        64.21        62.20        30.35        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       20.05        61.97        45.14        47.87        38.17        40.77 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F 
      150.35        27.95        40.44        60.66        19.43        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       15.72        65.98        66.74         9.21        77.88       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO 
       50.40        50.89        71.31        49.15        21.70        20.32 
TCGA-FX-A48G TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5NA 
       19.89         8.05        34.88         4.57        33.30         9.80 
TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       19.53        19.89        37.12        13.58        85.97         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       16.41         1.05         3.91       101.26        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        63.81        16.41        35.28 
TCGA-LI-A67I TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
       30.31        19.73        14.99        17.98        22.39        11.57 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
       10.45         7.36       122.96        38.63        81.01        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-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32       111.98        64.77         0.72        16.77        18.94 
TCGA-SI-A71P TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XQ 
       25.35        13.22        13.41        10.72        12.46         4.80 
TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       84.79        22.62         8.58        63.35        26.43        35.90 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       18.08        45.34        30.84        35.18        19.17        20.65 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       50.86        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.49               0.56 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            171.09             188.15 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            25.410             33.005 
[1] "0.5 - 171.1 (25.4)" "0.6 - 188.2 (33.0)"
[1] "hr=" "1.3"
D71V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  17P LOSS MUTATED                0                  3                   0
  17P LOSS WILD-TYPE              1                  4                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  17P LOSS MUTATED                     0                             1
  17P LOSS WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  17P LOSS MUTATED                       0                      6
  17P LOSS WILD-TYPE                     1                     22
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  17P LOSS MUTATED                      0                    0
  17P LOSS WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  17P LOSS MUTATED                                       0
  17P LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  17P LOSS MUTATED                                  0
  17P LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  17P LOSS MUTATED                                                1
  17P LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  17P LOSS MUTATED                                 1
  17P LOSS WILD-TYPE                               9
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  17P LOSS MUTATED                                         0
  17P LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  17P LOSS MUTATED                              1                       0
  17P LOSS WILD-TYPE                            3                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  17P LOSS MUTATED                                  3
  17P LOSS WILD-TYPE                               14
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  17P LOSS MUTATED                                         1
  17P LOSS WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  17P LOSS MUTATED                             13
  17P LOSS WILD-TYPE                           31
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  17P LOSS MUTATED                                         1
  17P LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  17P LOSS MUTATED                                           0
  17P LOSS WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  17P LOSS MUTATED                                                  1
  17P LOSS WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  17P LOSS MUTATED                                          3
  17P LOSS WILD-TYPE                                        5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  17P LOSS MUTATED                                                         0
  17P LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  17P LOSS MUTATED                                            1
  17P LOSS WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  17P LOSS MUTATED                                                  12
  17P LOSS WILD-TYPE                                                61
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  17P LOSS MUTATED                                                    1
  17P LOSS WILD-TYPE                                                  2
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  17P LOSS MUTATED                                    2
  17P LOSS WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  17P LOSS MUTATED                          1                           1
  17P LOSS WILD-TYPE                        4                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  17P LOSS MUTATED                           1
  17P LOSS WILD-TYPE                         0
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  17P LOSS MUTATED                                   1
  17P LOSS WILD-TYPE                                 6
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  17P LOSS MUTATED                                   2
  17P LOSS WILD-TYPE                                 3
D71V3, multiclass
                                                         clus
vv                                                        17P LOSS MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     3
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 6
  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                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        1
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          13
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            1
  SUPERFICIAL TRUNK - FLANK                                              1
  UPPER EXTREMITY - SHOULDER/AXILLA                                      1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        17P LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       4
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            1
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  22
  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                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          9
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        14
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            31
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       61
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              3
  SUPERFICIAL TRUNK - FLANK                                                0
  UPPER EXTREMITY - SHOULDER/AXILLA                                        6
  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"
D71V4, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    31  26
  17P LOSS WILD-TYPE 108  92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     31   26
  17P LOSS WILD-TYPE  108   92
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               31                108
  MALE                 26                 92
[1] 2 2
[1] FALSE
D71V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    34  19
  17P LOSS WILD-TYPE 145  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     34   19
  17P LOSS WILD-TYPE  145   53
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                34                145
  YES               19                 53
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  17P LOSS MUTATED                             10             0
  17P LOSS WILD-TYPE                           49             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  17P LOSS MUTATED                                                                          0
  17P LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  17P LOSS MUTATED                     24
  17P LOSS WILD-TYPE                   79
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  17P LOSS MUTATED                                                  4
  17P LOSS WILD-TYPE                                                5
                    vv
clus                 MYXOFIBROSARCOMA
  17P LOSS MUTATED                  4
  17P LOSS WILD-TYPE               20
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  17P LOSS MUTATED                                                         10
  17P LOSS WILD-TYPE                                                       18
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  17P LOSS MUTATED                                          0
  17P LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  17P LOSS MUTATED                             1                             0
  17P LOSS WILD-TYPE                           1                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  17P LOSS MUTATED                                            4
  17P LOSS WILD-TYPE                                         17
D71V6, multiclass
                                                                          clus
vv                                                                         17P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           10
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   24
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        4
  MYXOFIBROSARCOMA                                                                        4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             1
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              4
                                                                          clus
vv                                                                         17P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             49
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     79
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          5
  MYXOFIBROSARCOMA                                                                         20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 18
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               1
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               17
[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
  17P LOSS MUTATED    32  17   2   6
  17P LOSS WILD-TYPE 120  52   7  20
D71V7, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               32                120
  R1               17                 52
  R2                2                  7
  RX                6                 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
  17P LOSS MUTATED       0                         5    49
  17P LOSS WILD-TYPE     6                        13   175
D71V8, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   49                175
[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"
D71V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  48
  17P LOSS WILD-TYPE   4 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   48
  17P LOSS WILD-TYPE    4  172
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               48                172
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    26  23
  17Q LOSS WILD-TYPE 133  75
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                49                208 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                23                 75 
$`17Q LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2W 
       31.53        15.22        17.95        14.07        15.85       106.45 
TCGA-DX-AB35 TCGA-HS-A5N9 TCGA-KF-A41W TCGA-QC-A6FX TCGA-X6-A8C6 TCGA-3B-A9HI 
       30.51        52.11        11.70        20.94        35.08        50.01 
TCGA-3B-A9HR TCGA-3B-A9I3 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3U9 
       88.57        26.56        74.66         6.28        49.05        14.99 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6B8 TCGA-DX-A6BA 
       50.43        34.88        85.45        24.26        15.95        82.68 
TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BU TCGA-DX-A8BZ 
       16.87        21.30        34.49         9.34        36.69         6.58 
TCGA-DX-AATS TCGA-DX-AB2O TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A3OV 
        1.15        86.10        31.13        67.63         0.72        80.48 
TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-K1-A42W TCGA-K1-A6RV TCGA-MB-A8JK TCGA-PC-A5DL 
        3.22        25.22        62.17         5.19        21.73        37.55 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XX 
       10.52         3.88        22.82        32.75        19.63        38.27 
TCGA-X6-A7WC 
       45.34 

$`17Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        34.68        16.18        67.20        34.36        75.32 
TCGA-DX-A8BH TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
       14.43        40.60        12.07        13.28        22.85       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-LI-A9QH 
       26.93        52.27        28.21       159.29        22.62        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
        8.28         6.35        18.08       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       41.49        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       25.25        14.37        42.84        10.32        38.47        36.03 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64         0.56        14.04        32.71        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       45.11        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        95.38        79.17         9.04        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       10.68        73.87        68.55         9.73        45.99        35.28 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       37.41        36.33        28.96        31.96        36.85        26.99 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        41.00        78.28        50.50        86.30        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
      101.23        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       20.05        61.97        45.14        47.87        38.17        40.77 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E 
      150.35        27.95        40.44        60.66        19.43        17.79 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       12.00        15.72        65.98        66.74         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE 
      106.55        50.40        50.89        71.31        49.15        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV 
       20.32        19.89        15.48         8.05        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       33.30         9.80        19.53         1.38        19.89        37.12 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
      171.09        13.58        85.97         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
        3.91       101.26        53.33       123.78        17.36        23.38 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       63.81        16.41        35.28        30.31        25.41         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        22.39        11.57        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
        7.36       122.96        38.63        81.01        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-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32       111.98        64.77         0.72        16.77        18.94 
TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D 
       25.35         8.61        13.22        13.41        10.72        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       11.93         4.80        84.79        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       63.35        26.43        35.90        18.08        30.84        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       19.17        20.65        50.86        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.72               0.49 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            106.45             188.15 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            26.560             32.055 
[1] "0.7 - 106.5 (26.6)" "0.5 - 188.2 (32.1)"
[1] "hr=" "1.4"
D72V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  17Q LOSS MUTATED                0                  2                   0
  17Q LOSS WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  17Q LOSS MUTATED                     0                             1
  17Q LOSS WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  17Q LOSS MUTATED                       0                      3
  17Q LOSS WILD-TYPE                     1                     25
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  17Q LOSS MUTATED                      0                    0
  17Q LOSS WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  17Q LOSS MUTATED                                       0
  17Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  17Q LOSS MUTATED                                  0
  17Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  17Q LOSS MUTATED                                                1
  17Q LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  17Q LOSS MUTATED                                 1
  17Q LOSS WILD-TYPE                               9
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  17Q LOSS MUTATED                                         0
  17Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  17Q LOSS MUTATED                              0                       0
  17Q LOSS WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  17Q LOSS MUTATED                                  3
  17Q LOSS WILD-TYPE                               14
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  17Q LOSS MUTATED                                         1
  17Q LOSS WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  17Q LOSS MUTATED                             15
  17Q LOSS WILD-TYPE                           29
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  17Q LOSS MUTATED                                         0
  17Q LOSS WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  17Q LOSS MUTATED                                           0
  17Q LOSS WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  17Q LOSS MUTATED                                                  1
  17Q LOSS WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  17Q LOSS MUTATED                                          3
  17Q LOSS WILD-TYPE                                        5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  17Q LOSS MUTATED                                                         0
  17Q LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  17Q LOSS MUTATED                                            1
  17Q LOSS WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  17Q LOSS MUTATED                                                  10
  17Q LOSS WILD-TYPE                                                63
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  17Q LOSS MUTATED                                                    0
  17Q LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  17Q LOSS MUTATED                                    1
  17Q LOSS WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  17Q LOSS MUTATED                          2                           1
  17Q LOSS WILD-TYPE                        3                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  17Q LOSS MUTATED                           0
  17Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  17Q LOSS MUTATED                                   1
  17Q LOSS WILD-TYPE                                 6
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  17Q LOSS MUTATED                                   2
  17Q LOSS WILD-TYPE                                 3
D72V3, multiclass
                                                         clus
vv                                                        17Q LOSS MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     2
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 3
  HEAD AND NECK - HEAD                                                   0
  HEAD AND NECK - NECK                                                   0
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                  0
  LOWER ABDOMINAL/PELVIC - BLADDER                                       0
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                         1
  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                                       3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                0
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     10
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            1
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        17Q LOSS 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                           1
  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                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  4
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       63
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              3
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        6
  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"
D72V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    24  25
  17Q LOSS WILD-TYPE 115  93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     24   25
  17Q LOSS WILD-TYPE  115   93
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               24                115
  MALE                 25                 93
[1] 2 2
[1] FALSE
D72V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    25  22
  17Q LOSS WILD-TYPE 154  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     25   22
  17Q LOSS WILD-TYPE  154   50
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                25                154
  YES               22                 50
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  17Q LOSS MUTATED                              9             0
  17Q LOSS WILD-TYPE                           50             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  17Q LOSS MUTATED                                                                          0
  17Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  17Q LOSS MUTATED                     21
  17Q LOSS WILD-TYPE                   82
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  17Q LOSS MUTATED                                                  4
  17Q LOSS WILD-TYPE                                                5
                    vv
clus                 MYXOFIBROSARCOMA
  17Q LOSS MUTATED                  3
  17Q LOSS WILD-TYPE               21
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  17Q LOSS MUTATED                                                         10
  17Q LOSS WILD-TYPE                                                       18
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  17Q LOSS MUTATED                                          0
