[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/15087563/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/15098587/transformed.cor.cli.txt"

nPatients in clinical file=250, in cluster file=256, common to both=246
[1]  82 246
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               192 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               192 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               47               199 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               47               199 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               21               225 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               21               225 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21               225 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21               225 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               37               209 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               37               209 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               34               212 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               34               212 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               65               181 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               65               181 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               44               202 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               44               202 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               95               151 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               95               151 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               70               176 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               70               176 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               49               197 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               49               197 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               198 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               198 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               79               167 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               79               167 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               66               180 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               66               180 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               194 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               194 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               63               183 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               63               183 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               55               191 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               55               191 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               175 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               71               175 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                224 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                224 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                235 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                235 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                224 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                224 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                21                225 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                21                225 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                42                204 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                42                204 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                33                213 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                33                213 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                233 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                233 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                55                191 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                55                191 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                61                185 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                61                185 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                39                207 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                39                207 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                20                226 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                20                226 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                58                188 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                58                188 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                53                193 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                53                193 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                49                197 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                49                197 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                33                213 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                33                213 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                82                164 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                82                164 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                62                184 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                62                184 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                185 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                185 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                82                164 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                82                164 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                55                191 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                55                191 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                58                188 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                58                188 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               72               174 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               72               174 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               32               214 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               32               214 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               30               216 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               30               216 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               37               209 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               37               209 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               84               162 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               84               162 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               67               179 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               67               179 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               56               190 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               56               190 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               49               197 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               49               197 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               41               205 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               41               205 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               50               196 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               50               196 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               20               226 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               20               226 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               34               212 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               34               212 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               57               189 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               57               189 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               50               196 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               50               196 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               31               215 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               31               215 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               33               213 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               33               213 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               188 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               188 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               43               203 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               43               203 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               81               165 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               81               165 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               49               197 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               49               197 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               116                130 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               116                130 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               126                120 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               126                120 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                91                155 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                91                155 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                87                159 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                87                159 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                63                183 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                63                183 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                52                194 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                52                194 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               130                116 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               130                116 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                59                187 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                59                187 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                42                204 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                42                204 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                72                174 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                72                174 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               120                126 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               120                126 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                55                191 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                55                191 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                46                200 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                46                200 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                60                186 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                60                186 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                69                177 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                69                177 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                21                225 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                21                225 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                208 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                208 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                52                194 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                52                194 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                24                222 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                24                222 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                48                198 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                48                198 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                63                183 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                63                183 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               58               188 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               58               188 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               96               150 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               96               150 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "DCC_UPLOAD_DATE"                       
 [6] "GENDER"                                
 [7] "RADIATION_THERAPY"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCH_NUMBER"                          

Input Data has 11 rows and 246 columns.

[1] "Batch" "11"   
[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=78,	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=163,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              26-3-2015 29-1-2015 31-12-2014
freq.values   "244"     "1"       "1"       
freq.contrast "2"       "245"     "245"     
both >= 3     "FALSE"   "FALSE"   "FALSE"   
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "245"  
freq.contrast "245"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 9:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'BATCH_NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 246 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
GENDER, nv=2, 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    32  22
  1P GAIN WILD-TYPE 130  60
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               190 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               22                60 
$`1P GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U9 
       19.69        18.64        26.56         9.70        23.08        14.99 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A6B8 TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
       19.30        24.26        15.95        23.54        50.50        16.87 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BS 
        7.04        17.95         9.34        59.87        35.77        27.95 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2P TCGA-DX-AB2T TCGA-DX-AB2W TCGA-FX-A2QS 
       36.69         6.58        12.07        71.57       106.45         0.46 
TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N9 
       20.32         2.07        48.30         4.57        15.91        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-JV-A5VF 
        9.80        80.48        19.53        25.22        40.08         1.05 
TCGA-K1-A42W TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JK TCGA-N1-A6IA 
       27.29        10.85        11.70        13.35         4.34         4.08 
TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
        6.35         5.03        48.59         3.88         6.58        17.92 
TCGA-SI-AA8B TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A7W8 TCGA-X6-A8C4 
        5.06        26.17        72.72        38.27        26.43        16.83 

$`1P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX 
       25.25        42.84        10.32        31.00        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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 
       59.47        54.77         9.04        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       20.05        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
        9.73        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        25.15        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       66.31        67.20        74.10        64.21        88.31        21.30 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       34.49        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       48.20        14.07        14.43        33.07        44.68        38.17 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       14.07       124.37        35.54        60.66        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       12.99         8.75         4.67        12.39        40.60        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
       49.18         9.21        96.89        13.28        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
      101.98        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 
       71.31         0.10         0.07         0.07         0.07        34.88 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK 
       12.62        23.97         0.10        21.37         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       19.89        37.12        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN 
       73.28         5.92        22.62        16.41         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A5Y8 
       36.39       123.78         9.04         4.08        22.03         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        8.28         0.49        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
        7.46        10.45       120.20        37.55        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08        20.94         9.83         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-A71Q 
       10.52         0.72        11.18        18.94        19.82        27.22 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ 
        9.93        13.22         0.72        10.72        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        65.46        22.62         9.04        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 
       18.08        36.82        18.35        25.71        15.95        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       35.08        17.72        15.58        36.43 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.46              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           106.45            188.15 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           18.295            26.090 
[1] "0.5 - 106.5 (18.3)" "0.1 - 188.2 (26.1)"
[1] "hr=" "1.9"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    31  23
  1P GAIN WILD-TYPE 101  91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     31   23
  1P GAIN WILD-TYPE  101   91
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              31               101
  MALE                23                91
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         8    42
  1P GAIN WILD-TYPE     6                        10   152
D1V4, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               8                10
  WHITE                                  42               152
[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"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  47
  1P GAIN WILD-TYPE   5 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   47
  1P GAIN WILD-TYPE    5  144
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              47               144
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    33  14
  1Q GAIN WILD-TYPE 129  68
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               47               197 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               14                68 
$`1Q GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-DX-A1L2 TCGA-DX-A3LT 
       19.69        53.49        42.84        26.56        59.24        23.08 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48O TCGA-DX-A6YU 
       14.99        28.80        64.18        19.30        27.22        23.54 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-AB2T 
        7.04        17.95         9.34        35.77        27.95        71.57 
TCGA-DX-AB2W TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z 
      106.45        20.32         2.07        48.30        34.88        15.91 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ 
        0.10        41.33         9.80        80.48        19.53        25.22 
TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-K1-A42W TCGA-K1-A6RU TCGA-KF-A41W TCGA-PC-A5DN 
       40.08        22.62        27.29        10.85        11.70        38.63 
TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-WK-A8XS TCGA-WK-A8XX 
        5.03        48.59         3.88        17.92        72.72        38.27 
TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X9-A971 
       26.43        18.08        36.82        16.83        15.58 

$`1Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       54.77         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       34.68        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       44.45        39.35        34.88         9.73        24.26        12.26 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       14.96        26.47        72.72        25.08        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
       21.63        16.18         3.06        34.55        66.31        67.20 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       50.50        16.87        74.10        64.21        88.31        21.30 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       34.49        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.20        14.07        14.43        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       38.17        14.07       124.37        35.54        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       19.43         6.58         1.15        12.99         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.39        40.60        86.10        12.07        49.18         9.21 
TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       96.89        13.28        50.40        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3YV TCGA-HB-A5W3 
        0.10         0.07         0.07         0.07         4.57        12.62 
TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       23.97        21.37         3.22         1.38        19.89        37.12 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       16.41         1.05         3.91        71.70        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
        9.04         4.08        22.03        13.35         8.32         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49         4.34        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
        7.46        10.45         4.08       120.20        37.55         6.35 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        18.08        20.94         9.83         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        35.90        30.90       188.15       130.32        98.27 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 
       62.20        10.52         0.72        11.18        18.94         6.58 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       19.82        27.22         5.06         9.93        13.22         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY 
       10.72        26.17        11.93         4.80        41.49        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 
       22.62         9.04        57.80        29.92        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       15.95        38.96        35.08        17.72        36.43 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.10              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           106.45            188.15 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            25.22             22.62 
[1] "0.1 - 106.5 (25.2)" "0.1 - 188.2 (22.6)"
[1] "hr=" "1.1"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    30  17
  1Q GAIN WILD-TYPE 102  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     30   17
  1Q GAIN WILD-TYPE  102   97
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              30               102
  MALE                17                97
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         4    38
  1Q GAIN WILD-TYPE     5                        14   156
D2V4, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  38               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"
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     0  42
  1Q GAIN WILD-TYPE   5 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0   42
  1Q GAIN WILD-TYPE    5  149
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              42               149
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    12   9
  2P GAIN WILD-TYPE 150  73
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               21               223 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                9                73 
$`2P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A6YZ TCGA-DX-A7EF 
       14.04        32.71        74.66        23.08        74.10        21.30 
TCGA-DX-A7EI TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2X TCGA-FX-A2QS 
       34.49        12.99        86.10        49.18        13.28         0.46 
TCGA-IW-A3M5 TCGA-KF-A41W TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-RN-AAAQ 
        5.92        11.70        10.45        37.55         5.03        11.18 
TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q 
        3.88        19.82        27.22 

$`2P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       18.64        26.56         0.56        38.24        12.85        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       18.54        54.21        59.24        33.53        42.54         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        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       17.10        20.05        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       17.79        21.63        16.18         3.06        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       67.20        23.54        50.50        16.87        64.21        88.31 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       14.07         7.04        17.95        14.43         9.34        59.87 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
       33.07        44.68        38.17        35.77        14.07       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        35.54        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
        1.15         8.75         4.67        12.39        40.60        12.07 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 
        9.21        71.57        96.89       106.45        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
      101.98        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       71.31         0.10         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        2.07        48.30        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
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-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       40.08        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62        16.41         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I 
       27.29       123.78         9.04        10.85         4.08        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35         8.32         8.28         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        15.65         7.46         4.08       120.20 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N 
        6.35        38.63        81.01        18.08        20.94         9.83 
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        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
      188.15       130.32        98.27        62.20        10.52         0.72 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       18.94         6.58        17.92         5.06         9.93        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
        0.72        10.72        26.17        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       41.49        38.27        65.46        22.62         9.04        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       26.43        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       15.95        16.83        38.96        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.46              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            86.10            188.15 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            19.82             23.97 
[1] "0.5 - 86.1 (19.8)"  "0.1 - 188.2 (24.0)"
[1] "hr=" "1.6"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    12   9
  2P GAIN WILD-TYPE 120 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     12    9
  2P GAIN WILD-TYPE  120  105
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              12               120
  MALE                 9               105
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       1                         1    17
  2P GAIN WILD-TYPE     5                        17   177
D3V4, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               1                17
  WHITE                                  17               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"
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1  16
  2P GAIN WILD-TYPE   4 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   16
  2P GAIN WILD-TYPE    4  175
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              16               175
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    14   7
  2Q GAIN WILD-TYPE 148  75
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21               223 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                75 
$`2Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A6BA TCGA-DX-A6YZ 
       14.04        32.71        74.66        23.08        66.05        74.10 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BO TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2Q 
       21.30        34.49        35.77        12.99         8.75        49.18 
TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB37 TCGA-KF-A41W TCGA-MO-A47R TCGA-QQ-A8VB 
       71.57        13.28        84.66        11.70        10.45       188.15 
TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q 
       11.18        19.82        27.22 

$`2Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       18.64        26.56         0.56        38.24        12.85        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       18.54        54.21        59.24        33.53        42.54         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        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       17.10        20.05        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       15.95        11.47        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
       21.63        16.18         3.06        34.55        66.31        67.20 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL 
       23.54        50.50        16.87        64.21        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
        7.04        17.95        14.43         9.34        59.87        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       44.68        38.17        14.07       124.37        27.95        35.54 
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         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2V 
       12.39        40.60        86.10        12.07         9.21        96.89 
TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        50.40        22.85       101.98        19.20        60.00 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       32.15        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57        15.91        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
       19.89        37.12        25.22        40.08        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        1.05         3.91        71.70        36.39        27.29       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
        9.04        10.85         4.08        22.03        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         7.46         4.08       120.20        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
       38.63        81.01        18.08        20.94         5.03         9.83 
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        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 
      130.32        98.27        62.20        10.52         0.72        18.94 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
        3.88         6.58        17.92         5.06         9.93        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
        0.72        10.72        26.17        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       41.49        38.27        65.46        22.62         9.04        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       26.43        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       15.95        16.83        38.96        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             8.75              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           188.15            143.41 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            27.22             22.85 
[1] "8.8 - 188.2 (27.2)" "0.1 - 143.4 (22.9)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    14   7
  2Q GAIN WILD-TYPE 118 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14    7
  2Q GAIN WILD-TYPE  118  107
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              14               118
  MALE                 7               107
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       1                         2    16
  2Q GAIN WILD-TYPE     5                        16   178
D4V4, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  16               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"
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     1  16
  2Q GAIN WILD-TYPE   4 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   16
  2Q GAIN WILD-TYPE    4  175
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              16               175
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    25  12
  3P GAIN WILD-TYPE 137  70
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               37               207 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12                70 
$`3P GAIN MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A3U7 
       88.57        42.84        18.64        26.56         0.56        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UF TCGA-DX-A6YX TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BN 
        4.54        64.18        16.87         7.04        59.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB2V 
       35.77        14.07        27.95        36.69        12.99        96.89 
TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-HB-A2OT TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ 
      106.45        50.40        48.30        80.48        19.53        25.22 
TCGA-KF-A41W TCGA-MJ-A68H TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z4 
       11.70        14.99        18.08         5.03        48.59        18.94 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8Y0 
        6.58         5.06         0.72        26.17        72.72        22.62 
TCGA-X6-A7WC 
       36.82 

$`3P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KU TCGA-DX-A1KW 
       25.25        10.32        31.00        36.03        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       38.24        12.85        36.69        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A3UA 
       20.05        34.68        15.06        17.75        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        34.88         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       25.08        25.15        15.95        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         9.11        17.79        21.63        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ 
       34.55        66.31        67.20        23.54        50.50        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG 
       15.62       135.48        29.49        48.20        14.07        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BR TCGA-DX-A8BT 
       14.43         9.34        33.07        44.68       124.37        35.54 
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         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.39        40.60        86.10        12.07        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       71.57        13.28        22.85       101.98        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
        0.07        20.32         0.07         0.07         2.07        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57        15.91        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
        9.80        21.37         3.22         1.38        19.89        37.12 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       40.08        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62        16.41         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       36.39        27.29       123.78         9.04        10.85         4.08 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
       22.03        13.35         8.32         8.28         0.49         4.34 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       19.73        17.98        15.65         7.46        10.45         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX 
      120.20        37.55         6.35        38.63        81.01        20.94 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
        9.83         1.84        46.82        18.08        35.90        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
      188.15       130.32        98.27        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
       11.18         3.88        17.92        19.82        27.22         9.93 
TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
       13.22        10.72        11.93         4.80        41.49        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46         9.04        57.80        26.43        29.92        18.08 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.35        25.71        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.56              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           106.45            188.15 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            26.17             22.85 
[1] "0.6 - 106.5 (26.2)" "0.1 - 188.2 (22.9)"
[1] "hr=" "1.1"
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    22  15
  3P GAIN WILD-TYPE 110  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     22   15
  3P GAIN WILD-TYPE  110   99
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              22               110
  MALE                15                99
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       1                         6    27
  3P GAIN WILD-TYPE     5                        12   167
D5V4, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  27               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"
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  32
  3P GAIN WILD-TYPE   5 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   32
  3P GAIN WILD-TYPE    5  159
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              32               159
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    23  11
  3Q GAIN WILD-TYPE 139  71
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               34               210 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               11                71 
$`3Q GAIN MUTATED`
TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A3U7 TCGA-DX-A3U8 
       88.57        18.64        26.56         0.56        42.77         4.54 
TCGA-DX-A3UF TCGA-DX-A6YX TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BN 
       64.18        16.87         7.04        17.95        59.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB2V 
       35.77        14.07        27.95        36.69        12.99        96.89 
TCGA-DX-AB2Z TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-KF-A41W 
       50.40        48.30         0.10        19.53        25.22        11.70 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-UE-A6QU 
       18.08         5.03        48.59        18.94         6.58         0.72 
TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A7WC 
       26.17        72.72        22.62        36.82 