  17Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  17Q LOSS MUTATED                             0                             0
  17Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  17Q LOSS MUTATED                                            2
  17Q LOSS WILD-TYPE                                         19
D72V6, multiclass
                                                                          clus
vv                                                                         17Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            9
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   21
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        4
  MYXOFIBROSARCOMA                                                                        3
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              2
                                                                          clus
vv                                                                         17Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             50
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     82
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          5
  MYXOFIBROSARCOMA                                                                         21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 18
  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
  17Q LOSS MUTATED    27  15   1   6
  17Q LOSS WILD-TYPE 125  54   8  20
D72V7, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               27                125
  R1               15                 54
  R2                1                  8
  RX                6                 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
  17Q LOSS MUTATED       0                         5    41
  17Q LOSS WILD-TYPE     6                        13   183
D72V8, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   41                183
[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"
D72V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  43
  17Q LOSS WILD-TYPE   5 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   43
  17Q LOSS WILD-TYPE    5  177
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               43                177
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    32  29
  18P LOSS WILD-TYPE 127  69
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                61                196 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                29                 69 
$`18P LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB2P TCGA-DX-AB32 
       31.53        67.20        15.22        14.43        12.07       101.98 
TCGA-DX-AB36 TCGA-DX-AB3A TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DP 
       60.00        32.15        26.93        22.62        11.70        18.08 
TCGA-QC-A6FX TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3R-A8YX 
       20.94        26.17        35.08        44.91        42.84         0.56 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U9 
       68.61        12.85        18.54         9.70        49.05        14.99 
TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48P TCGA-DX-A6BF TCGA-DX-A6YZ 
       10.68        68.55        85.45        46.03        31.96        86.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ 
       34.49        62.20         9.34        40.44        36.69         6.58 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2Q TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-IE-A3OV 
       17.79        15.72        66.74        67.63        33.30        80.48 
TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-KD-A5QU TCGA-MB-A5Y8 
        3.22       171.09        85.97         1.05        35.28        25.41 
TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-AA8C 
       37.55        13.08        10.52         3.88        25.35        19.63 
TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WB 
       10.72        84.79        38.27        22.62        26.43        18.08 
TCGA-X6-A8C4 
       20.65 

$`18P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        34.68        16.18        34.36        75.32        17.95 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       14.07        15.85        40.60       106.45        13.28        22.85 
TCGA-DX-AB35 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       30.51        84.66        16.60        37.02        12.62        52.11 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM 
       52.27        28.21       159.29        17.75         8.28         6.35 
TCGA-QQ-A8VB TCGA-SG-A849 TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP 
      188.15        17.52        41.49        50.01        19.69        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY 
       68.55        88.57        54.74        25.25        14.37        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW 
       38.47        36.03        18.64        26.56        14.04        32.71 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       45.11        54.21        85.02        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58        95.38        79.17         9.04        86.83       136.44 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       33.44        44.68        31.86        35.77        51.02         4.54 
TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       73.87        50.43        34.88         9.73        45.99        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       35.28        52.77        26.47       108.82        59.84        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       15.95        37.41        82.68        36.33        28.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX 
       26.99         3.06        41.00        78.28        50.50        16.87 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       64.21       101.23        21.30        30.35       152.12        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       48.20        20.05        61.97        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       40.77       150.35        27.95        60.66        19.43         1.15 
TCGA-DX-AB2F TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       12.00        65.98        86.10         9.21        77.88       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV 
       20.32        19.89        15.48         8.05        34.88         4.57 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
        0.72         9.80        19.53         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN 
       25.22        13.58         5.92        16.41         3.91       101.26 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       53.33        62.17       123.78        17.36        23.38         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       63.81        16.41        30.31         0.49        21.73        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        22.39        11.57        10.45         7.36 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
      122.96        38.63        81.01        17.65         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71Q 
       64.77         0.72        16.77        18.94        22.82        32.75 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ 
        8.61        13.22        13.41        12.46        11.93         4.80 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD 
       65.46         8.58        63.35        35.90        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       35.18        19.17        50.86        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.56               0.49 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            171.09             188.15 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            26.430             32.285 
[1] "0.6 - 171.1 (26.4)" "0.5 - 188.2 (32.3)"
[1] "hr=" "1.4"
D73V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  18P LOSS MUTATED                0                  4                   0
  18P LOSS WILD-TYPE              1                  3                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  18P LOSS MUTATED                     0                             1
  18P LOSS WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  18P LOSS MUTATED                       0                      7
  18P LOSS WILD-TYPE                     1                     21
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  18P LOSS MUTATED                      1                    0
  18P LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  18P LOSS MUTATED                                       0
  18P LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  18P LOSS MUTATED                                  0
  18P LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  18P LOSS MUTATED                                                1
  18P LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  18P LOSS MUTATED                                 2
  18P LOSS WILD-TYPE                               8
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  18P LOSS MUTATED                                         0
  18P LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  18P LOSS MUTATED                              1                       0
  18P LOSS WILD-TYPE                            3                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  18P LOSS MUTATED                                  4
  18P LOSS WILD-TYPE                               13
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  18P LOSS MUTATED                                         1
  18P LOSS WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  18P LOSS MUTATED                             10
  18P LOSS WILD-TYPE                           34
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  18P LOSS MUTATED                                         1
  18P LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  18P LOSS MUTATED                                           1
  18P LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  18P LOSS MUTATED                                                  1
  18P LOSS WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  18P LOSS MUTATED                                          1
  18P LOSS WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  18P LOSS MUTATED                                                         0
  18P LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  18P LOSS MUTATED                                            0
  18P LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  18P LOSS MUTATED                                                  17
  18P LOSS WILD-TYPE                                                56
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  18P LOSS MUTATED                                                    0
  18P LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  18P LOSS MUTATED                                    2
  18P LOSS WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  18P LOSS MUTATED                          1                           1
  18P LOSS WILD-TYPE                        4                           3
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  18P LOSS MUTATED                           0
  18P LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  18P LOSS MUTATED                                   2
  18P LOSS WILD-TYPE                                 5
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  18P LOSS MUTATED                                   1
  18P LOSS WILD-TYPE                                 4
D73V3, multiclass
                                                         clus
vv                                                        18P LOSS MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     4
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 7
  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                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        2
  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                                1
  LOWER EXTREMITY - THIGH/KNEE                                          10
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            1
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        18P LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       3
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            1
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  21
  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                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        13
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            34
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  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                       56
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              3
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    32  29
  18P LOSS WILD-TYPE 107  89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     32   29
  18P LOSS WILD-TYPE  107   89
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               32                107
  MALE                 29                 89
[1] 2 2
[1] FALSE
D73V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    39  21
  18P LOSS WILD-TYPE 140  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     39   21
  18P LOSS WILD-TYPE  140   51
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                39                140
  YES               21                 51
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  18P LOSS MUTATED                             13             0
  18P LOSS WILD-TYPE                           46             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  18P LOSS MUTATED                                                                          0
  18P LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  18P LOSS MUTATED                     23
  18P LOSS WILD-TYPE                   80
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  18P LOSS MUTATED                                                  3
  18P LOSS WILD-TYPE                                                6
                    vv
clus                 MYXOFIBROSARCOMA
  18P LOSS MUTATED                  6
  18P LOSS WILD-TYPE               18
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  18P LOSS MUTATED                                                          9
  18P LOSS WILD-TYPE                                                       19
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  18P LOSS MUTATED                                          0
  18P LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  18P LOSS MUTATED                             0                             0
  18P LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  18P LOSS MUTATED                                            7
  18P LOSS WILD-TYPE                                         14
D73V6, multiclass
                                                                          clus
vv                                                                         18P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           13
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   23
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        3
  MYXOFIBROSARCOMA                                                                        6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                9
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              7
                                                                          clus
vv                                                                         18P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             46
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     80
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          6
  MYXOFIBROSARCOMA                                                                         18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 19
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               14
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    35  18   2   6
  18P LOSS WILD-TYPE 117  51   7  20
D73V7, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               35                117
  R1               18                 51
  R2                2                  7
  RX                6                 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
  18P LOSS MUTATED       1                         4    54
  18P LOSS WILD-TYPE     5                        14   170
D73V8, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   54                170
[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"
D73V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1  54
  18P LOSS WILD-TYPE   4 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   54
  18P LOSS WILD-TYPE    4  166
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               54                166
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    37  32
  18Q LOSS WILD-TYPE 122  66
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                69                188 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                32                 66 
$`18Q LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-AB2P TCGA-DX-AB2X 
       31.53        67.20        15.22        14.43        12.07        13.28 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DM 
      101.98        60.00        32.15        22.62        11.70         6.35 
TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HS TCGA-3B-A9HX 
       18.08       188.15        26.17        35.08        44.91        42.84 
TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A2J0 
        0.56        68.61        12.85        18.54         6.28         9.70 
TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48P 
       49.05        14.99        10.68        85.45        45.99        46.03 
TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z0 
       82.68        31.96         3.06        78.28        16.87        64.21 
TCGA-DX-A7EM TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BU TCGA-DX-A8BZ 
       62.20         9.34        61.97        40.77        36.69         6.58 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2Q TCGA-FX-A48G TCGA-HB-A2OT TCGA-HS-A5N7 
       17.79        15.72        66.74        19.89        67.63        33.30 
TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-JV-A5VF TCGA-KD-A5QU 
       80.48         3.22        25.22       171.09         1.05        35.28 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-QC-A7B5 TCGA-QQ-A8VH TCGA-RN-AAAQ 
       30.31        25.41        21.73        13.08        10.52        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XS 
       18.94         3.88        25.35        19.63        10.72        84.79 
TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-Z4-AAPG 
       22.62        26.43        15.98 

$`18Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BG 
       36.30        34.68        16.18        34.36        75.32        17.95 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 
       14.07        15.85        40.60       106.45        22.85        30.51 
TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH 
       84.66        16.60        37.02        12.62        52.11        26.93 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-QC-A6FX 
       52.27        28.21       159.29        17.75         8.28        20.94 
TCGA-SG-A849 TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ 
       17.52        41.49        50.01        19.69        53.49        68.55 
TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ 
       88.57        54.74        25.25        14.37        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ 
       36.03        18.64        26.56        14.04        32.71        45.11 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        85.02        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 
       76.41        66.87        27.81        60.30         8.58        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       79.17         9.04        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       31.86        35.77        51.02         4.54        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       50.43        34.88         9.73        24.26        35.28        52.77 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YV 
       36.33        28.96        36.85        26.99        41.00        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO 
       86.30       101.23        21.30        34.49        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       29.49        48.20        20.05        45.14        47.87        38.17 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
      150.35        27.95        40.44        60.66        19.43         1.15 
TCGA-DX-AB2F TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       12.00        65.98        86.10         9.21        77.88       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 
       20.32        15.48         8.05        34.88         4.57         0.72 
TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA 
        9.80        19.53         1.38        19.89        37.12        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       85.97         5.92        16.41         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS 
       62.17       123.78        17.36        23.38         5.19        63.81 
TCGA-KD-A5QT TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       16.41         0.49        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       81.01        17.65         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       35.90        37.12       130.32       111.98        64.77         0.72 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D 
       22.82        32.75         8.61        13.22        13.41        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
       11.93         4.80        38.27        65.46         8.58        63.35 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       35.90        18.08        45.34        30.84        35.18        19.17 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB 
       20.65        50.86        29.46        27.32        36.43         4.37 
TCGA-Z4-A9VC TCGA-Z4-AAPF 
       13.38        15.95 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.56               0.49 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            188.15             159.29 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            25.220             33.945 
[1] "0.6 - 188.2 (25.2)" "0.5 - 159.3 (33.9)"
[1] "hr=" "1.5"
D74V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  18Q LOSS MUTATED                0                  4                   0
  18Q LOSS WILD-TYPE              1                  3                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  18Q LOSS MUTATED                     0                             1
  18Q LOSS WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  18Q LOSS MUTATED                       0                      5
  18Q LOSS WILD-TYPE                     1                     23
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  18Q LOSS MUTATED                      1                    0
  18Q LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  18Q LOSS MUTATED                                       0
  18Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  18Q LOSS MUTATED                                  0
  18Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  18Q LOSS MUTATED                                                1
  18Q LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  18Q LOSS MUTATED                                 3
  18Q LOSS WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  18Q LOSS MUTATED                                         0
  18Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  18Q LOSS MUTATED                              1                       0
  18Q LOSS WILD-TYPE                            3                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  18Q LOSS MUTATED                                  7
  18Q LOSS WILD-TYPE                               10
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  18Q LOSS MUTATED                                         4
  18Q LOSS WILD-TYPE                                       1
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  18Q LOSS MUTATED                             15
  18Q LOSS WILD-TYPE                           29
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  18Q LOSS MUTATED                                         1
  18Q LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  18Q LOSS MUTATED                                           1
  18Q LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  18Q LOSS MUTATED                                                  1
  18Q LOSS WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  18Q LOSS MUTATED                                          1
  18Q LOSS WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  18Q LOSS MUTATED                                                         0
  18Q LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  18Q LOSS MUTATED                                            0
  18Q LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  18Q LOSS MUTATED                                                  15
  18Q LOSS WILD-TYPE                                                58
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  18Q LOSS MUTATED                                                    0
  18Q LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  18Q LOSS MUTATED                                    2
  18Q LOSS WILD-TYPE                                  0
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  18Q LOSS MUTATED                          0                           2
  18Q LOSS WILD-TYPE                        5                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  18Q LOSS MUTATED                           0
  18Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  18Q LOSS MUTATED                                   2
  18Q LOSS WILD-TYPE                                 5
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  18Q LOSS MUTATED                                   1
  18Q LOSS WILD-TYPE                                 4
D74V3, multiclass
                                                         clus
vv                                                        18Q LOSS MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     4
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  0
  GYNECOLOGICAL - UTERUS                                                 5
  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                         1
  LOWER ABDOMINAL/PELVIC - PELVIC                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           1
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                4
  LOWER EXTREMITY - THIGH/KNEE                                          15
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               1
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     15
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     2
  SUPERFICIAL TRUNK - BACK                                               0
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        18Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       3
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            1
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  23
  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                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             3
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  1
  LOWER EXTREMITY - THIGH/KNEE                                            29
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                1
  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                       58
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       0
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        4
[1] 33  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V4, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    36  33
  18Q LOSS WILD-TYPE 103  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     36   33
  18Q LOSS WILD-TYPE  103   85
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               36                103
  MALE                 33                 85
[1] 2 2
[1] FALSE
D74V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    42  26
  18Q LOSS WILD-TYPE 137  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     42   26
  18Q LOSS WILD-TYPE  137   46
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                42                137
  YES               26                 46
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  18Q LOSS MUTATED                             13             0
  18Q LOSS WILD-TYPE                           46             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  18Q LOSS MUTATED                                                                          0
  18Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  18Q LOSS MUTATED                     22
  18Q LOSS WILD-TYPE                   81
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  18Q LOSS MUTATED                                                  5
  18Q LOSS WILD-TYPE                                                4
                    vv
clus                 MYXOFIBROSARCOMA
  18Q LOSS MUTATED                 10
  18Q LOSS WILD-TYPE               14
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  18Q LOSS MUTATED                                                         12
  18Q LOSS WILD-TYPE                                                       16
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  18Q LOSS MUTATED                                          0
  18Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  18Q LOSS MUTATED                             0                             0
  18Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  18Q LOSS MUTATED                                            7
  18Q LOSS WILD-TYPE                                         14
D74V6, multiclass
                                                                          clus
vv                                                                         18Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           13
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   22
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        5
  MYXOFIBROSARCOMA                                                                       10
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              7
                                                                          clus
vv                                                                         18Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             46
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     81
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          4
  MYXOFIBROSARCOMA                                                                         14
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               14
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    38  19   2   9
  18Q LOSS WILD-TYPE 114  50   7  17
D74V7, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               38                114
  R1               19                 50
  R2                2                  7
  RX                9                 17
[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
  18Q LOSS MUTATED       1                         4    60
  18Q LOSS WILD-TYPE     5                        14   164
D74V8, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   60                164
[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"
D74V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1  59
  18Q LOSS WILD-TYPE   4 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1   59
  18Q LOSS WILD-TYPE    4  161
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               59                161
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    16   8
  19P LOSS WILD-TYPE 143  90
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                24                233 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 90 
$`19P LOSS MUTATED`
TCGA-DX-A7ET TCGA-DX-AB2W TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-KF-A41W TCGA-PC-A5DM 
       15.22       106.45        26.93        22.62        11.70         6.35 
TCGA-3B-A9HL TCGA-3B-A9HX TCGA-DX-A3LT TCGA-DX-A48K TCGA-DX-A7EN TCGA-K1-A6RV 
       19.69        42.84        49.05        45.99        30.35         5.19 
TCGA-LI-A67I TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-AA8B 
       30.31        81.01        13.08        16.77         3.88         8.61 
TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C4 
       19.63        10.72        22.62        26.43        35.18        20.65 

$`19P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J 
       75.32        17.95        14.43        14.07        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       12.07        13.28        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       84.66        32.15        16.60        37.02        12.62        52.11 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP 
       52.27        28.21       159.29        17.75         8.28        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       20.94       188.15        17.52        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       50.01        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        14.37        10.32        38.47        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       26.56         0.56        14.04        32.71        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       45.11        18.54        54.21        85.02        33.53        66.94 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        95.38        79.17         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       86.83       136.44        33.44        44.68        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       51.02         4.54        14.99        10.68        73.87        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       50.43        34.88        85.45         9.73        24.26        35.28 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        37.41        82.68        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       36.85        26.99         3.06        41.00        78.28        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        86.30        64.21       101.23        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       62.20       152.12        29.49        48.20        20.05         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       61.97        45.14        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        1.15        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       66.74         9.21        77.88       106.55        50.40        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31        49.15        31.13        21.70        20.32        19.89 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       15.48         8.05        67.63        34.88         4.57        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.72         9.80        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
       19.89        37.12        25.22       171.09        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        16.41         1.05         3.91       101.26        53.33 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QS TCGA-KD-A5QT 
       62.17       123.78        17.36        23.38        63.81        16.41 
TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       35.28        25.41         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       37.55        38.63        17.65         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        35.90        37.12       130.32       111.98        64.77 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       10.52         0.72        18.94        22.82        25.35        32.75 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.22        13.41        12.46        11.93         4.80        84.79 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46         8.58        63.35        35.90        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       45.34        30.84        19.17        50.86        29.46        27.32 
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 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3.88               0.49 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            106.45             188.15 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            21.635             32.750 
[1] "3.9 - 106.5 (21.6)" "0.5 - 188.2 (32.8)"
[1] "hr=" "1.2"
D75V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  19P LOSS MUTATED                0                  1                   0
  19P LOSS WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  19P LOSS MUTATED                     0                             0
  19P LOSS WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  19P LOSS MUTATED                       0                      3
  19P LOSS WILD-TYPE                     1                     25
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  19P LOSS MUTATED                      1                    0
  19P LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  19P LOSS MUTATED                                       0
  19P LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  19P LOSS MUTATED                                  0
  19P LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  19P LOSS MUTATED                                                0
  19P LOSS WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  19P LOSS MUTATED                                 0
  19P LOSS WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  19P LOSS MUTATED                                         0
  19P LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  19P LOSS MUTATED                              0                       0
  19P LOSS WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  19P LOSS MUTATED                                  3
  19P LOSS WILD-TYPE                               14
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  19P LOSS MUTATED                                         2
  19P LOSS WILD-TYPE                                       3
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  19P LOSS MUTATED                              6
  19P LOSS WILD-TYPE                           38
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  19P LOSS MUTATED                                         1
  19P LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  19P LOSS MUTATED                                           0
  19P LOSS WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  19P LOSS MUTATED                                                  0
  19P LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  19P LOSS MUTATED                                          1
  19P LOSS WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  19P LOSS MUTATED                                                         0
  19P LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  19P LOSS MUTATED                                            0
  19P LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  19P LOSS MUTATED                                                   3
  19P LOSS WILD-TYPE                                                70
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  19P LOSS MUTATED                                                    0
  19P LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  19P LOSS MUTATED                                    1
  19P LOSS WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  19P LOSS MUTATED                          0                           0
  19P LOSS WILD-TYPE                        5                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  19P LOSS MUTATED                           0
  19P LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  19P LOSS MUTATED                                   1
  19P LOSS WILD-TYPE                                 6
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  19P LOSS MUTATED                                   1
  19P LOSS WILD-TYPE                                 4
D75V3, multiclass
                                                         clus
vv                                                        19P LOSS 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                                                 3
  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                                       3
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                2
  LOWER EXTREMITY - THIGH/KNEE                                           6
  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                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      3
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               0
  SUPERFICIAL TRUNK - BUTTOCK                                            0
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        19P LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  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                                         10
  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                                            38
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  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                                       1
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        6
  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"
D75V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    13  11
  19P LOSS WILD-TYPE 126 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     13   11
  19P LOSS WILD-TYPE  126  107
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               13                126
  MALE                 11                107
[1] 2 2
[1] FALSE
D75V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    12  12
  19P LOSS WILD-TYPE 167  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     12   12
  19P LOSS WILD-TYPE  167   60
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                12                167
  YES               12                 60
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  19P LOSS MUTATED                              3             0
  19P LOSS WILD-TYPE                           56             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  19P LOSS MUTATED                                                                          0
  19P LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  19P LOSS MUTATED                      9
  19P LOSS WILD-TYPE                   94
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  19P LOSS MUTATED                                                  2
  19P LOSS WILD-TYPE                                                7
                    vv
clus                 MYXOFIBROSARCOMA
  19P LOSS MUTATED                  2
  19P LOSS WILD-TYPE               22
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  19P LOSS MUTATED                                                          3
  19P LOSS WILD-TYPE                                                       25
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  19P LOSS MUTATED                                          0
  19P LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  19P LOSS MUTATED                             0                             0
  19P LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  19P LOSS MUTATED                                            5
  19P LOSS WILD-TYPE                                         16
D75V6, multiclass
                                                                          clus
vv                                                                         19P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            3
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    9
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        2
  MYXOFIBROSARCOMA                                                                        2
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              5
                                                                          clus
vv                                                                         19P LOSS 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)                                          7
  MYXOFIBROSARCOMA                                                                         22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 25
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               16
[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
  19P LOSS MUTATED    10   9   0   4
  19P LOSS WILD-TYPE 142  60   9  22
D75V7, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               10                142
  R1                9                 60
  R2                0                  9
  RX                4                 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
  19P LOSS MUTATED       1                         1    22
  19P LOSS WILD-TYPE     5                        17   202
D75V8, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                 17
  WHITE                                   22                202
[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"
D75V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  24
  19P LOSS WILD-TYPE   5 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   24
  19P LOSS WILD-TYPE    5  196
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               24                196
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    24  17
  19Q LOSS WILD-TYPE 135  81
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                41                216 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                17                 81 
$`19Q LOSS MUTATED`
TCGA-DX-A7ET TCGA-DX-AB2W TCGA-DX-AB3A TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-PC-A5DM 
       15.22       106.45        32.15        26.93        22.62         6.35 
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HX TCGA-3B-A9I0 TCGA-DX-A1L0 TCGA-DX-A2J0 
       19.69        68.55        42.84        36.03        18.54         9.70 
TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48K TCGA-DX-A6Z2 TCGA-DX-A7EI 
       49.05        51.02        50.43        45.99       101.23        34.49 
TCGA-DX-A7EN TCGA-DX-A8BO TCGA-DX-AB2Q TCGA-FX-A48G TCGA-HB-A3YV TCGA-IW-A3M4 
       30.35        40.77        66.74        19.89         4.57        85.97 
TCGA-JV-A75J TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-PC-A5DK TCGA-PC-A5DO TCGA-QC-A7B5 
        3.91        30.31        25.41       122.96        81.01        13.08 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8Y0 
       18.94         3.88         8.61        19.63        10.72        22.62 
TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-Z4-AAPG 
       26.43        18.08        35.18        20.65        15.98 

$`19Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J 
       75.32        17.95        14.43        14.07        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       12.07        13.28        22.85       101.98        30.51        60.00 
TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK 
       84.66        16.60        37.02        12.62        52.11        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DP 
       28.21       159.29        11.70        17.75         8.28        18.08 
TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
       20.94       188.15        17.52        26.17        41.49        35.08 
TCGA-3B-A9HI TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       50.01        53.49        88.57        44.91        54.74        25.25 
TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       14.37        10.32        38.47        18.64        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04        32.71        68.61        12.85        45.11        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       85.02        33.53        66.94        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 
       66.87         6.28        27.81        60.30         8.58        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       79.17         9.04        86.83       136.44        33.44        44.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       31.86        35.77         4.54        14.99        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       68.55        34.88        85.45         9.73        24.26        35.28 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       52.77        46.03        26.47       108.82        59.84        37.58 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        37.41        82.68        36.33        28.96        31.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       36.85        26.99         3.06        41.00        78.28        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EO 
       16.87        86.30        64.21        21.30        62.20       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       29.49        48.20        20.05         9.34        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       47.87        38.17       150.35        27.95        40.44        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        17.79        12.00 
TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       15.72        65.98        86.10         9.21        77.88       106.55 
TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       50.40        50.89        71.31        49.15        31.13        21.70 
TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HS-A5N7 
       20.32        15.48         8.05        67.63        34.88        33.30 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.72         9.80        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 
       19.89        37.12        25.22       171.09        13.58         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       16.41         1.05       101.26        53.33        62.17       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU 
       17.36        23.38         5.19        63.81        16.41        35.28 
TCGA-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-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-AA9N 
       11.57        10.45         7.36        37.55        38.63        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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32       111.98        64.77        10.52         0.72        16.77 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-AB3D 
       22.82        25.35        32.75        13.22        13.41        12.46 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB 
       11.93         4.80        84.79        38.27        65.46         8.58 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 
       63.35        35.90        45.34        30.84        19.17        50.86 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       29.46        27.32        36.43         4.37        13.38        15.95 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              3.88               0.49 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            122.96             188.15 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            26.430             32.335 
[1] "3.9 - 123.0 (26.4)" "0.5 - 188.2 (32.3)"
[1] "hr=" "1.2"
D76V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  19Q LOSS MUTATED                0                  1                   0
  19Q LOSS WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  19Q LOSS MUTATED                     0                             0
  19Q LOSS WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  19Q LOSS MUTATED                       0                      6
  19Q LOSS WILD-TYPE                     1                     22
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  19Q LOSS MUTATED                      1                    0
  19Q LOSS WILD-TYPE                    1                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  19Q LOSS MUTATED                                       0
  19Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  19Q LOSS MUTATED                                  0
  19Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  19Q LOSS MUTATED                                                0
  19Q LOSS WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  19Q LOSS MUTATED                                 0
  19Q LOSS WILD-TYPE                              10
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  19Q LOSS MUTATED                                         0
  19Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  19Q LOSS MUTATED                              0                       0
  19Q LOSS WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  19Q LOSS MUTATED                                  6
  19Q LOSS WILD-TYPE                               11
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  19Q LOSS MUTATED                                         2
  19Q LOSS WILD-TYPE                                       3
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  19Q LOSS MUTATED                              7
  19Q LOSS WILD-TYPE                           37
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  19Q LOSS MUTATED                                         1
  19Q LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  19Q LOSS MUTATED                                           0
  19Q LOSS WILD-TYPE                                         2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  19Q LOSS MUTATED                                                  0
  19Q LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  19Q LOSS MUTATED                                          3
  19Q LOSS WILD-TYPE                                        5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  19Q LOSS MUTATED                                                         0
  19Q LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  19Q LOSS MUTATED                                            0
  19Q LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  19Q LOSS MUTATED                                                  12
  19Q LOSS WILD-TYPE                                                61
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  19Q LOSS MUTATED                                                    0
  19Q LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  19Q LOSS MUTATED                                    1
  19Q LOSS WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  19Q LOSS MUTATED                          0                           0
  19Q LOSS WILD-TYPE                        5                           4
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  19Q LOSS MUTATED                           0
  19Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  19Q LOSS MUTATED                                   0
  19Q LOSS WILD-TYPE                                 7
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  19Q LOSS MUTATED                                   1
  19Q LOSS WILD-TYPE                                 4
D76V3, multiclass
                                                         clus
vv                                                        19Q LOSS 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                                                 6
  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                                       6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                2
  LOWER EXTREMITY - THIGH/KNEE                                           7
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     12
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  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                                                        19Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  22
  HEAD AND NECK - HEAD                                                     1
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           2
  LOWER ABDOMINAL/PELVIC - PELVIC                                         10
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  3
  LOWER EXTREMITY - THIGH/KNEE                                            37
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       61
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 5
  SUPERFICIAL TRUNK - BUTTOCK                                              4
  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"
D76V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    23  18
  19Q LOSS WILD-TYPE 116 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     23   18
  19Q LOSS WILD-TYPE  116  100
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               23                116
  MALE                 18                100
[1] 2 2
[1] FALSE
D76V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    27  14
  19Q LOSS WILD-TYPE 152  58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     27   14
  19Q LOSS WILD-TYPE  152   58
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                27                152
  YES               14                 58
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  19Q LOSS MUTATED                              7             0
  19Q LOSS WILD-TYPE                           52             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  19Q LOSS MUTATED                                                                          0
  19Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  19Q LOSS MUTATED                     17
  19Q LOSS WILD-TYPE                   86
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  19Q LOSS MUTATED                                                  1
  19Q LOSS WILD-TYPE                                                8
                    vv
clus                 MYXOFIBROSARCOMA
  19Q LOSS MUTATED                  2
  19Q LOSS WILD-TYPE               22
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  19Q LOSS MUTATED                                                          6
  19Q LOSS WILD-TYPE                                                       22
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  19Q LOSS MUTATED                                          0
  19Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  19Q LOSS MUTATED                             0                             0
  19Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  19Q LOSS MUTATED                                            8
  19Q LOSS WILD-TYPE                                         13
D76V6, multiclass
                                                                          clus
vv                                                                         19Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            7
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   17
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        1
  MYXOFIBROSARCOMA                                                                        2
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                6
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              8
                                                                          clus
vv                                                                         19Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             52
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     86
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          8
  MYXOFIBROSARCOMA                                                                         22
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 22
  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
  19Q LOSS MUTATED    21  15   1   4
  19Q LOSS WILD-TYPE 131  54   8  22
D76V7, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               21                131
  R1               15                 54
  R2                1                  8
  RX                4                 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
  19Q LOSS MUTATED       1                         1    39
  19Q LOSS WILD-TYPE     5                        17   185
D76V8, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                 17
  WHITE                                   39                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  38
  19Q LOSS WILD-TYPE   3 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   38
  19Q LOSS WILD-TYPE    3  182
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               38                182
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    35  20
  20P LOSS WILD-TYPE 124  78
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                55                202 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                 78 
$`20P LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-AB2P TCGA-DX-AB2X 
       31.53        67.20        15.22        17.95        12.07        13.28 
TCGA-DX-AB32 TCGA-FX-A3NK TCGA-QC-A6FX TCGA-SG-A849 TCGA-3B-A9HI TCGA-3B-A9HS 
      101.98        16.60        20.94        17.52        50.01        44.91 
TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY 
       42.84        38.47        36.03         9.04        49.05        33.44 
TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       44.68        14.99        34.88        85.45        45.99        24.26 
TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A8BJ TCGA-DX-A8BK 
       59.84        15.95        16.87       101.23         9.34        61.97 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2Q TCGA-DX-AB2T 
       38.17        40.77        60.66         6.58        66.74        77.88 
TCGA-DX-AB2Z TCGA-FX-A2QS TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A6RU 
       50.40        49.15        19.89        16.41       101.26        23.38 
TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-PC-A5DK TCGA-PC-A5DO TCGA-QQ-A5VC TCGA-SI-AA8B 
       25.41        21.73       122.96        81.01        35.90         8.61 
TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-X6-A7WB TCGA-X6-A8C4 TCGA-X9-A971 
       11.93        84.79        65.46        18.08        20.65        27.32 
TCGA-Z4-AAPG 
       15.98 

$`20P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EL TCGA-DX-A8BH 
       36.30        34.68        16.18        34.36        75.32        14.43 
TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 
       14.07        15.85        40.60       106.45        22.85        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 
       60.00        84.66        32.15        37.02        12.62        52.11 
TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W 
       26.93        52.27        28.21       159.29        22.62        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A8VB TCGA-VT-A80J 
       17.75         8.28         6.35        18.08       188.15        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        35.08        19.69        53.49        68.55        88.57 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9I1 TCGA-3B-A9I3 
       54.74        25.25        14.37        10.32        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
        0.56        14.04        32.71        68.61        12.85        45.11 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       18.54        54.21        85.02        33.53        66.94        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58         9.70        95.38        79.17        86.83       136.44 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       31.86        35.77        51.02         4.54        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       68.55        50.43         9.73        35.28        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       26.47       108.82        37.58        37.41        82.68        36.33 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI 
       78.28        50.50        86.30        64.21        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       62.20        30.35       152.12        29.49        48.20        20.05 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       45.14        47.87       150.35        27.95        40.44        36.69 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L 
       19.43         1.15        17.79        12.00        15.72        65.98 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
       86.10         9.21       106.55        50.89        71.31        31.13 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       21.70        20.32        19.89        15.48         8.05        67.63 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       34.88         4.57        33.30         0.72         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
       19.53         3.22         1.38        37.12        25.22       171.09 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO 
       13.58        85.97         5.92         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        63.81        16.41 
TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       35.28        30.31         0.49        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DN 
       22.39        11.57        10.45         7.36        37.55        38.63 
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-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       16.77        18.94         3.88        22.82        25.35        32.75 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XQ 
       19.63        13.22        13.41        10.72        12.46         4.80 
TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       38.27        22.62         8.58        63.35        26.43        35.90 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
       45.34        30.84        35.18        19.17        50.86        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       36.43         4.37        13.38        15.95 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              6.58               0.49 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            122.96             188.15 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             34.88              30.43 
[1] "6.6 - 123.0 (34.9)" "0.5 - 188.2 (30.4)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  20P LOSS MUTATED                0                  2                   0
  20P LOSS WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  20P LOSS MUTATED                     1                             0
  20P LOSS WILD-TYPE                   0                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  20P LOSS MUTATED                       0                      2
  20P LOSS WILD-TYPE                     1                     26
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  20P LOSS MUTATED                      0                    0
  20P LOSS WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  20P LOSS MUTATED                                       0
  20P LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  20P LOSS MUTATED                                  0
  20P LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  20P LOSS MUTATED                                                1
  20P LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  20P LOSS MUTATED                                 1
  20P LOSS WILD-TYPE                               9
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  20P LOSS MUTATED                                         0
  20P LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  20P LOSS MUTATED                              0                       0
  20P LOSS WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  20P LOSS MUTATED                                  7
  20P LOSS WILD-TYPE                               10
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  20P LOSS MUTATED                                         0
  20P LOSS WILD-TYPE                                       5
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  20P LOSS MUTATED                             12
  20P LOSS WILD-TYPE                           32
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  20P LOSS MUTATED                                         1
  20P LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  20P LOSS MUTATED                                           2
  20P LOSS WILD-TYPE                                         0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  20P LOSS MUTATED                                                  1
  20P LOSS WILD-TYPE                                                4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  20P LOSS MUTATED                                          0
  20P LOSS WILD-TYPE                                        8
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  20P LOSS MUTATED                                                         1
  20P LOSS WILD-TYPE                                                       1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  20P LOSS MUTATED                                            0
  20P LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  20P LOSS MUTATED                                                  13
  20P LOSS WILD-TYPE                                                60
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  20P LOSS MUTATED                                                    1
  20P LOSS WILD-TYPE                                                  2
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  20P LOSS MUTATED                                    1
  20P LOSS WILD-TYPE                                  1
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  20P LOSS MUTATED                          2                           2
  20P LOSS WILD-TYPE                        3                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  20P LOSS MUTATED                           0
  20P LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  20P LOSS MUTATED                                   2
  20P LOSS WILD-TYPE                                 5
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  20P LOSS MUTATED                                   3
  20P LOSS WILD-TYPE                                 2
D77V3, multiclass
                                                         clus
vv                                                        20P LOSS MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     2
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    1
  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                         1
  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                                       7
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                0
  LOWER EXTREMITY - THIGH/KNEE                                          12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               0
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     13