$`3Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        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-DX-A1KU 
       25.25        42.84        10.32        31.00        36.03        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 
       17.10        20.05        34.68        15.06        17.75        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       72.72        25.08        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV 
        3.06        34.55        66.31        67.20        23.54        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       74.10        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BR TCGA-DX-A8BT 
       14.43         9.34        33.07        44.68       124.37        35.54 
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         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.39        40.60        86.10        12.07        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       71.57       106.45        13.28        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.10         0.07        20.32         0.07         0.07         2.07 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
       34.88         4.57        15.91        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
        9.80        80.48        21.37         3.22         1.38        19.89 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       37.12        40.08        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
       71.70        36.39        27.29       123.78         9.04        10.85 
TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        4.08        22.03        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
       10.45         4.08       120.20        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       81.01        20.94         9.83         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
       10.52         0.72        11.18         3.88        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XO 
       27.22         5.06         9.93        13.22        10.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
        4.80        41.49        38.27        65.46         9.04        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       26.43        29.92        18.08        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            96.89            188.15 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            23.92             23.26 
[1] "0.1 - 96.9 (23.9)"  "0.1 - 188.2 (23.3)"
[1] "hr=" "1"  
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    20  14
  3Q GAIN WILD-TYPE 112 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     20   14
  3Q GAIN WILD-TYPE  112  100
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              20               112
  MALE                14               100
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       1                         5    24
  3Q GAIN WILD-TYPE     5                        13   170
D6V4, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  24               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"
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0  28
  3Q GAIN WILD-TYPE   5 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0   28
  3Q GAIN WILD-TYPE    5  163
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              28               163
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    40  24
  4P GAIN WILD-TYPE 122  58
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               64               180 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24                58 
$`4P GAIN MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1L0 
       44.91        42.84        18.64         0.56        38.24        18.54 
TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A3M2 TCGA-DX-A48K TCGA-DX-A6BA TCGA-DX-A6YQ 
       54.21        74.66        34.68        19.30        66.05         3.06 
TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EL TCGA-DX-A8BH 
       34.55        23.54        74.10        64.21        75.32        14.43 
TCGA-DX-A8BL TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2P TCGA-DX-AB2Q 
       33.07        36.69         1.15         8.75        12.07        49.18 
TCGA-DX-AB2X TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 
       13.28         4.57        41.33        19.89        25.22       143.41 
TCGA-JV-A5VE TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A8JK TCGA-MJ-A68H 
       16.41        10.85         4.08        11.70         4.34        14.99 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5VA 
        4.08        37.55        81.01         5.03         9.83        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 
       48.59        35.90       188.15        10.52        11.18        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
        3.88        17.92         5.06        13.22         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC 
       26.17        72.72        22.62         9.04        26.43        36.82 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X9-A971 
       25.71        16.83        35.08        15.58 

$`4P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU 
       25.25        10.32        31.00        36.03        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       32.71        12.85        36.69        59.24        33.53        42.54 
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        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       28.80        34.88        64.18         9.73        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       15.95        11.47        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX 
       21.63        16.18        66.31        67.20        50.50        16.87 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       88.31        21.30        34.49        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ 
       29.49        48.20        14.07         7.04        17.95         9.34 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
       59.87        44.68        38.17        35.77        14.07       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E 
       27.95        35.54        60.66        19.43         6.58        12.99 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T 
        4.67        12.39        40.60        86.10         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       96.89       106.45        50.40        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.10         0.07        20.32         0.07         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       48.30        34.88        15.91        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37        19.53         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       37.12        40.08        28.21       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
       27.29       123.78         9.04        22.03        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        8.28         0.49        19.73        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX 
       10.45       120.20         6.35        38.63        18.08        20.94 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
        1.84        46.82        30.90       130.32        98.27        62.20 
TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XO 
        0.72         6.58        19.82        27.22         9.93        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA 
        4.80        41.49        38.27        65.46        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       18.08        18.35        15.95        38.96        17.72        36.43 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.56              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           188.15            135.48 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            19.12             24.67 
[1] "0.6 - 188.2 (19.1)" "0.1 - 135.5 (24.7)"
[1] "hr=" "1.4"
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   37 28
  4P GAIN WILD-TYPE 95 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     37   28
  4P GAIN WILD-TYPE   95   86
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              37                95
  MALE                28                86
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       2                         5    51
  4P GAIN WILD-TYPE     4                        13   143
D7V4, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  51               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"
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  53
  4P GAIN WILD-TYPE   4 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   53
  4P GAIN WILD-TYPE    4  138
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              53               138
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    25  18
  4Q GAIN WILD-TYPE 137  64
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               43               201 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18                64 
$`4Q GAIN MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 
       44.91        42.84        18.64        38.24        18.54        54.21 
TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A6YV TCGA-DX-A6Z2 
       17.10        34.68        19.30        15.95        50.50        88.31 
TCGA-DX-A7EL TCGA-DX-A8BL TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2P TCGA-DX-AB2Q 
       75.32        33.07        36.69         1.15        12.07        49.18 
TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 
        4.57        41.33         3.22        19.89        25.22       143.41 
TCGA-JV-A5VE TCGA-K1-A6RU TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DL TCGA-PC-A5DO 
       16.41        10.85         4.34        14.99        37.55        81.01 
TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 
        5.03        18.08        48.59        10.52        11.18        18.94 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8Y0 TCGA-X6-A7W8 
        5.06        13.22        10.72        26.17        22.62        26.43 
TCGA-X6-A8C2 
       25.71 

$`4Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX 
       25.25        10.32        31.00        36.03        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        32.71        12.85        36.69        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        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        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        23.08        70.49       108.13        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.15        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       17.79        21.63        16.18         3.06        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
       67.20        23.54        16.87        74.10        64.21        21.30 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       14.07         7.04        17.95        14.43         9.34        59.87 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS 
       44.68        38.17        35.77        14.07       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       35.54        60.66        19.43         6.58        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T 
        4.67        12.39        40.60        86.10         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
       96.89       106.45        13.28        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       19.20        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        2.07        48.30        34.88        15.91        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
        0.10         9.80        80.48        21.37        19.53         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       37.12        40.08        28.21       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I 
       27.29       123.78         9.04         4.08        11.70        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       13.35         8.32         8.28         0.49        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM 
       15.65         7.46        10.45         4.08       120.20         6.35 
TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        18.08        20.94         9.83         1.84        46.82 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
        0.72         3.88         6.58        17.92        19.82        27.22 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
        9.93         0.72        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46         9.04        57.80        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       36.82        18.35        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.15              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           143.41            188.15 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            19.89             23.54 
[1] "1.1 - 143.4 (19.9)" "0.1 - 188.2 (23.5)"
[1] "hr=" "1.5"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    21  23
  4Q GAIN WILD-TYPE 111  91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     21   23
  4Q GAIN WILD-TYPE  111   91
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              21               111
  MALE                23                91
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         3    36
  4Q GAIN WILD-TYPE     5                        15   158
D8V4, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  36               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"
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  35
  4Q GAIN WILD-TYPE   4 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   35
  4Q GAIN WILD-TYPE    4  156
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              35               156
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   64 31
  5P GAIN WILD-TYPE 98 51
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               95               149 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               31                51 
$`5P GAIN MUTATED`
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9I1 TCGA-3B-A9I3 
       68.55        88.57        44.91        54.74        18.64        26.56 
TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3M2 
       38.24        54.21        33.53         6.28        17.10        34.68 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L 
       42.77         4.54        14.99        28.80        64.18        24.26 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BG TCGA-DX-A6YR TCGA-DX-A6YS 
       14.96        26.47        15.95        17.79        34.55        66.31 
TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       23.54        16.87        74.10        21.30        34.49        75.32 
TCGA-DX-A7EN TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BS 
       15.62        59.87        33.07        38.17        14.07        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E 
       35.54        36.69        60.66        19.43         1.15        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W 
        8.75         4.67        12.07        49.18        96.89       106.45 
TCGA-DX-AB2Z TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV 
       50.40        19.20        32.15        20.32        48.30         4.57 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
        0.10        19.53         3.22        19.89        25.22        40.08 
TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       71.70        27.29         4.08        11.70        22.03        13.35 
TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX 
       14.99        10.45         4.08         6.35        18.08        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VF 
        5.03        46.82        18.08        35.90       188.15        98.27 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QT 
       11.18        18.94         3.88        17.92         5.06        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T 
        0.72        10.72        72.72        38.27         9.04        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X9-A971 
       26.43        36.82        25.71        16.83        15.58 