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     1
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      2
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      3
                                                         clus
vv                                                        20P LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      0
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  26
  HEAD AND NECK - HEAD                                                     2
  HEAD AND NECK - NECK                                                     1
  HEAD AND NECK - OTHER (PLEASE SPECIFY                                    2
  LOWER ABDOMINAL/PELVIC - BLADDER                                         1
  LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY                           1
  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                                        10
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  5
  LOWER EXTREMITY - THIGH/KNEE                                            32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 8
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                  1
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                               1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       60
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       1
  SUPERFICIAL TRUNK - BACK                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        5
  UPPER EXTREMITY - UPPER ARM/ELBOW                                        2
[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"
D77V4, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    33  22
  20P LOSS WILD-TYPE 106  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     33   22
  20P LOSS WILD-TYPE  106   96
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               33                106
  MALE                 22                 96
[1] 2 2
[1] FALSE
D77V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    32  23
  20P LOSS WILD-TYPE 147  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     32   23
  20P LOSS WILD-TYPE  147   49
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                32                147
  YES               23                 49
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  20P LOSS MUTATED                              9             0
  20P LOSS WILD-TYPE                           50             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  20P LOSS MUTATED                                                                          0
  20P LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  20P LOSS MUTATED                     22
  20P LOSS WILD-TYPE                   81
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  20P LOSS MUTATED                                                  0
  20P LOSS WILD-TYPE                                                9
                    vv
clus                 MYXOFIBROSARCOMA
  20P LOSS MUTATED                  7
  20P LOSS WILD-TYPE               17
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  20P LOSS MUTATED                                                         11
  20P LOSS WILD-TYPE                                                       17
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  20P LOSS MUTATED                                          0
  20P LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  20P LOSS MUTATED                             0                             0
  20P LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  20P LOSS MUTATED                                            6
  20P LOSS WILD-TYPE                                         15
D77V6, multiclass
                                                                          clus
vv                                                                         20P LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            9
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   22
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        0
  MYXOFIBROSARCOMA                                                                        7
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               11
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              6
                                                                          clus
vv                                                                         20P LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             50
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     81
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          9
  MYXOFIBROSARCOMA                                                                         17
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 17
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                  2
  SYNOVIAL SARCOMA - BIPHASIC                                                               2
  SYNOVIAL SARCOMA - MONOPHASIC                                                             6
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                               15
[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
  20P LOSS MUTATED    38  15   1   1
  20P LOSS WILD-TYPE 114  54   8  25
D77V7, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               38                114
  R1               15                 54
  R2                1                  8
  RX                1                 25
[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
  20P LOSS MUTATED       0                         4    50
  20P LOSS WILD-TYPE     6                        14   174
D77V8, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   50                174
[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"
D77V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  51
  20P LOSS WILD-TYPE   4 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   51
  20P LOSS WILD-TYPE    4  169
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               51                169
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    16   9
  20Q LOSS WILD-TYPE 143  89
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                25                232 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 9                 89 
$`20Q LOSS MUTATED`
TCGA-DX-A8BG TCGA-DX-AB2X TCGA-DX-AB32 TCGA-FX-A3NK TCGA-3B-A9HI TCGA-3B-A9HX 
       17.95        13.28       101.98        16.60        50.01        42.84 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UE TCGA-DX-A6YX 
       49.05        33.44        44.68        14.99        34.88        16.87 
TCGA-DX-A6Z2 TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2T 
      101.23         9.34        61.97        60.66         6.58        77.88 
TCGA-DX-AB2Z TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-K1-A6RU TCGA-WK-A8XO TCGA-WK-A8XS 
       50.40        19.89        16.41        23.38        11.93        84.79 
TCGA-X9-A971 
       27.32 

$`20Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J 
       75.32        15.22        14.43        14.07        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       12.07       106.45        22.85        30.51        60.00        84.66 
TCGA-DX-AB3A TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK 
       32.15        37.02        12.62        52.11        26.93        52.27 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       28.21       159.29        22.62        11.70        17.75         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 TCGA-VT-A80J 
        6.35        18.08        20.94       188.15        17.52        26.17 
TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR 
       41.49        35.08        19.69        53.49        68.55        88.57 
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ 
       44.91        54.74        25.25        14.37        10.32        38.47 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       68.61        12.85        45.11        18.54        54.21        85.02 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        66.94        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        95.38 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 
       79.17         9.04        86.83       136.44        31.86        35.77 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       51.02         4.54        10.68        73.87        68.55        50.43 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       85.45         9.73        45.99        24.26        35.28        52.77 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       46.03        26.47       108.82        59.84        37.58        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       37.41        82.68        36.33        28.96        31.96        36.85 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ 
       26.99         3.06        41.00        78.28        50.50        86.30 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       64.21        21.30        34.49        62.20        30.35       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       29.49        48.20        20.05        45.14        47.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX 
       40.77       150.35        27.95        40.44        36.69        19.43 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        1.15        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       66.74         9.21       106.55        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       31.13        21.70        20.32        19.89        15.48         8.05 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
       67.63        34.88         4.57        33.30         0.72         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        19.53         3.22         1.38        37.12        25.22 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
      171.09        13.58        85.97         5.92         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
      101.26        53.33        62.17       123.78        17.36         5.19 
TCGA-KD-A5QS TCGA-KD-A5QT TCGA-KD-A5QU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA 
       63.81        16.41        35.28        30.31        25.41         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
       21.73        19.73        14.99        17.98        22.39        11.57 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       10.45         7.36       122.96        37.55        38.63        81.01 
TCGA-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-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90        37.12       130.32       111.98        64.77        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        16.77        18.94         3.88        22.82        25.35 
TCGA-SI-A71Q TCGA-SI-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-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       12.46         4.80        38.27        65.46        22.62         8.58 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       63.35        26.43        35.90        18.08        45.34        30.84 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       35.18        19.17        20.65        50.86        29.46        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
        4.37        13.38        15.95        15.98 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              6.58               0.49 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            101.98             188.15 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            33.440             30.985 
[1] "6.6 - 102.0 (33.4)" "0.5 - 188.2 (31.0)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  20Q LOSS MUTATED                0                  2                   0
  20Q LOSS WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  20Q LOSS MUTATED                     0                             0
  20Q LOSS WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  20Q LOSS MUTATED                       0                      0
  20Q LOSS WILD-TYPE                     1                     28
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  20Q LOSS MUTATED                      0                    0
  20Q LOSS WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  20Q LOSS MUTATED                                  0
  20Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  20Q LOSS MUTATED                                                1
  20Q LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  20Q LOSS MUTATED                                 1
  20Q LOSS WILD-TYPE                               9
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  20Q LOSS MUTATED                                         0
  20Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  20Q LOSS MUTATED                              0                       0
  20Q LOSS WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  20Q LOSS MUTATED                                  1
  20Q LOSS WILD-TYPE                               16
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  20Q LOSS MUTATED                                         0
  20Q LOSS WILD-TYPE                                       5
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  20Q LOSS MUTATED                              6
  20Q LOSS WILD-TYPE                           38
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  20Q LOSS MUTATED                                         1
  20Q LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  20Q LOSS MUTATED                                           2
  20Q LOSS WILD-TYPE                                         0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  20Q LOSS MUTATED                                                  0
  20Q LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  20Q LOSS MUTATED                                          0
  20Q LOSS WILD-TYPE                                        8
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  20Q LOSS MUTATED                                                         0
  20Q LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  20Q LOSS MUTATED                                            0
  20Q LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  20Q LOSS MUTATED                                                   5
  20Q LOSS WILD-TYPE                                                68
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  20Q LOSS MUTATED                                                    0
  20Q LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  20Q LOSS MUTATED                                    0
  20Q LOSS WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  20Q LOSS MUTATED                          1                           2
  20Q LOSS WILD-TYPE                        4                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  20Q LOSS MUTATED                           0
  20Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  20Q LOSS MUTATED                                   1
  20Q LOSS WILD-TYPE                                 6
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  20Q LOSS MUTATED                                   2
  20Q LOSS WILD-TYPE                                 3
D78V3, multiclass
                                                         clus
vv                                                        20Q LOSS 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                         1
  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                                       1
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                0
  LOWER EXTREMITY - THIGH/KNEE                                           6
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              2
  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                      5
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               1
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        20Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  GYNECOLOGICAL - OVARY                                                    1
  GYNECOLOGICAL - UTERUS                                                  28
  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                           1
  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                                        16
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  5
  LOWER EXTREMITY - THIGH/KNEE                                            38
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                                0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                         5
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                 8
  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                                                 4
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        6
  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"
D78V4, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    16   9
  20Q LOSS WILD-TYPE 123 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     16    9
  20Q LOSS WILD-TYPE  123  109
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               16                123
  MALE                  9                109
[1] 2 2
[1] FALSE
D78V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    15  10
  20Q LOSS WILD-TYPE 164  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     15   10
  20Q LOSS WILD-TYPE  164   62
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                15                164
  YES               10                 62
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  20Q LOSS MUTATED                              6             0
  20Q LOSS WILD-TYPE                           53             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  20Q LOSS MUTATED                                                                          0
  20Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  20Q LOSS MUTATED                      8
  20Q LOSS WILD-TYPE                   95
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  20Q LOSS MUTATED                                                  0
  20Q LOSS WILD-TYPE                                                9
                    vv
clus                 MYXOFIBROSARCOMA
  20Q LOSS MUTATED                  6
  20Q LOSS WILD-TYPE               18
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  20Q LOSS MUTATED                                                          4
  20Q LOSS WILD-TYPE                                                       24
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  20Q LOSS MUTATED                                          0
  20Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  20Q LOSS MUTATED                             0                             0
  20Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  20Q LOSS MUTATED                                            1
  20Q LOSS WILD-TYPE                                         20
D78V6, multiclass
                                                                          clus
vv                                                                         20Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                            6
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                    8
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        0
  MYXOFIBROSARCOMA                                                                        6
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                4
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              1
                                                                          clus
vv                                                                         20Q LOSS 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)                                          9
  MYXOFIBROSARCOMA                                                                         18
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 24
  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
  20Q LOSS MUTATED    21   3   1   0
  20Q LOSS WILD-TYPE 131  66   8  26
D78V7, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               21                131
  R1                3                 66
  R2                1                  8
  RX                0                 26
[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
  20Q LOSS MUTATED       0                         3    21
  20Q LOSS WILD-TYPE     6                        15   203
D78V8, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                3                 15
  WHITE                                   21                203
[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"
D78V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  23
  20Q LOSS WILD-TYPE   5 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   23
  20Q LOSS WILD-TYPE    5  197
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               23                197
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    32  18
  21Q LOSS WILD-TYPE 127  80
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                50                207 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                18                 80 
$`21Q LOSS MUTATED`
TCGA-DX-AB32 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SG-A849 
      101.98        22.62        11.70        20.94       188.15        17.52 
TCGA-VT-A80J TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HR TCGA-DX-A1KX TCGA-DX-A1L0 
       26.17        35.08        19.69        88.57        68.61        18.54 
TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       85.02        74.66         6.28        33.44        44.68        31.86 
TCGA-DX-A3UF TCGA-DX-A48V TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YX TCGA-DX-A7EF 
       85.45        59.84        36.33        31.96        16.87        21.30 
TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS 
        9.34        47.87        40.77        36.69         6.58         1.15 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-FX-A3TO TCGA-HB-A2OT TCGA-IS-A3K7 TCGA-JV-A5VE 
       86.10        66.74        20.32        67.63       171.09        16.41 
TCGA-K1-A3PN TCGA-K1-A42W TCGA-KD-A5QU TCGA-PC-A5DO TCGA-QQ-A8VG TCGA-RN-AAAQ 
      101.26        62.17        35.28        81.01        64.77        16.77 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XS TCGA-X6-A8C2 
       18.94         3.88         8.61        10.72        84.79        35.18 
TCGA-X6-A8C4 TCGA-Z4-AAPG 
       20.65        15.98 

$`21Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       36.30        31.53        34.68        16.18        67.20        34.36 
TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H 
       75.32        15.22        17.95        14.43        14.07        15.85 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 
       40.60        12.07       106.45        13.28        22.85        30.51 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HB-A5W3 
       60.00        84.66        32.15        16.60        37.02        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-LI-A9QH 
       52.11        26.93        52.27        28.21       159.29        17.75 
TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-WK-A8XT TCGA-3B-A9HI TCGA-3B-A9HP 
        8.28         6.35        18.08        41.49        50.01        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       68.55        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-A1L1 TCGA-DX-A1L3 
       14.04        32.71        12.85        45.11        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       66.94         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        95.38        79.17         9.04        49.05 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       86.83       136.44        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-A48J 
       10.68        73.87        68.55        50.43        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       45.99        24.26        35.28        52.77        46.03        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE 
      108.82        37.58        15.95        37.41        82.68        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       36.85        26.99         3.06        41.00        78.28        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN 
       86.30        64.21       101.23        34.49        62.20        30.35 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL 
      152.12        29.49        48.20        20.05        61.97        45.14 
TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX 
       38.17       150.35        27.95        40.44        60.66        19.43 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2S TCGA-DX-AB2T 
       17.79        12.00        15.72        65.98         9.21        77.88 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      106.55        50.40        50.89        71.31        49.15        31.13 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV 
       21.70        19.89        15.48         8.05        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       33.30         0.72         9.80        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        19.89        37.12        25.22        13.58        85.97 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
        5.92         1.05         3.91        53.33       123.78        17.36 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5Y8 
       23.38         5.19        63.81        16.41        30.31        25.41 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49        21.73        19.73        14.99        17.98        22.39 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       11.57        10.45         7.36       122.96        37.55        38.63 
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-A8VF TCGA-QQ-A8VH TCGA-RN-A68Q 
       35.90        37.12       130.32       111.98        10.52         0.72 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       22.82        25.35        32.75        19.63        13.22        13.41 
TCGA-VT-AB3D TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       12.46        11.93         4.80        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
        8.58        63.35        26.43        35.90        18.08        45.34 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       30.84        19.17        50.86        29.46        27.32        36.43 
TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
        4.37        13.38        15.95 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.15               0.49 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            188.15             159.29 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             34.26              30.35 
[1] "1.1 - 188.2 (34.3)" "0.5 - 159.3 (30.4)"
[1] "hr=" "1.3"
D79V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  21Q LOSS MUTATED                0                  2                   0
  21Q LOSS WILD-TYPE              1                  5                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  21Q LOSS MUTATED                     0                             0
  21Q LOSS WILD-TYPE                   1                             2
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  21Q LOSS MUTATED                       0                      5
  21Q LOSS WILD-TYPE                     1                     23
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  21Q LOSS MUTATED                      0                    0
  21Q LOSS WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  21Q LOSS MUTATED                                       0
  21Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  21Q LOSS MUTATED                                  0
  21Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  21Q LOSS MUTATED                                                0
  21Q LOSS WILD-TYPE                                              2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  21Q LOSS MUTATED                                 3
  21Q LOSS WILD-TYPE                               7
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  21Q LOSS MUTATED                                         0
  21Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  21Q LOSS MUTATED                              0                       0
  21Q LOSS WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  21Q LOSS MUTATED                                  6
  21Q LOSS WILD-TYPE                               11
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  21Q LOSS MUTATED                                         1
  21Q LOSS WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  21Q LOSS MUTATED                              9
  21Q LOSS WILD-TYPE                           35
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  21Q LOSS MUTATED                                         0
  21Q LOSS WILD-TYPE                                       4
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  21Q LOSS MUTATED                                           1
  21Q LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  21Q LOSS MUTATED                                                  0
  21Q LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  21Q LOSS MUTATED                                          1
  21Q LOSS WILD-TYPE                                        7
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  21Q LOSS MUTATED                                                         0
  21Q LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  21Q LOSS MUTATED                                            1
  21Q LOSS WILD-TYPE                                          0
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  21Q LOSS MUTATED                                                  15
  21Q LOSS WILD-TYPE                                                58
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  21Q LOSS MUTATED                                                    0
  21Q LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  21Q LOSS MUTATED                                    0
  21Q LOSS WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  21Q LOSS MUTATED                          2                           2
  21Q LOSS WILD-TYPE                        3                           2
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  21Q LOSS MUTATED                           0
  21Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  21Q LOSS MUTATED                                   1
  21Q LOSS WILD-TYPE                                 6
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  21Q LOSS MUTATED                                   1
  21Q LOSS WILD-TYPE                                 4
D79V3, multiclass
                                                         clus
vv                                                        21Q LOSS 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                                                 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                                        3
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                0
  LOWER EXTREMITY - FOOT/ANKLE                                           0
  LOWER EXTREMITY - GROIN                                                0
  LOWER EXTREMITY - LOWER LEG/CALF                                       6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                           9
  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                             1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     15
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               2
  SUPERFICIAL TRUNK - BUTTOCK                                            2
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      1
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      1
                                                         clus
vv                                                        21Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       5
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            2
  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                                          7
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            35
  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                               0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                       58
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                       3
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                       2
  SUPERFICIAL TRUNK - BACK                                                 3
  SUPERFICIAL TRUNK - BUTTOCK                                              2
  SUPERFICIAL TRUNK - FLANK                                                1
  UPPER EXTREMITY - SHOULDER/AXILLA                                        6
  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"
D79V4, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    27  23
  21Q LOSS WILD-TYPE 112  95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     27   23
  21Q LOSS WILD-TYPE  112   95
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               27                112
  MALE                 23                 95
[1] 2 2
[1] FALSE
D79V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    32  18
  21Q LOSS WILD-TYPE 147  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     32   18
  21Q LOSS WILD-TYPE  147   54
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                32                147
  YES               18                 54
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  21Q LOSS MUTATED                             11             0
  21Q LOSS WILD-TYPE                           48             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  21Q LOSS MUTATED                                                                          0
  21Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  21Q LOSS MUTATED                     14
  21Q LOSS WILD-TYPE                   89
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  21Q LOSS MUTATED                                                  3
  21Q LOSS WILD-TYPE                                                6
                    vv
clus                 MYXOFIBROSARCOMA
  21Q LOSS MUTATED                  3
  21Q LOSS WILD-TYPE               21
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  21Q LOSS MUTATED                                                         10
  21Q LOSS WILD-TYPE                                                       18
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  21Q LOSS MUTATED                                          0
  21Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  21Q LOSS MUTATED                             0                             0
  21Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  21Q LOSS MUTATED                                            9
  21Q LOSS WILD-TYPE                                         12
D79V6, multiclass
                                                                          clus
vv                                                                         21Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           11
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   14
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        3
  MYXOFIBROSARCOMA                                                                        3
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               10
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              9
                                                                          clus
vv                                                                         21Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             48
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     89
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          6
  MYXOFIBROSARCOMA                                                                         21
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 18
  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
  21Q LOSS MUTATED    25  19   1   4
  21Q LOSS WILD-TYPE 127  50   8  22
D79V7, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               25                127
  R1               19                 50
  R2                1                  8
  RX                4                 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
  21Q LOSS MUTATED       1                         4    44
  21Q LOSS WILD-TYPE     5                        14   180
D79V8, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   44                180
[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"
D79V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  44
  21Q LOSS WILD-TYPE   4 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   44
  21Q LOSS WILD-TYPE    4  176
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               44                176
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    42  25
  22Q LOSS WILD-TYPE 117  73
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                67                190 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                25                 73 
$`22Q LOSS MUTATED`
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A8BG TCGA-DX-AB2H TCGA-DX-AB3A 
       16.18        67.20        34.36        17.95        15.85        32.15 
TCGA-IE-A4EH TCGA-IS-A3K8 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-QQ-A8VB TCGA-3B-A9HI 
       26.93       159.29        22.62        11.70       188.15        50.01 
TCGA-3B-A9HR TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A1L2 
       88.57        42.84        26.56        32.71        54.21        85.02 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW 
       66.87         6.28         8.58         9.04        49.05       136.44 
TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA 
       44.68        14.99        24.26        26.47        15.95        82.68 
TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-AB2O 
       31.96        78.28        50.50        61.97        45.14        86.10 
TCGA-DX-AB2T TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV 
       77.88        21.70        20.32        19.89        34.88         4.57 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M5 
        0.72         9.80        19.89        25.22       171.09         5.92 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QT TCGA-LI-A67I 
        1.05       101.26        23.38         5.19        16.41        30.31 
TCGA-MB-A5Y8 TCGA-QC-AA9N TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-SI-AA8C 
       25.41        17.65        10.52         3.88         8.61        19.63 
TCGA-WK-A8XS TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X9-A971 
       84.79        63.35        26.43        18.08        35.18        27.32 
TCGA-Z4-AAPG 
       15.98 

$`22Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HO TCGA-DX-A3M2 TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BH 
       36.30        31.53        34.68        75.32        15.22        14.43 
TCGA-DX-A8BP TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       14.07        40.60        12.07       106.45        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3NK TCGA-HB-A43Z 
      101.98        30.51        60.00        84.66        16.60        37.02 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-LI-A9QH TCGA-MB-A5Y9 
       12.62        52.11        52.27        28.21        17.75         8.28 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT 
        6.35        18.08        20.94        17.52        26.17        41.49 
TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       35.08        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        14.37        10.32        38.47        36.03        18.64 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        14.04        68.61        12.85        45.11        18.54 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z 
       33.53        66.94        74.66         5.26        76.41        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY 
       60.30         9.70        95.38        79.17        86.83        33.44 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       31.86        35.77        51.02         4.54        10.68        73.87 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       68.55        50.43        34.88        85.45         9.73        45.99 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       35.28        52.77        46.03       108.82        59.84        37.58 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       37.41        36.33        28.96        36.85        26.99         3.06 
TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       41.00        16.87        86.30        64.21       101.23        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        62.20        30.35       152.12        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       20.05         9.34        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        40.44        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q 
        1.15        17.79        12.00        15.72        65.98        66.74 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
        9.21       106.55        50.40        50.89        71.31        49.15 
TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-IE-A3OV 
       31.13        15.48         8.05        67.63        33.30        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M4 
       19.53         3.22         1.38        37.12        13.58        85.97 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
       16.41         3.91        53.33        62.17       123.78        17.36 
TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       63.81        35.28         0.49        21.73        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55        38.63        81.01        13.08         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        48.59        35.90        37.12       130.32       111.98 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P 
       64.77         0.72        16.77        18.94        22.82        25.35 
TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D TCGA-WK-A8XO 
       32.75        13.22        13.41        10.72        12.46        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WA 
        4.80        38.27        65.46        22.62         8.58        35.90 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       45.34        30.84        19.17        20.65        50.86        29.46 
TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF 
       36.43         4.37        13.38        15.95 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.72               0.49 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            188.15             152.12 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             26.47              33.37 
[1] "0.7 - 188.2 (26.5)" "0.5 - 152.1 (33.4)"
[1] "hr=" "1"  
D80V2, continuous
                    vv
clus                 CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  22Q LOSS MUTATED                0                  1                   0
  22Q LOSS WILD-TYPE              1                  6                   2
                    vv
clus                 CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  22Q LOSS MUTATED                     0                             1
  22Q LOSS WILD-TYPE                   1                             1
                    vv
clus                 GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  22Q LOSS MUTATED                       1                     14
  22Q LOSS WILD-TYPE                     0                     14
                    vv
clus                 HEAD AND NECK - HEAD HEAD AND NECK - NECK
  22Q LOSS MUTATED                      0                    0
  22Q LOSS WILD-TYPE                    2                    1
                    vv
clus                 HEAD AND NECK - OTHER (PLEASE SPECIFY
  22Q LOSS MUTATED                                       0
  22Q LOSS WILD-TYPE                                     2
                    vv
clus                 LOWER ABDOMINAL/PELVIC - BLADDER
  22Q LOSS MUTATED                                  0
  22Q LOSS WILD-TYPE                                1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  22Q LOSS MUTATED                                                1
  22Q LOSS WILD-TYPE                                              1
                    vv
clus                 LOWER ABDOMINAL/PELVIC - PELVIC
  22Q LOSS MUTATED                                 2
  22Q LOSS WILD-TYPE                               8
                    vv
clus                 LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  22Q LOSS MUTATED                                         0
  22Q LOSS WILD-TYPE                                       2
                    vv
clus                 LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  22Q LOSS MUTATED                              0                       0
  22Q LOSS WILD-TYPE                            4                       2
                    vv
clus                 LOWER EXTREMITY - LOWER LEG/CALF
  22Q LOSS MUTATED                                  5
  22Q LOSS WILD-TYPE                               12
                    vv
clus                 LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  22Q LOSS MUTATED                                         1
  22Q LOSS WILD-TYPE                                       4
                    vv
clus                 LOWER EXTREMITY - THIGH/KNEE
  22Q LOSS MUTATED                             12
  22Q LOSS WILD-TYPE                           32
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - COLON
  22Q LOSS MUTATED                                         1
  22Q LOSS WILD-TYPE                                       3
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  22Q LOSS MUTATED                                           1
  22Q LOSS WILD-TYPE                                         1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  22Q LOSS MUTATED                                                  0
  22Q LOSS WILD-TYPE                                                5
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  22Q LOSS MUTATED                                          2
  22Q LOSS WILD-TYPE                                        6
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  22Q LOSS MUTATED                                                         0
  22Q LOSS WILD-TYPE                                                       2
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  22Q LOSS MUTATED                                            0
  22Q LOSS WILD-TYPE                                          1
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  22Q LOSS MUTATED                                                  17
  22Q LOSS WILD-TYPE                                                56
                    vv
clus                 RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  22Q LOSS MUTATED                                                    0
  22Q LOSS WILD-TYPE                                                  3
                    vv
clus                 SUPERFICIAL TRUNK - ABDOMINAL WALL
  22Q LOSS MUTATED                                    0
  22Q LOSS WILD-TYPE                                  2
                    vv