$`5P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       36.30        19.69        53.49        25.25        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY 
       31.00        36.03         0.56        14.04        32.71        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       36.69        18.54        59.24        42.54        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 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       20.05        15.06        17.75        10.68        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U 
       34.88         9.73        19.30        12.26        27.22        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        25.15        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YV 
        9.11        21.63        16.18         3.06        67.20        50.50 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       64.21        88.31        48.36       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM 
       14.07         7.04        17.95        14.43         9.34        44.68 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BZ TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       35.77       124.37         6.58        12.39        40.60        86.10 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
        9.21        71.57        13.28        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       84.66        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07         2.07        34.88        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK 
       23.97        41.33         9.80        80.48        21.37         1.38 
TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       37.12        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO 
        5.92        22.62        16.41         1.05         3.91        36.39 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
      123.78         9.04        10.85         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK 
        4.34        19.73        17.98        15.65         7.46       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB 
       37.55        38.63        81.01         9.83         1.84        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 
       30.90       130.32        62.20        10.52         0.72         6.58 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.82        27.22         9.93        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       41.49        65.46        22.62        29.92        18.08        18.35 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       15.95        38.96        35.08        17.72        36.43 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.10              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           188.15            143.41 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            22.03             23.44 
[1] "0.1 - 188.2 (22.0)" "0.1 - 143.4 (23.4)"
[1] "hr=" "1"  
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   49 46
  5P GAIN WILD-TYPE 83 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     49   46
  5P GAIN WILD-TYPE   83   68
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              49                83
  MALE                46                68
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       3                         6    79
  5P GAIN WILD-TYPE     3                        12   115
D9V4, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 3
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  79               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"
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     2  79
  5P GAIN WILD-TYPE   3 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   79
  5P GAIN WILD-TYPE    3  112
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              79               112
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    44  26
  5Q GAIN WILD-TYPE 118  56
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               70               174 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               26                56 
$`5Q GAIN MUTATED`
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        38.24 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3M2 TCGA-DX-A3U8 TCGA-DX-A3U9 
       54.21        33.53         6.28        34.68         4.54        14.99 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B8 
       28.80        64.18        24.26        14.96        26.47        15.95 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18         3.06        66.31        23.54        16.87        74.10 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BS 
       34.49        75.32        59.87        33.07        38.17        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2P TCGA-DX-AB2V 
       35.54        36.69        60.66        19.43        12.07        96.89 
TCGA-DX-AB35 TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A3OV 
       19.20        20.32        48.30         4.57         0.10        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-K1-A42W 
       19.53         3.22        40.08       143.41        13.58        27.29 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA 
        4.08        11.70        22.03        14.99        10.45         4.08 
TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VF 
        6.35         5.03        18.08        35.90       188.15        98.27 
TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
       11.18         3.88        17.92         5.06        13.22         0.72 
TCGA-WK-A8XS TCGA-X6-A7W8 TCGA-X6-A8C4 TCGA-X9-A971 
       72.72        26.43        16.83        15.58 

$`5Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        19.69        53.49        44.91        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       10.32        31.00        36.03         0.56        14.04        32.71 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L4 TCGA-DX-A23R 
       12.85        36.69        18.54        59.24        42.54        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        59.47        54.77         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       10.68        44.45        39.35        34.88         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       12.26        27.22        72.72        25.08        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       34.55        67.20        50.50        64.21        88.31        21.30 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO 
        7.04        17.95        14.43         9.34        44.68        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       14.07       124.37         6.58         1.15        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
        4.67        12.39        40.60        86.10        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
       71.57       106.45        13.28        50.40        22.85       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
        0.10         0.07         0.07         0.07         2.07        34.88 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
       15.91        12.62        23.97        41.33         9.80        21.37 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 
        1.38        19.89        37.12        25.22        28.21       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A9QH 
       71.70        36.39       123.78         9.04        10.85        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
        8.32         8.28         0.49         4.34        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       15.65         7.46       120.20        37.55        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       18.08        20.94         9.83         1.84        46.82        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 
       30.90       130.32        62.20        10.52         0.72        18.94 
TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-A80J 
        6.58        19.82        27.22         9.93        10.72        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        41.49        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        9.04        57.80        29.92        18.08        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       25.71        15.95        38.96        35.08        17.72        36.43 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.10              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           188.15            135.48 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           22.785            23.260 
[1] "0.1 - 188.2 (22.8)" "0.1 - 135.5 (23.3)"
[1] "hr=" "1.2"
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   41 29
  5Q GAIN WILD-TYPE 91 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     41   29
  5Q GAIN WILD-TYPE   91   85
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              41                91
  MALE                29                85
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       3                         6    53
  5Q GAIN WILD-TYPE     3                        12   141
D10V4, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   3                 3
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  53               141
[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"
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  54
  5Q GAIN WILD-TYPE   4 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   54
  5Q GAIN WILD-TYPE    4  137
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              54               137
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    25  24
  6P GAIN WILD-TYPE 137  58
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               49               195 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               24                58 
$`6P GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX 
       19.69        88.57        44.91         0.56        32.71        38.24 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3M2 TCGA-DX-A3U9 TCGA-DX-A6B8 TCGA-DX-A6YR 
       59.24         6.28        34.68        14.99        15.95        34.55 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7ET TCGA-DX-A8BS 
       23.54        50.50        74.10        21.30         7.04        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB35 TCGA-HB-A2OT 
       36.69        60.66        19.43         1.15        19.20        48.30 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
        4.57         0.10        41.33         3.22        19.89        37.12 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-MB-A5Y9 
      143.41         5.92         9.04        10.85        22.03         8.28 
TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-SG-A6Z7 
        4.34         4.08         6.35        46.82        35.90         3.88 
TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A8C2 TCGA-X6-A8C6 
        5.06         0.72        22.62         9.04        25.71        35.08 
TCGA-X9-A971 
       15.58 

$`6P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        53.49        68.55        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64        26.56        14.04 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       12.85        36.69        18.54        54.21        33.53        42.54 
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        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YX 
       21.63        16.18         3.06        66.31        67.20        16.87 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       64.21        88.31        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BH 
      135.48        29.49        48.20        14.07        17.95        14.43 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        59.87        33.07        44.68        38.17        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       14.07       124.37        35.54         6.58        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        4.67        12.39        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
        9.21        71.57        96.89       106.45        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85       101.98        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         2.07        34.88        15.91        12.62        23.97 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
        9.80        80.48        21.37        19.53         1.38        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 
       40.08        28.21       116.88        13.58        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       16.41         1.05         3.91        71.70        36.39        27.29 
TCGA-K1-A42X TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5YA 
      123.78         4.08        11.70        13.35         8.32         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        15.65         7.46        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
      120.20        37.55        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
        5.03         9.83         1.84        18.08        48.59        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
      188.15       130.32        98.27        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       11.18        18.94         6.58        17.92        19.82        27.22 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
        9.93        13.22        10.72        26.17        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7W8 
       72.72        41.49        38.27        65.46        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       29.92        18.08        36.82        18.35        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       38.96        17.72        36.43 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.10              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           143.41            188.15 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            19.89             25.08 
[1] "0.1 - 143.4 (19.9)" "0.1 - 188.2 (25.1)"
[1] "hr=" "2.2"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    23  26
  6P GAIN WILD-TYPE 109  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     23   26
  6P GAIN WILD-TYPE  109   88
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              23               109
  MALE                26                88
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         5    36
  6P GAIN WILD-TYPE     5                        13   158
D11V4, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  36               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"
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1  37
  6P GAIN WILD-TYPE   4 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   37
  6P GAIN WILD-TYPE    4  154
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              37               154
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    26  21
  6Q GAIN WILD-TYPE 136  61
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               47               197 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21                61 
$`6Q GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       19.69        44.91         0.56        32.71        38.24        18.54 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U9 TCGA-DX-A6YR TCGA-DX-A6YU 
       23.08        17.10        34.68        14.99        34.55        23.54 
TCGA-DX-A6YV TCGA-DX-A6Z0 TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BS TCGA-DX-A8BU 
       50.50        64.21         7.04        59.87        27.95        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB35 TCGA-HB-A2OT TCGA-HB-A3YV 
       60.66        19.43         1.15        19.20        48.30         4.57 
TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 
       41.33         3.22        19.89        37.12       143.41         5.92 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A8JK 
        9.04        10.85        22.03        13.35         8.28         4.34 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A5VC TCGA-SI-A71Q TCGA-UE-A6QU 
        4.08        37.55         6.35        35.90        27.22         0.72 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A8C2 TCGA-X6-A8C6 TCGA-X9-A971 
       38.27         9.04        25.71        35.08        15.58 

$`6Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        88.57        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        31.00        36.03        18.64        26.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        12.85        36.69        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        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        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YT 
       17.79        21.63        16.18         3.06        66.31        67.20 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       16.87        74.10        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       17.95        14.43         9.34        33.07        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E 
       35.77        14.07       124.37        35.54         6.58        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
        8.75         4.67        12.39        40.60        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       49.18         9.21        71.57        96.89       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       50.40        22.85       101.98        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07         2.07        34.88        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       23.97         0.10         9.80        80.48        21.37        19.53 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        1.38        25.22        40.08        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28        22.62        16.41         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 
       36.39        27.29       123.78         4.08        11.70         8.32 
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        15.65         7.46 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
       10.45       120.20        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.03         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       30.90       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
        0.72        11.18        18.94         3.88         6.58        17.92 
TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-A80J 
       19.82         5.06         9.93        13.22        10.72        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        72.72        41.49        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       57.80        26.43        29.92        18.08        36.82        18.35 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       15.95        16.83        38.96        17.72        36.43 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.56              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           143.41            188.15 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            22.03             23.97 
[1] "0.6 - 143.4 (22.0)" "0.1 - 188.2 (24.0)"
[1] "hr=" "1.9"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    21  27
  6Q GAIN WILD-TYPE 111  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     21   27
  6Q GAIN WILD-TYPE  111   87
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              21               111
  MALE                27                87
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       1                         5    37
  6Q GAIN WILD-TYPE     5                        13   157
D12V4, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  37               157
[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"
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1  38
  6Q GAIN WILD-TYPE   4 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   38
  6Q GAIN WILD-TYPE    4  153
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              38               153
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    50  29
  7P GAIN WILD-TYPE 112  53
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               79               165 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               29                53 
$`7P GAIN MUTATED`
TCGA-3B-A9HX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R 
       42.84        38.24        12.85        36.69        59.24        74.66 
TCGA-DX-A3LT TCGA-DX-A3M2 TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6B8 
       23.08        34.68        14.99        64.18        24.26        15.95 
TCGA-DX-A6BB TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
       23.44        34.55        66.31        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BG 
       74.10        64.21        34.49        48.36         7.04        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT 
       14.43         9.34        44.68        35.77        27.95        35.54 
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        12.99        49.18 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-FX-A3RE 
       71.57        96.89       106.45        13.28        19.20         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
       48.30         4.57        41.33        19.53         3.22        19.89 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A42X 
       40.08       143.41        13.58         5.92         1.05       123.78 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QC-A6FX 
       13.35         8.28        10.45        37.55        18.08        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z7 
        5.03        46.82        98.27        10.52        11.18         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80J 
        6.58        17.92        27.22         5.06         0.72        26.17 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       22.62         9.04        26.43        25.71        15.95        16.83 
TCGA-X9-A973 
       36.43 

$`7P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       54.74        25.25        10.32        31.00        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L1 
       26.56         0.56        14.04        32.71        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        42.54         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        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       28.80        34.88         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       66.05        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EN 
        3.06        67.20        88.31        21.30        75.32        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL 
      135.48        29.49        48.20        14.07        59.87        33.07 
TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2G 
       38.17        14.07       124.37        60.66         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2Z 
       12.39        40.60        86.10        12.07         9.21        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85       101.98        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       71.31         0.46         0.10        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        2.07        34.88        15.91        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
        9.80        80.48        21.37         1.38        37.12        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
       28.21       116.88        73.28        22.62        16.41         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       71.70        36.39        27.29         9.04        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       11.70        22.03         8.32         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        15.65         7.46         4.08       120.20 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA 
        6.35        38.63        81.01         9.83         1.84        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG 
       48.59        35.90        30.90       188.15       130.32        62.20 
TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G 
        0.72        18.94        19.82         9.93        13.22        10.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C5 
       57.80        29.92        18.08        36.82        18.35        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       35.08        17.72        15.58 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           143.41            188.15 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            23.08             23.97 
[1] "0.1 - 143.4 (23.1)" "0.1 - 188.2 (24.0)"
[1] "hr=" "1.2"
D13V2, continuous
D13V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   43 36
  7P GAIN WILD-TYPE 89 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     43   36
  7P GAIN WILD-TYPE   89   78
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              43                89
  MALE                36                78
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       3                         7    62
  7P GAIN WILD-TYPE     3                        11   132
D13V4, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   3                 3
  BLACK OR AFRICAN AMERICAN               7                11
  WHITE                                  62               132
[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"
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     2  62
  7P GAIN WILD-TYPE   3 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   62
  7P GAIN WILD-TYPE    3  129
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              62               129
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    39  27
  7Q GAIN WILD-TYPE 123  55
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               66               178 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               27                55 
$`7Q GAIN MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 
       44.91        42.84        38.24        12.85        36.69        59.24 
TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3M2 TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L 
        6.28        23.08        34.68        14.99        64.18        24.26 
TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       15.95        23.44        34.55        50.50        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM 
       64.21        34.49        48.36        14.43         9.34        44.68 
TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ 
       35.77        27.95        35.54        36.69        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W 
        1.15        12.99        49.18         9.21        96.89       106.45 
TCGA-DX-AB2X TCGA-DX-AB35 TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IE-A4EI 
       13.28        19.20         0.07        48.30         4.57        19.53 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-JV-A5VF TCGA-K1-A6RU 
        3.22        19.89        40.08        13.58         1.05        10.85 
TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A8VB 
        8.28        10.45        37.55        20.94         5.03       188.15 
TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SG-A849 TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO 
       98.27        11.18         6.58         0.72        26.17        11.93 
TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C6 TCGA-X9-A973 
       22.62        26.43        36.82        25.71        35.08        36.43 

$`7Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       25.25        10.32        31.00        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 
       42.54        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        59.47        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        19.30        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        72.72        25.08        25.15        11.47        66.05 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         9.11        17.79        21.63        16.18         3.06 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL 
       66.31        67.20        23.54        88.31        21.30        75.32 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR 
       17.95        59.87        33.07        38.17        14.07       124.37 
TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       60.66         8.75         4.67        12.39        40.60        86.10 
TCGA-DX-AB2P TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       12.07        71.57        50.40        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A43Z 
       20.32         0.07         0.07         2.07        34.88        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 
       21.37         1.38        37.12        25.22        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        73.28         5.92        22.62        16.41         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
       71.70        36.39        27.29       123.78         9.04         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       11.70        22.03        13.35         8.32         0.49         4.34 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        15.65         7.46         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N 
      120.20         6.35        38.63        81.01        18.08         9.83 
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        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 
      130.32        62.20        10.52         0.72        18.94         3.88 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       17.92        19.82        27.22         5.06         9.93        13.22 
TCGA-VT-A80G TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       10.72         4.80        72.72        41.49        38.27        65.46 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 
        9.04        57.80        29.92        18.08        18.35        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       16.83        38.96        17.72        15.58 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           188.15            143.41 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           23.850            22.735 
[1] "0.1 - 188.2 (23.9)" "0.1 - 143.4 (22.7)"
[1] "hr=" "1.4"
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    30  36
  7Q GAIN WILD-TYPE 102  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     30   36
  7Q GAIN WILD-TYPE  102   78
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              30               102
  MALE                36                78
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       2                         4    54
  7Q GAIN WILD-TYPE     4                        14   140
D14V4, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  54               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     3  52
  7Q GAIN WILD-TYPE   2 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3   52
  7Q GAIN WILD-TYPE    2  139
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              52               139
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    30  22
  8P GAIN WILD-TYPE 132  60
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               52               192 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               22                60 
$`8P GAIN MUTATED`
TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R 
       53.49        54.74        26.56        14.04        12.85        74.66 
TCGA-DX-A3M2 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A6BA TCGA-DX-A6YQ 
       34.68         4.54        14.99        64.18        66.05         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A8BJ 
       34.55        66.31        23.54        88.31        48.36         9.34 
TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AB2P TCGA-DX-AB2W 
       38.17        14.07        36.69        19.43        12.07       106.45 
TCGA-DX-AB30 TCGA-FX-A3NJ TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       22.85         0.10         4.57        80.48        19.53         3.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RU 
       40.08        13.58         5.92         1.05         3.91        10.85 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM 
       14.99        17.98        10.45         4.08        37.55         6.35 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
       11.18        18.94         6.58         5.06        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C3 
       26.17        22.62        26.43        15.95 