clus                 SUPERFICIAL TRUNK - BACK SUPERFICIAL TRUNK - BUTTOCK
  22Q LOSS MUTATED                          0                           3
  22Q LOSS WILD-TYPE                        5                           1
                    vv
clus                 SUPERFICIAL TRUNK - FLANK
  22Q LOSS MUTATED                           0
  22Q LOSS WILD-TYPE                         1
                    vv
clus                 UPPER EXTREMITY - SHOULDER/AXILLA
  22Q LOSS MUTATED                                   3
  22Q LOSS WILD-TYPE                                 4
                    vv
clus                 UPPER EXTREMITY - UPPER ARM/ELBOW
  22Q LOSS MUTATED                                   2
  22Q LOSS WILD-TYPE                                 3
D80V3, multiclass
                                                         clus
vv                                                        22Q LOSS MUTATED
  CHEST - BREAST                                                         0
  CHEST - CHEST WALL                                                     1
  CHEST - LUNG/PLEURA                                                    0
  CHEST - MEDIASTINUM                                                    0
  CHEST - OTHER (PLEASE SPECIFY                                          1
  GYNECOLOGICAL - OVARY                                                  1
  GYNECOLOGICAL - UTERUS                                                14
  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                         1
  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                                       5
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                1
  LOWER EXTREMITY - THIGH/KNEE                                          12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                              1
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                       0
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                               2
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                             0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                     17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                     0
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                     0
  SUPERFICIAL TRUNK - BACK                                               0
  SUPERFICIAL TRUNK - BUTTOCK                                            3
  SUPERFICIAL TRUNK - FLANK                                              0
  UPPER EXTREMITY - SHOULDER/AXILLA                                      3
  UPPER EXTREMITY - UPPER ARM/ELBOW                                      2
                                                         clus
vv                                                        22Q LOSS WILD-TYPE
  CHEST - BREAST                                                           1
  CHEST - CHEST WALL                                                       6
  CHEST - LUNG/PLEURA                                                      2
  CHEST - MEDIASTINUM                                                      1
  CHEST - OTHER (PLEASE SPECIFY                                            1
  GYNECOLOGICAL - OVARY                                                    0
  GYNECOLOGICAL - UTERUS                                                  14
  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                           1
  LOWER ABDOMINAL/PELVIC - PELVIC                                          8
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                  2
  LOWER EXTREMITY - FOOT/ANKLE                                             4
  LOWER EXTREMITY - GROIN                                                  2
  LOWER EXTREMITY - LOWER LEG/CALF                                        12
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                  4
  LOWER EXTREMITY - THIGH/KNEE                                            32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                  3
  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                       56
  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                                        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"
D80V4, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   44 23
  22Q LOSS WILD-TYPE 95 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     44   23
  22Q LOSS WILD-TYPE   95   95
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               44                 95
  MALE                 23                 95
[1] 2 2
[1] FALSE
D80V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    47  19
  22Q LOSS WILD-TYPE 132  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     47   19
  22Q LOSS WILD-TYPE  132   53
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                47                132
  YES               19                 53
[1] 2 2
[1] FALSE
                    vv
clus                 DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  22Q LOSS MUTATED                             16             0
  22Q LOSS WILD-TYPE                           43             2
                    vv
clus                 GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  22Q LOSS MUTATED                                                                          0
  22Q LOSS WILD-TYPE                                                                        1
                    vv
clus                 LEIOMYOSARCOMA (LMS)
  22Q LOSS MUTATED                     28
  22Q LOSS WILD-TYPE                   75
                    vv
clus                 MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  22Q LOSS MUTATED                                                  3
  22Q LOSS WILD-TYPE                                                6
                    vv
clus                 MYXOFIBROSARCOMA
  22Q LOSS MUTATED                  9
  22Q LOSS WILD-TYPE               15
                    vv
clus                 PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  22Q LOSS MUTATED                                                          3
  22Q LOSS WILD-TYPE                                                       25
                    vv
clus                 SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  22Q LOSS MUTATED                                          0
  22Q LOSS WILD-TYPE                                        2
                    vv
clus                 SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  22Q LOSS MUTATED                             0                             0
  22Q LOSS WILD-TYPE                           2                             6
                    vv
clus                 UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  22Q LOSS MUTATED                                            8
  22Q LOSS WILD-TYPE                                         13
D80V6, multiclass
                                                                          clus
vv                                                                         22Q LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           16
  DESMOID TUMOR                                                                           0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                0
  LEIOMYOSARCOMA (LMS)                                                                   28
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                        3
  MYXOFIBROSARCOMA                                                                        9
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                3
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                0
  SYNOVIAL SARCOMA - BIPHASIC                                                             0
  SYNOVIAL SARCOMA - MONOPHASIC                                                           0
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              8
                                                                          clus
vv                                                                         22Q LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                             43
  DESMOID TUMOR                                                                             2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                  1
  LEIOMYOSARCOMA (LMS)                                                                     75
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                          6
  MYXOFIBROSARCOMA                                                                         15
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                 25
  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
  22Q LOSS MUTATED    35  20   3   9
  22Q LOSS WILD-TYPE 117  49   6  17
D80V7, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               35                117
  R1               20                 49
  R2                3                  6
  RX                9                 17
[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
  22Q LOSS MUTATED       1                         4    59
  22Q LOSS WILD-TYPE     5                        14   165
D80V8, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   59                165
[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"
D80V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     0  55
  22Q LOSS WILD-TYPE   5 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0   55
  22Q LOSS WILD-TYPE    5  165
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               55                165
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    37  26
  XP LOSS WILD-TYPE 122  72
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               63               194 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               26                72 
$`XP LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-AB32 TCGA-DX-AB35 TCGA-HB-A5W3 TCGA-IE-A4EH TCGA-IS-A3K6 
       31.53       101.98        30.51        12.62        26.93        28.21 
TCGA-LI-A9QH TCGA-QQ-A8VB TCGA-3B-A9HI TCGA-3B-A9HS TCGA-3B-A9HV TCGA-3B-A9HY 
       17.75       188.15        50.01        44.91        14.37        10.32 
TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A2J0 TCGA-DX-A3LY 
       36.03         0.56        18.54        85.02         9.70        33.44 
TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       50.43         9.73        52.77        46.03        26.47       108.82 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EF 
       59.84        37.58        37.41         3.06        16.87        21.30 
TCGA-DX-A7EN TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BZ TCGA-DX-AB3C 
       30.35        38.17        40.77       150.35         6.58        71.31 
TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IF-A4AJ TCGA-IS-A3K7 
       19.89        34.88         4.57         9.80        25.22       171.09 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-K1-A42X TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KD-A5QU 
       85.97        16.41       123.78        23.38         5.19        35.28 
TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-PC-A5DO TCGA-QC-AA9N TCGA-SI-A71O TCGA-SI-A71Q 
       25.41        19.73        81.01        17.65        22.82        32.75 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WB 
        8.61        19.63        38.27        65.46        63.35        18.08 
TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 
       30.84        20.65        50.86 

$`XP LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A7EL 
       36.30        34.68        16.18        67.20        34.36        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J 
       15.22        17.95        14.43        14.07        15.85        40.60 
TCGA-DX-AB2P TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 
       12.07       106.45        13.28        22.85        60.00        84.66 
TCGA-DX-AB3A TCGA-FX-A3NK TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K8 
       32.15        16.60        37.02        52.11        52.27       159.29 
TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX 
       22.62        11.70         8.28         6.35        18.08        20.94 
TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 TCGA-3B-A9HL TCGA-3B-A9HP 
       17.52        26.17        41.49        35.08        19.69        53.49 
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ 
       68.55        88.57        54.74        25.25        42.84        38.47 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64        26.56        14.04        32.71        68.61        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       45.11        54.21        33.53        66.94        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       95.38        79.17         9.04        49.05        86.83       136.44 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       44.68        31.86        35.77        51.02         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K 
       10.68        73.87        68.55        34.88        85.45        45.99 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       24.26        35.28        15.95        82.68        36.33        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV 
       31.96        36.85        26.99        41.00        78.28        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EO 
       86.30        64.21       101.23        34.49        62.20       152.12 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       29.49        48.20        20.05         9.34        61.97        45.14 
TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
       47.87        27.95        40.44        36.69        60.66        19.43 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2O 
        1.15        17.79        12.00        15.72        65.98        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B 
       66.74         9.21        77.88       106.55        50.40        50.89 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO 
       49.15        31.13        21.70        20.32        15.48         8.05 
TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       67.63        33.30         0.72        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF 
        1.38        19.89        37.12        13.58         5.92         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-KD-A5QS 
        3.91       101.26        53.33        62.17        17.36        63.81 
TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J 
       16.41        30.31         0.49        21.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       22.39        11.57        10.45         7.36       122.96        37.55 
TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       38.63        13.08         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90        37.12       130.32       111.98        64.77        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-UE-A6QT 
        0.72        16.77        18.94         3.88        25.35        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        84.79 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C2 
       22.62         8.58        26.43        35.90        45.34        35.18 
TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 TCGA-Z4-A8JB TCGA-Z4-A9VC 
       19.17        29.46        27.32        36.43         4.37        13.38 
TCGA-Z4-AAPF TCGA-Z4-AAPG 
       15.95        15.98 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.56              0.49 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           188.15            159.29 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            30.51             31.91 
[1] "0.6 - 188.2 (30.5)" "0.5 - 159.3 (31.9)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  XP LOSS MUTATED                1                  2                   0
  XP LOSS WILD-TYPE              0                  5                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  XP LOSS MUTATED                     0                             0
  XP LOSS WILD-TYPE                   1                             2
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  XP LOSS MUTATED                       0                     12
  XP LOSS WILD-TYPE                     1                     16
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  XP LOSS MUTATED                      0                    0
  XP LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  XP LOSS MUTATED                                       0
  XP LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  XP LOSS MUTATED                                  0
  XP LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  XP LOSS MUTATED                                                0
  XP LOSS WILD-TYPE                                              2
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  XP LOSS MUTATED                                 1
  XP LOSS WILD-TYPE                               9
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  XP LOSS MUTATED                                         0
  XP LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  XP LOSS MUTATED                              0                       0
  XP LOSS WILD-TYPE                            4                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  XP LOSS MUTATED                                  6
  XP LOSS WILD-TYPE                               11
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  XP LOSS MUTATED                                         2
  XP LOSS WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  XP LOSS MUTATED                             10
  XP LOSS WILD-TYPE                           34
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  XP LOSS MUTATED                                         2
  XP LOSS WILD-TYPE                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  XP LOSS MUTATED                                           0
  XP LOSS WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  XP LOSS MUTATED                                                  1
  XP LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  XP LOSS MUTATED                                          3
  XP LOSS WILD-TYPE                                        5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  XP LOSS MUTATED                                                         0
  XP LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  XP LOSS MUTATED                                            0
  XP LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  XP LOSS MUTATED                                                  17
  XP LOSS WILD-TYPE                                                56
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  XP LOSS MUTATED                                                    2
  XP LOSS WILD-TYPE                                                  1
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  XP LOSS MUTATED                                    0                        0
  XP LOSS WILD-TYPE                                  2                        5
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  XP LOSS MUTATED                             3                         0
  XP LOSS WILD-TYPE                           1                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  XP LOSS MUTATED                                   0
  XP LOSS WILD-TYPE                                 7
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  XP LOSS MUTATED                                   1
  XP LOSS WILD-TYPE                                 4
D81V3, multiclass
                                                         clus
vv                                                        XP LOSS MUTATED
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    2
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   0
  CHEST - OTHER (PLEASE SPECIFY                                         0
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                               12
  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                                      6
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                         10
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    17
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              0
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     0
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     1
                                                         clus
vv                                                        XP LOSS WILD-TYPE
  CHEST - BREAST                                                          0
  CHEST - CHEST WALL                                                      5
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     1
  CHEST - OTHER (PLEASE SPECIFY                                           2
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 16
  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                                       11
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           34
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 2
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      56
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                5
  SUPERFICIAL TRUNK - BUTTOCK                                             1
  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"
D81V4, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    39  24
  XP LOSS WILD-TYPE 100  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     39   24
  XP LOSS WILD-TYPE  100   94
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              39               100
  MALE                24                94
[1] 2 2
[1] FALSE
D81V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    44  18
  XP LOSS WILD-TYPE 135  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     44   18
  XP LOSS WILD-TYPE  135   54
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               44               135
  YES              18                54
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  XP LOSS MUTATED                              8             0
  XP LOSS WILD-TYPE                           51             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  XP LOSS MUTATED                                                                          0
  XP LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  XP LOSS MUTATED                     36
  XP LOSS WILD-TYPE                   67
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  XP LOSS MUTATED                                                  4
  XP LOSS WILD-TYPE                                                5
                   vv
clus                MYXOFIBROSARCOMA
  XP LOSS MUTATED                  4
  XP LOSS WILD-TYPE               20
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  XP LOSS MUTATED                                                          5
  XP LOSS WILD-TYPE                                                       23
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  XP LOSS MUTATED                                          0
  XP LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  XP LOSS MUTATED                             0                             1
  XP LOSS WILD-TYPE                           2                             5
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  XP LOSS MUTATED                                            5
  XP LOSS WILD-TYPE                                         16
D81V6, multiclass
                                                                          clus
vv                                                                         XP LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                           8
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  36