$`8P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU 
       36.30        19.69        68.55        88.57        44.91        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       42.84        10.32        31.00        36.03        18.64         0.56 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       32.71        38.24        36.69        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        42.54         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        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       28.80        34.88         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       15.95        11.47        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       21.63        16.18        67.20        50.50        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO 
       64.21        21.30        34.49        75.32        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       29.49        48.20        14.07         7.04        17.95        14.43 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       59.87        33.07        44.68        35.77       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       35.54        60.66         6.58         1.15        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
        4.67        12.39        40.60        86.10        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB35 
       71.57        96.89        13.28        50.40       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.07        20.32         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
       34.88        15.91        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        9.80        21.37         1.38        19.89        37.12        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
       28.21       143.41       116.88        73.28        22.62        16.41 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
       71.70        36.39        27.29       123.78         9.04         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       11.70        22.03        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN 
        4.34        19.73        15.65         7.46       120.20        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       81.01        18.08        20.94         5.03         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
       46.82        18.08        48.59        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
      130.32        98.27        62.20        10.52         0.72         3.88 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XO 
       17.92        19.82        27.22         9.93        10.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB 
        4.80        72.72        41.49        38.27        65.46         9.04 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.10              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           106.45            188.15 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           16.965            25.235 
[1] "0.1 - 106.5 (17.0)" "0.1 - 188.2 (25.2)"
[1] "hr=" "1.8"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    28  24
  8P GAIN WILD-TYPE 104  90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     28   24
  8P GAIN WILD-TYPE  104   90
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              28               104
  MALE                24                90
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       4                         4    40
  8P GAIN WILD-TYPE     2                        14   154
D15V4, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   4                 2
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  40               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"
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  44
  8P GAIN WILD-TYPE   3 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   44
  8P GAIN WILD-TYPE    3  147
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              44               147
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    36  27
  8Q GAIN WILD-TYPE 126  55
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               63               181 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               27                55 
$`8Q GAIN MUTATED`
TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       53.49        54.74        42.84        26.56         0.56        14.04 
TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UF 
       12.85        74.66         4.54        14.99        10.68        64.18 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6Z2 TCGA-DX-A7EM 
       15.95        66.05        34.55        23.54        88.31        48.36 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BX TCGA-DX-AB2E 
       14.43         9.34        35.77        14.07        19.43        12.99 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       86.10        12.07        49.18       106.45        13.28        22.85 
TCGA-DX-AB35 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A3OV 
       19.20         0.46         0.10         4.57        41.33        80.48 
TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
       19.53        25.22        40.08         5.92         1.05         3.91 
TCGA-K1-A6RU TCGA-MB-A5Y8 TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R TCGA-N1-A6IA 
       10.85         8.32        14.99        17.98        10.45         4.08 
TCGA-PC-A5DL TCGA-QQ-A5VB TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 
       37.55        48.59        11.18        18.94         3.88         6.58 
TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8Y0 
       27.22        13.22         0.72        10.72        26.17        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A8C3 
        9.04        26.43        15.95 

$`8Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU 
       36.30        19.69        68.55        88.57        44.91        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KW TCGA-DX-A1KX 
       10.32        31.00        36.03        18.64        32.71        38.24 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.69        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-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        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       70.49       108.13        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       17.75        42.77        44.45        39.35        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB 
       26.47        72.72        25.08        25.15        11.47        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         9.11        17.79        21.63        16.18         3.06 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       66.31        67.20        50.50        16.87        74.10        64.21 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       21.30        34.49        75.32        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL 
       48.20        14.07         7.04        17.95        59.87        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       44.68        38.17       124.37        27.95        35.54        36.69 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       60.66         6.58         1.15         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB32 
       40.60         9.21        71.57        96.89        50.40       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3RE 
       60.00        84.66        32.15        50.89        71.31         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH 
       15.91        12.62        23.97         0.10         9.80        21.37 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 
        3.22         1.38        19.89        37.12        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
      116.88        13.58        73.28        22.62        16.41        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W 
       36.39        27.29       123.78         9.04         4.08        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       22.03        13.35         8.28         0.49         4.34        19.73 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
       15.65         7.46       120.20         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       18.08        20.94         5.03         9.83         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        35.90        30.90       188.15       130.32        98.27 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B 
       62.20        10.52         0.72        17.92        19.82         5.06 
TCGA-SI-AA8C TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
        9.93        11.93         4.80        72.72        41.49        38.27 
TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       65.46        57.80        29.92        18.08        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       25.71        16.83        38.96        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           106.45            188.15 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            15.95             26.47 
[1] "0.1 - 106.5 (15.9)" "0.1 - 188.2 (26.5)"
[1] "hr=" "1.9"
D16V2, continuous
D16V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   36 27
  8Q GAIN WILD-TYPE 96 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     36   27
  8Q GAIN WILD-TYPE   96   87
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              36                96
  MALE                27                87
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       4                         5    49
  8Q GAIN WILD-TYPE     2                        13   145
D16V4, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   4                 2
  BLACK OR AFRICAN AMERICAN               5                13
  WHITE                                  49               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"
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3  52
  8Q GAIN WILD-TYPE   2 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3   52
  8Q GAIN WILD-TYPE    2  139
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              52               139
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    29  25
  9P GAIN WILD-TYPE 133  57
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               54               190 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               25                57 
$`9P GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 
       19.69        42.84        32.71        38.24        36.69        59.24 
TCGA-DX-A3LU TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B8 
       70.49        14.99        10.68        24.26        12.26        15.95 
TCGA-DX-A6BB TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A7ET TCGA-DX-A8BG 
       23.44        67.20        23.54        50.50         7.04        17.95 
TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX 
       14.43        59.87        33.07        27.95        36.69        19.43 
TCGA-DX-AATS TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB35 
        1.15        86.10        96.89        13.28        50.40        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A3TO TCGA-HB-A3L4 TCGA-IE-A6BZ TCGA-IF-A4AK 
       60.00        84.66        20.32        34.88        19.89        40.08 
TCGA-IS-A3KA TCGA-JV-A5VF TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A8JK 
       13.58         1.05         4.08        11.70        22.03         4.34 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A5V9 TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 
       18.08        20.94        46.82        18.94         3.88         6.58 
TCGA-SI-A71O TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A8C6 
       17.92        11.93        72.72         9.04        26.43        35.08 

$`9P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       25.25        10.32        31.00        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
        0.56        14.04        12.85        18.54        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        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        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
        9.04        23.08       108.13        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77         4.54        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48O 
       28.80        34.88        64.18         9.73        19.30        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       66.05        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        34.55        66.31        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       88.31        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BM 
      135.48        29.49        48.20        14.07         9.34        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV 
       38.17        35.77        14.07       124.37        35.54        60.66 
TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        6.58        12.99         8.75         4.67        12.39        40.60 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB30 
       12.07        49.18         9.21        71.57       106.45        22.85 
TCGA-DX-AB32 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
      101.98        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3YV 
        0.07         0.07         0.07         2.07        48.30         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
       15.91        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
       80.48        21.37        19.53         3.22         1.38        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 
       25.22        28.21       143.41       116.88        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       22.62        16.41         3.91        71.70        36.39        27.29 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
      123.78         9.04        10.85        13.35         8.32         8.28 
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        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
       10.45         4.08       120.20        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       81.01         5.03         9.83         1.84        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       10.52         0.72        11.18        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XQ 
        9.93        13.22         0.72        10.72        26.17         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        38.27        65.46        22.62        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       18.08        36.82        18.35        25.71        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       38.96        17.72        15.58        36.43 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.05              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            96.89            188.15 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           21.485            24.525 
[1] "1.1 - 96.9 (21.5)"  "0.1 - 188.2 (24.5)"
[1] "hr=" "1.6"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    25  30
  9P GAIN WILD-TYPE 107  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     25   30
  9P GAIN WILD-TYPE  107   84
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              25               107
  MALE                30                84
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         3    48
  9P GAIN WILD-TYPE     6                        15   146
D17V4, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  48               146
[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"
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  48
  9P GAIN WILD-TYPE   4 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   48
  9P GAIN WILD-TYPE    4  143
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              48               143
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    46  24
  9Q GAIN WILD-TYPE 116  58
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               70               174 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24                58 
$`9Q GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ 
       19.69        88.57        42.84        32.71        38.24        36.69 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3U7 
       54.21        59.24        74.66        70.49        20.05        42.77 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB 
       14.99        10.68        12.26        15.95        66.05        23.44 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A7ET 
        3.06        34.55        67.20        23.54        50.50         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BP 
       17.95        14.43        59.87        33.07        35.77        14.07 
TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O 
       27.95        36.69        19.43         1.15         8.75        86.10 
TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB35 
       12.07        96.89       106.45        13.28        50.40        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A3L4 TCGA-IE-A4EI 
       60.00        84.66         0.46        20.32        34.88        19.53 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I 
        3.22        19.89        40.08         1.05        11.70        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A8JK TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A5V9 
       13.35         8.28         4.34        18.08        20.94        46.82 
TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-WK-A8XO TCGA-WK-A8XS 
       35.90        18.94         6.58        17.92        11.93        72.72 
TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X9-A971 
       26.43        25.71        15.95        15.58 

$`9Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       10.32        31.00        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        42.54         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        59.47        54.77         9.04        23.08       108.13 
TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB 
       17.10        34.68        15.06        17.75         4.54        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       25.15        11.47        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       16.18        66.31        16.87        74.10        64.21        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       21.30        34.49        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN 
       29.49        48.20        14.07         9.34        44.68        38.17 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G 
      124.37        35.54        60.66         6.58        12.99         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB30 
       12.39        40.60        49.18         9.21        71.57        22.85 
TCGA-DX-AB32 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE 
      101.98        32.15        50.89        71.31         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         0.07         2.07        48.30         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 
       21.37         1.38        37.12        25.22        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       10.85         4.08         8.32         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        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
       37.55         6.35        38.63        81.01         5.03         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
        1.84        18.08        48.59        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 
       98.27        62.20        10.52         0.72        11.18         3.88 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       19.82        27.22         5.06         9.93        13.22         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       10.72        26.17         4.80        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62         9.04        57.80        29.92        18.08        36.82 
TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       18.35        16.83        38.96        35.08        17.72        36.43 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.46              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           106.45            188.15 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           21.485            24.115 
[1] "0.5 - 106.5 (21.5)" "0.1 - 188.2 (24.1)"
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   35 36
  9Q GAIN WILD-TYPE 97 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     35   36
  9Q GAIN WILD-TYPE   97   78
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              35                97
  MALE                36                78
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       1                         4    59
  9Q GAIN WILD-TYPE     5                        14   135
D18V4, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  59               135
[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"
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  62
  9Q GAIN WILD-TYPE   4 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   62
  9Q GAIN WILD-TYPE    4  129
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              62               129
[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 150  72
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                222 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                10                 72 
$`10P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A6YV TCGA-DX-A8BK TCGA-DX-A8BL 
       14.04        42.77         4.54        50.50        59.87        33.07 
TCGA-DX-AB2E TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-HS-A5N9 
       12.99        71.57       106.45        13.28        50.40        41.33 
TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-JV-A5VF TCGA-LI-A67I TCGA-PC-A5DP TCGA-QQ-A5VA 
       19.89        13.58         1.05        22.03        18.08        18.08 
TCGA-SG-A6Z4 TCGA-WK-A8Y0 TCGA-X6-A8C2 TCGA-X6-A8C6 
       18.94        22.62        25.71        35.08 

$`10P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64        26.56         0.56        32.71        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.69        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
       23.08        70.49       108.13        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        14.99        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.15        15.95        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       66.31        67.20        23.54        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       88.31        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
      135.48        29.49        48.20        14.07         7.04        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP 
       14.43         9.34        44.68        38.17        35.77        14.07 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      124.37        27.95        35.54        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        6.58         1.15         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB30 
       86.10        12.07        49.18         9.21        96.89        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
      101.98        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         2.07        48.30        34.88         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97         0.10         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
       19.53         3.22         1.38        37.12        25.22        40.08 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       143.41       116.88        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       16.41         3.91        71.70        36.39        27.29       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 
        9.04        10.85         4.08        11.70        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
        6.35        38.63        81.01        20.94         5.03         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        1.84        46.82        48.59        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32        98.27        62.20        10.52         0.72        11.18 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
        3.88         6.58        17.92        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
        9.93        13.22         0.72        10.72        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB 
        4.80        72.72        41.49        38.27        65.46         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       57.80        26.43        29.92        18.08        36.82        18.35 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       15.95        16.83        38.96        17.72        15.58        36.43 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.05               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            106.45             188.15 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            22.325             23.490 
[1] "1.1 - 106.5 (22.3)" "0.1 - 188.2 (23.5)"
[1] "hr=" "1.4"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    13   9
  10P GAIN WILD-TYPE 119 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     13    9
  10P GAIN WILD-TYPE  119  105
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               13                119
  MALE                  9                105
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         2    18
  10P GAIN WILD-TYPE     6                        16   176
D19V4, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                2                 16
  WHITE                                   18                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"
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  20
  10P GAIN WILD-TYPE   5 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   20
  10P GAIN WILD-TYPE    5  171
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               20                171
[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 156  77
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                233 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 5                 77 
$`10Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A3U8 TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-AB2X 
       14.04         4.54        59.87        33.07        44.68        13.28 
TCGA-DX-AB2Z TCGA-DX-AB35 TCGA-HS-A5N9 TCGA-SG-A6Z7 TCGA-X6-A8C6 
       50.40        19.20        41.33         3.88        35.08 

$`10Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64        26.56         0.56        32.71        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.69        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
       23.08        70.49       108.13        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75        42.77        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       25.08        25.15        15.95        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         9.11        17.79        21.63        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
       34.55        66.31        67.20        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       74.10        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO 
        7.04        17.95        14.43         9.34        38.17        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       14.07       124.37        27.95        35.54        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       19.43         6.58         1.15        12.99         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.39        40.60        86.10        12.07        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       71.57        96.89       106.45        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.07        20.32         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
       19.89        37.12        25.22        40.08        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        1.05         3.91        71.70        36.39        27.29       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
        9.04        10.85         4.08        11.70        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
        8.32         8.28         0.49         4.34        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
       37.55         6.35        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.03         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O 
       10.52         0.72        11.18        18.94         6.58        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       19.82        27.22         5.06         9.93        13.22         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       10.72        26.17        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       38.27        65.46        22.62         9.04        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       29.92        18.08        36.82        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        17.72        15.58        36.43 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              3.88               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             59.87             188.15 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             33.07              23.08 
[1] "3.9 - 59.9 (33.1)"  "0.1 - 188.2 (23.1)"
[1] "hr=" "1.5"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5   6
  10Q GAIN WILD-TYPE 127 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    6
  10Q GAIN WILD-TYPE  127  108
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                5                127
  MALE                  6                108
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     9
  10Q GAIN WILD-TYPE     6                        18   185
D20V4, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                    9                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"
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   9
  10Q GAIN WILD-TYPE   5 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    9
  10Q GAIN WILD-TYPE    5  182
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                9                182
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     9  13
  11P GAIN WILD-TYPE 153  69
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                22                222 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                 69 
$`11P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EF 
       14.04        16.18        34.55        50.50        16.87        21.30 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-AATS TCGA-DX-AB2O TCGA-DX-AB2W TCGA-IE-A4EJ 
       14.43         9.34         1.15        86.10       106.45         3.22 
TCGA-IS-A3KA TCGA-K1-A42X TCGA-K1-A6RU TCGA-KF-A41W TCGA-PC-A5DP TCGA-QC-A7B5 
       13.58       123.78        10.85        11.70        18.08         5.03 
TCGA-QQ-A5VA TCGA-QQ-A8VH TCGA-X6-A7W8 TCGA-X6-A8C3 
       18.08        10.52        26.43        15.95 

$`11P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64        26.56         0.56        32.71        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.69        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
       23.08        70.49       108.13        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       15.06        17.75        42.77         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       72.72        25.08        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       23.44        28.96         9.11        17.79        21.63         3.06 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       66.31        67.20        23.54        74.10        64.21        88.31 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       34.49        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL 
       48.20        14.07         7.04        17.95        59.87        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS 
       44.68        38.17        35.77        14.07       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E 
       35.54        36.69        60.66        19.43         6.58        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q 
        8.75         4.67        12.39        40.60        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
        9.21        71.57        96.89        13.28        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
      101.98        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         2.07        48.30        34.88         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       21.37        19.53         1.38        19.89        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 
       40.08        28.21       143.41       116.88        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62        16.41         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
       27.29         9.04         4.08        22.03        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 
        6.35        38.63        81.01        20.94         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       46.82        48.59        35.90        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       98.27        62.20         0.72        11.18        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        6.58        17.92        19.82        27.22         5.06         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22         0.72        10.72        26.17        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       72.72        41.49        38.27        65.46        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.15               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            123.78             188.15 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            16.065             25.115 
[1] "1.1 - 123.8 (16.1)" "0.1 - 188.2 (25.1)"
[1] "hr=" "2.3"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    14   8
  11P GAIN WILD-TYPE 118 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     14    8
  11P GAIN WILD-TYPE  118  106
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               14                118
  MALE                  8                106
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       1                         0    20
  11P GAIN WILD-TYPE     5                        18   174
D21V4, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   20                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"
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  19
  11P GAIN WILD-TYPE   5 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   19
  11P GAIN WILD-TYPE    5  172
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               19                172
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     7  14
  11Q GAIN WILD-TYPE 155  68
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                21                223 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                 68 
$`11Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A3M2 TCGA-DX-A48L TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 
       14.04        34.68        24.26        50.50        16.87        64.21 
TCGA-DX-A7EF TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-AATS TCGA-DX-AB2W TCGA-DX-AB2X 
       21.30        14.43         9.34         1.15       106.45        13.28 
TCGA-HB-A43Z TCGA-IE-A4EH TCGA-K1-A42X TCGA-KF-A41W TCGA-PC-A5DP TCGA-QC-A7B5 
       15.91        21.37       123.78        11.70        18.08         5.03 
TCGA-QQ-A5VA TCGA-QQ-A8VH TCGA-X6-A7W8 
       18.08        10.52        26.43 