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       4
  MYXOFIBROSARCOMA                                                                       4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                               5
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                             5
                                                                          clus
vv                                                                         XP LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            51
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    67
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         5
  MYXOFIBROSARCOMA                                                                        20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                23
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              16
[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
  XP LOSS MUTATED    38  16   3   6
  XP LOSS WILD-TYPE 114  53   6  20
D81V7, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              38               114
  R1              16                53
  R2               3                 6
  RX               6                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
  XP LOSS MUTATED       0                         7    52
  XP LOSS WILD-TYPE     6                        11   172
D81V8, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               7                11
  WHITE                                  52               172
[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"
D81V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0  51
  XP LOSS WILD-TYPE   5 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   51
  XP LOSS WILD-TYPE    5  169
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              51               169
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   66 36
  XQ LOSS WILD-TYPE 93 62
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              102               155 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               36                62 
$`XQ LOSS MUTATED`
TCGA-3B-A9HO TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-AB32 TCGA-DX-AB35 TCGA-HB-A5W3 
       31.53        67.20        34.36       101.98        30.51        12.62 
TCGA-IE-A4EH TCGA-IS-A3K6 TCGA-IW-A3M6 TCGA-LI-A9QH TCGA-PC-A5DP TCGA-QQ-A8VB 
       26.93        28.21        22.62        17.75        18.08       188.15 
TCGA-3B-A9HI TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HV TCGA-3B-A9HX 
       50.01        19.69        44.91        25.25        14.37        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 
       10.32        38.47        36.03        68.61        12.85        18.54 
TCGA-DX-A1L2 TCGA-DX-A2J0 TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UC 
       85.02         9.70        33.44        44.68        10.68        68.55 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P 
       50.43        34.88        85.45         9.73        52.77        46.03 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47       108.82        59.84        37.58        15.95        37.41 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN 
       82.68        36.33        16.87        21.30        62.20        30.35 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
        9.34        45.14        47.87        38.17        40.77       150.35 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O 
       27.95        40.44         6.58         1.15        12.00        86.10 
TCGA-DX-AB3C TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 
       71.31        20.32        19.89        34.88         4.57        33.30 
TCGA-HS-A5NA TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A5VE 
        9.80        37.12        25.22       171.09        85.97        16.41 
TCGA-K1-A42X TCGA-K1-A6RV TCGA-KD-A5QS TCGA-KD-A5QU TCGA-MB-A5Y8 TCGA-MB-A8JL 
      123.78         5.19        63.81        35.28        25.41        19.73 
TCGA-MJ-A68H TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5VC TCGA-RN-AAAQ 
       14.99        38.63        81.01        17.65        35.90        16.77 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-AB3D 
       22.82        32.75        19.63        13.41        10.72        12.46 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46         8.58        63.35        35.90        18.08 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X9-A971 TCGA-X9-A973 
       30.84        35.18        20.65        50.86        27.32        36.43 

$`XQ LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-DX-A3M2 TCGA-DX-A6BK TCGA-DX-A7EL TCGA-DX-A7ET TCGA-DX-A8BG 
       36.30        34.68        16.18        75.32        15.22        17.95 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2W 
       14.43        14.07        15.85        40.60        12.07       106.45 
TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3NK 
       13.28        22.85        60.00        84.66        32.15        16.60 
TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-KF-A41W TCGA-MB-A5Y9 
       37.02        52.11        52.27       159.29        11.70         8.28 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-SG-A849 TCGA-VT-A80J TCGA-WK-A8XT TCGA-X6-A8C6 
        6.35        20.94        17.52        26.17        41.49        35.08 
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9I1 TCGA-3B-A9I3 
       53.49        68.55        88.57        54.74        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        0.56        14.04        32.71        45.11        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       66.94        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        95.38        79.17         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       49.05        86.83       136.44        31.86        35.77        51.02 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
        4.54        14.99        73.87        45.99        24.26        35.28 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96        31.96        36.85        26.99         3.06        41.00 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       78.28        50.50        86.30        64.21       101.23        34.49 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BU 
      152.12        29.49        48.20        20.05        61.97        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2L TCGA-DX-AB2Q 
       60.66        19.43        17.79        15.72        65.98        66.74 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB3B TCGA-FX-A2QS 
        9.21        77.88       106.55        50.40        50.89        49.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HS-A5N8 
       31.13        21.70        15.48         8.05        67.63         0.72 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IS-A3KA 
       80.48        19.53         3.22         1.38        19.89        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        5.92         1.05         3.91       101.26        53.33        62.17 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KD-A5QT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK 
       17.36        23.38        16.41        30.31         0.49        21.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        22.39        11.57        10.45         7.36       122.96 
TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       37.55        13.08         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       37.12       130.32       111.98        64.77        10.52         0.72 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO 
       18.94         3.88        25.35         8.61        13.22        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C3 
        4.80        84.79        22.62        26.43        45.34        19.17 
TCGA-X6-A8C7 TCGA-Z4-A8JB TCGA-Z4-A9VC TCGA-Z4-AAPF TCGA-Z4-AAPG 
       29.46         4.37        13.38        15.95        15.98 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             1.15              0.49 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           188.15            159.29 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            33.37             29.46 
[1] "1.1 - 188.2 (33.4)" "0.5 - 159.3 (29.5)"
[1] "hr=" "1.2"
D82V2, continuous
                   vv
clus                CHEST - BREAST CHEST - CHEST WALL CHEST - LUNG/PLEURA
  XQ LOSS MUTATED                1                  4                   0
  XQ LOSS WILD-TYPE              0                  3                   2
                   vv
clus                CHEST - MEDIASTINUM CHEST - OTHER (PLEASE SPECIFY
  XQ LOSS MUTATED                     1                             1
  XQ LOSS WILD-TYPE                   0                             1
                   vv
clus                GYNECOLOGICAL - OVARY GYNECOLOGICAL - UTERUS
  XQ LOSS MUTATED                       0                     15
  XQ LOSS WILD-TYPE                     1                     13
                   vv
clus                HEAD AND NECK - HEAD HEAD AND NECK - NECK
  XQ LOSS MUTATED                      0                    0
  XQ LOSS WILD-TYPE                    2                    1
                   vv
clus                HEAD AND NECK - OTHER (PLEASE SPECIFY
  XQ LOSS MUTATED                                       0
  XQ LOSS WILD-TYPE                                     2
                   vv
clus                LOWER ABDOMINAL/PELVIC - BLADDER
  XQ LOSS MUTATED                                  0
  XQ LOSS WILD-TYPE                                1
                   vv
clus                LOWER ABDOMINAL/PELVIC - OTHER (PLEASE SPECIFY
  XQ LOSS MUTATED                                                1
  XQ LOSS WILD-TYPE                                              1
                   vv
clus                LOWER ABDOMINAL/PELVIC - PELVIC
  XQ LOSS MUTATED                                 5
  XQ LOSS WILD-TYPE                               5
                   vv
clus                LOWER ABDOMINAL/PELVIC - SPERMATIC CORD
  XQ LOSS MUTATED                                         0
  XQ LOSS WILD-TYPE                                       2
                   vv
clus                LOWER EXTREMITY - FOOT/ANKLE LOWER EXTREMITY - GROIN
  XQ LOSS MUTATED                              1                       0
  XQ LOSS WILD-TYPE                            3                       2
                   vv
clus                LOWER EXTREMITY - LOWER LEG/CALF
  XQ LOSS MUTATED                                  8
  XQ LOSS WILD-TYPE                                9
                   vv
clus                LOWER EXTREMITY - OTHER (PLEASE SPECIFY
  XQ LOSS MUTATED                                         2
  XQ LOSS WILD-TYPE                                       3
                   vv
clus                LOWER EXTREMITY - THIGH/KNEE
  XQ LOSS MUTATED                             12
  XQ LOSS WILD-TYPE                           32
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - COLON
  XQ LOSS MUTATED                                         3
  XQ LOSS WILD-TYPE                                       1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC
  XQ LOSS MUTATED                                           0
  XQ LOSS WILD-TYPE                                         2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL
  XQ LOSS MUTATED                                                  1
  XQ LOSS WILD-TYPE                                                4
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY
  XQ LOSS MUTATED                                          3
  XQ LOSS WILD-TYPE                                        5
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY
  XQ LOSS MUTATED                                                         0
  XQ LOSS WILD-TYPE                                                       2
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS
  XQ LOSS MUTATED                                            0
  XQ LOSS WILD-TYPE                                          1
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM
  XQ LOSS MUTATED                                                  30
  XQ LOSS WILD-TYPE                                                43
                   vv
clus                RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES
  XQ LOSS MUTATED                                                    2
  XQ LOSS WILD-TYPE                                                  1
                   vv
clus                SUPERFICIAL TRUNK - ABDOMINAL WALL SUPERFICIAL TRUNK - BACK
  XQ LOSS MUTATED                                    0                        1
  XQ LOSS WILD-TYPE                                  2                        4
                   vv
clus                SUPERFICIAL TRUNK - BUTTOCK SUPERFICIAL TRUNK - FLANK
  XQ LOSS MUTATED                             3                         0
  XQ LOSS WILD-TYPE                           1                         1
                   vv
clus                UPPER EXTREMITY - SHOULDER/AXILLA
  XQ LOSS MUTATED                                   6
  XQ LOSS WILD-TYPE                                 1
                   vv
clus                UPPER EXTREMITY - UPPER ARM/ELBOW
  XQ LOSS MUTATED                                   2
  XQ LOSS WILD-TYPE                                 3
D82V3, multiclass
                                                         clus
vv                                                        XQ LOSS MUTATED
  CHEST - BREAST                                                        1
  CHEST - CHEST WALL                                                    4
  CHEST - LUNG/PLEURA                                                   0
  CHEST - MEDIASTINUM                                                   1
  CHEST - OTHER (PLEASE SPECIFY                                         1
  GYNECOLOGICAL - OVARY                                                 0
  GYNECOLOGICAL - UTERUS                                               15
  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                        1
  LOWER ABDOMINAL/PELVIC - PELVIC                                       5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                               0
  LOWER EXTREMITY - FOOT/ANKLE                                          1
  LOWER EXTREMITY - GROIN                                               0
  LOWER EXTREMITY - LOWER LEG/CALF                                      8
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                               2
  LOWER EXTREMITY - THIGH/KNEE                                         12
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                               3
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                             0
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                      1
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                              3
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY               0
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                            0
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                    30
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                    2
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                    0
  SUPERFICIAL TRUNK - BACK                                              1
  SUPERFICIAL TRUNK - BUTTOCK                                           3
  SUPERFICIAL TRUNK - FLANK                                             0
  UPPER EXTREMITY - SHOULDER/AXILLA                                     6
  UPPER EXTREMITY - UPPER ARM/ELBOW                                     2
                                                         clus
vv                                                        XQ LOSS WILD-TYPE
  CHEST - BREAST                                                          0
  CHEST - CHEST WALL                                                      3
  CHEST - LUNG/PLEURA                                                     2
  CHEST - MEDIASTINUM                                                     0
  CHEST - OTHER (PLEASE SPECIFY                                           1
  GYNECOLOGICAL - OVARY                                                   1
  GYNECOLOGICAL - UTERUS                                                 13
  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                          1
  LOWER ABDOMINAL/PELVIC - PELVIC                                         5
  LOWER ABDOMINAL/PELVIC - SPERMATIC CORD                                 2
  LOWER EXTREMITY - FOOT/ANKLE                                            3
  LOWER EXTREMITY - GROIN                                                 2
  LOWER EXTREMITY - LOWER LEG/CALF                                        9
  LOWER EXTREMITY - OTHER (PLEASE SPECIFY                                 3
  LOWER EXTREMITY - THIGH/KNEE                                           32
  RETROPERITONEUM/UPPER ABDOMINAL - COLON                                 1
  RETROPERITONEUM/UPPER ABDOMINAL - GASTRIC                               2
  RETROPERITONEUM/UPPER ABDOMINAL - INTRAABDOMINAL                        4
  RETROPERITONEUM/UPPER ABDOMINAL - KIDNEY                                5
  RETROPERITONEUM/UPPER ABDOMINAL - OTHER (PLEASE SPECIFY                 2
  RETROPERITONEUM/UPPER ABDOMINAL - PANCREAS                              1
  RETROPERITONEUM/UPPER ABDOMINAL - RETROPERITONEUM                      43
  RETROPERITONEUM/UPPER ABDOMINAL - SMALL INTESTINES                      1
  SUPERFICIAL TRUNK - ABDOMINAL WALL                                      2
  SUPERFICIAL TRUNK - BACK                                                4
  SUPERFICIAL TRUNK - BUTTOCK                                             1
  SUPERFICIAL TRUNK - FLANK                                               1
  UPPER EXTREMITY - SHOULDER/AXILLA                                       1
  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"
D82V4, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   62 40
  XQ LOSS WILD-TYPE 77 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     62   40
  XQ LOSS WILD-TYPE   77   78
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              62                77
  MALE                40                78
[1] 2 2
[1] FALSE
D82V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    72  29
  XQ LOSS WILD-TYPE 107  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     72   29
  XQ LOSS WILD-TYPE  107   43
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               72               107
  YES              29                43
[1] 2 2
[1] FALSE
                   vv
clus                DEDIFFERENTIATED LIPOSARCOMA DESMOID TUMOR
  XQ LOSS MUTATED                             13             0
  XQ LOSS WILD-TYPE                           46             2
                   vv
clus                GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS
  XQ LOSS MUTATED                                                                          0
  XQ LOSS WILD-TYPE                                                                        1
                   vv
clus                LEIOMYOSARCOMA (LMS)
  XQ LOSS MUTATED                     57
  XQ LOSS WILD-TYPE                   46
                   vv
clus                MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)
  XQ LOSS MUTATED                                                  5
  XQ LOSS WILD-TYPE                                                4
                   vv
clus                MYXOFIBROSARCOMA
  XQ LOSS MUTATED                  4
  XQ LOSS WILD-TYPE               20
                   vv
clus                PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA
  XQ LOSS MUTATED                                                         12
  XQ LOSS WILD-TYPE                                                       16
                   vv
clus                SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED
  XQ LOSS MUTATED                                          0
  XQ LOSS WILD-TYPE                                        2
                   vv
clus                SYNOVIAL SARCOMA - BIPHASIC SYNOVIAL SARCOMA - MONOPHASIC
  XQ LOSS MUTATED                             0                             1
  XQ LOSS WILD-TYPE                           2                             5
                   vv
clus                UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)
  XQ LOSS MUTATED                                           10
  XQ LOSS WILD-TYPE                                         11
D82V6, multiclass
                                                                          clus
vv                                                                         XQ LOSS MUTATED
  DEDIFFERENTIATED LIPOSARCOMA                                                          13
  DESMOID TUMOR                                                                          0
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS               0
  LEIOMYOSARCOMA (LMS)                                                                  57
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                       5
  MYXOFIBROSARCOMA                                                                       4
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                              12
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                               0
  SYNOVIAL SARCOMA - BIPHASIC                                                            0
  SYNOVIAL SARCOMA - MONOPHASIC                                                          1
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                            10
                                                                          clus
vv                                                                         XQ LOSS WILD-TYPE
  DEDIFFERENTIATED LIPOSARCOMA                                                            46
  DESMOID TUMOR                                                                            2
  GIANT CELL 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA WITH GIANT CELLS                 1
  LEIOMYOSARCOMA (LMS)                                                                    46
  MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNST)                                         4
  MYXOFIBROSARCOMA                                                                        20
  PLEOMORPHIC 'MFH' / UNDIFFERENTIATED PLEOMORPHIC SARCOMA                                16
  SARCOMA; SYNOVIAL; POORLY DIFFERENTIATED                                                 2
  SYNOVIAL SARCOMA - BIPHASIC                                                              2
  SYNOVIAL SARCOMA - MONOPHASIC                                                            5
  UNDIFFERENTIATED PLEOMORPHIC SARCOMA (UPS)                                              11
[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
  XQ LOSS MUTATED   64 26  3  8
  XQ LOSS WILD-TYPE 88 43  6 18
D82V7, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              64                88
  R1              26                43
  R2               3                 6
  RX               8                18
[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
  XQ LOSS MUTATED       2                        10    87
  XQ LOSS WILD-TYPE     4                         8   137
D82V8, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN              10                 8
  WHITE                                  87               137
[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"
D82V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  89
  XQ LOSS WILD-TYPE   5 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   89
  XQ LOSS WILD-TYPE    5  131
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              89               131
[1] 2 2
[1] FALSE