$`11Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64        26.56         0.56        32.71        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.69        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.15        15.95        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EI 
       66.31        67.20        23.54        74.10        88.31        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       14.07         7.04        17.95        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        35.77        14.07       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       36.69        60.66        19.43         6.58        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        4.67        12.39        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
        9.21        71.57        96.89        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       19.20        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 
        2.07        48.30        34.88         4.57        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10        41.33         9.80        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38        19.89        37.12        25.22        40.08        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       16.41         1.05         3.91        71.70        36.39        27.29 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
        9.04        10.85         4.08        22.03        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 
        6.35        38.63        81.01        20.94         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       46.82        48.59        35.90        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       98.27        62.20         0.72        11.18        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        6.58        17.92        19.82        27.22         5.06         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22         0.72        10.72        26.17        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       72.72        41.49        38.27        65.46        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       15.95        16.83        38.96        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.15               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            123.78             188.15 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             18.08              25.08 
[1] "1.1 - 123.8 (18.1)" "0.1 - 188.2 (25.1)"
[1] "hr=" "2.6"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    13   8
  11Q GAIN WILD-TYPE 119 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     13    8
  11Q GAIN WILD-TYPE  119  106
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               13                119
  MALE                  8                106
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0    20
  11Q GAIN WILD-TYPE     6                        18   174
D22V4, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   20                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"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  18
  11Q GAIN WILD-TYPE   5 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   18
  11Q GAIN WILD-TYPE    5  173
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               18                173
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    21  21
  12P GAIN WILD-TYPE 141  61
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                42                202 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                21                 61 
$`12P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A3LS TCGA-DX-A6YS TCGA-DX-A6YX 
       14.04        38.24        12.85         9.04        66.31        16.87 
TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BX TCGA-DX-AATS 
       64.21        34.49        14.43         9.34        19.43         1.15 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       40.60        86.10        49.18        96.89       106.45        13.28 
TCGA-DX-AB3A TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-K1-A42W 
       32.15         4.57         0.10        25.22         5.92        27.29 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QQ-A5VA TCGA-QQ-A8VF 
        8.32         8.28        10.45        37.55        18.08        98.27 
TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU 
       10.52        11.18         6.58        19.82         5.06         0.72 
TCGA-VT-A80G TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X9-A971 TCGA-X9-A973 
       10.72        25.71        16.83        35.08        15.58        36.43 

$`12P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        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        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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        59.47        54.77        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       17.10        20.05        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT 
       17.79        21.63        16.18         3.06        34.55        67.20 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL 
       23.54        50.50        74.10        88.31        21.30        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
        7.04        17.95        59.87        33.07        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       35.77        14.07       124.37        27.95        35.54        36.69 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       60.66         6.58        12.99         8.75         4.67        12.39 
TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
       12.07         9.21        71.57        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       19.20        60.00        84.66        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.10         0.07        20.32         0.07         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
       48.30        34.88        15.91        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       19.89        37.12        40.08        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28        22.62        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       71.70        36.39       123.78         9.04        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       11.70        22.03        13.35         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        15.65         7.46         4.08       120.20 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
        6.35        38.63        81.01        18.08        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        9.83         1.84        46.82        48.59        35.90        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 
      188.15       130.32        62.20         0.72        18.94         3.88 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XO 
       17.92        27.22         9.93        13.22        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        4.80        72.72        41.49        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
        9.04        57.80        26.43        29.92        18.08        36.82 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
       18.35        15.95        38.96        17.72 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.10               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            106.45             188.15 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             16.85              24.67 
[1] "0.1 - 106.5 (16.9)" "0.1 - 188.2 (24.7)"
[1] "hr=" "2"  
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    21  21
  12P GAIN WILD-TYPE 111  93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     21   21
  12P GAIN WILD-TYPE  111   93
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               21                111
  MALE                 21                 93
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       2                         0    36
  12P GAIN WILD-TYPE     4                        18   158
D23V4, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   36                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"
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     2  31
  12P GAIN WILD-TYPE   3 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   31
  12P GAIN WILD-TYPE    3  160
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               31                160
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    20  13
  12Q GAIN WILD-TYPE 142  69
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                33                211 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                13                 69 
$`12Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A3M2 TCGA-DX-A6YS TCGA-DX-A6Z0 TCGA-DX-A8BH TCGA-DX-A8BJ 
       38.24        34.68        66.31        64.21        14.43         9.34 
TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2J 
       33.07        35.77        60.66        19.43         1.15        40.60 
TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 
       49.18        96.89       106.45         4.57         0.10        41.33 
TCGA-IF-A4AJ TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A6FX TCGA-QQ-A8VF TCGA-QQ-A8VH 
       25.22        10.45        37.55        20.94        98.27        10.52 
TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-UE-A6QU TCGA-VT-A80G 
       11.18         6.58        17.92        19.82         0.72        10.72 
TCGA-X6-A8C3 TCGA-X6-A8C6 TCGA-X9-A973 
       15.95        35.08        36.43 

$`12Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        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-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.69        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       25.08        25.15        15.95        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         9.11        17.79        21.63        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       34.55        67.20        23.54        50.50        16.87        74.10 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       88.31        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
      135.48        29.49        48.20        14.07         7.04        17.95 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS 
       59.87        44.68        38.17        14.07       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       35.54        36.69         6.58        12.99         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2X 
       12.39        86.10        12.07         9.21        71.57        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       50.40        22.85       101.98        19.20        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       32.15        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       15.91        12.62        23.97         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK 
       19.53         3.22         1.38        19.89        37.12        40.08 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62        16.41         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W 
       27.29       123.78         9.04        10.85         4.08        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
       22.03        13.35         8.32         8.28         0.49         4.34 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        15.65         7.46         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
      120.20         6.35        38.63        81.01        18.08         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        9.83         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 
       30.90       188.15       130.32        62.20         0.72        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J 
        3.88        27.22         5.06         9.93        13.22        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       22.62         9.04        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       36.82        18.35        25.71        16.83        38.96        17.72 
TCGA-X9-A971 
       15.58 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.10               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            106.45             188.15 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             25.22              23.08 
[1] "0.1 - 106.5 (25.2)" "0.1 - 188.2 (23.1)"
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    12  21
  12Q GAIN WILD-TYPE 120  93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12   21
  12Q GAIN WILD-TYPE  120   93
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               12                120
  MALE                 21                 93
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       3                         0    27
  12Q GAIN WILD-TYPE     3                        18   167
D24V4, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    3                  3
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   27                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"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  25
  12Q GAIN WILD-TYPE   3 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   25
  12Q GAIN WILD-TYPE    3  166
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               25                166
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     9   4
  13Q GAIN WILD-TYPE 153  78
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                231 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 78 
$`13Q GAIN MUTATED`
TCGA-DX-A6YR TCGA-DX-A8BS TCGA-DX-AB2P TCGA-DX-AB2T TCGA-HS-A5N9 TCGA-IF-A4AK 
       34.55        27.95        12.07        71.57        41.33        40.08 
TCGA-JV-A5VE TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MJ-A68H TCGA-PC-A5DP TCGA-WP-A9GB 
       16.41         4.08        13.35        14.99        18.08         9.04 
TCGA-X9-A971 
       15.58 

$`13Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       18.64        26.56         0.56        14.04        32.71        38.24 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        36.69        18.54        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        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        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       34.68        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47        72.72        25.08        25.15        15.95        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV 
       16.18         3.06        66.31        67.20        23.54        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        74.10        64.21        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       14.07         7.04        17.95        14.43         9.34        59.87 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
       33.07        44.68        38.17        35.77        14.07       124.37 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.54        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       12.99         8.75         4.67        12.39        40.60        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
       49.18         9.21        96.89       106.45        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
        0.07         0.07         2.07        48.30        34.88         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       15.91        12.62        23.97         0.10         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A67I 
       27.29       123.78         9.04        10.85        11.70        22.03 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
        8.32         8.28         0.49         4.34        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
        6.35        38.63        81.01        20.94         5.03         9.83 
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        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
      188.15       130.32        98.27        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       11.18        18.94         3.88         6.58        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       27.22         5.06         9.93        13.22         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
       26.17        11.93         4.80        72.72        41.49        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46        22.62        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       36.82        18.35        25.71        15.95        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       35.08        17.72        36.43 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              4.08               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             71.57             188.15 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             16.41              23.54 
[1] "4.1 - 71.6 (16.4)"  "0.1 - 188.2 (23.5)"
[1] "hr=" "1.2"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    10   3
  13Q GAIN WILD-TYPE 122 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     10    3
  13Q GAIN WILD-TYPE  122  111
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               10                122
  MALE                  3                111
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         4     8
  13Q GAIN WILD-TYPE     6                        14   186
D25V4, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                    8                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"
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  12
  13Q GAIN WILD-TYPE   5 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   12
  13Q GAIN WILD-TYPE    5  179
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               12                179
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    28  27
  14Q GAIN WILD-TYPE 134  55
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                55                189 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                27                 55 
$`14Q GAIN MUTATED`
TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A240 
       88.57        18.64         0.56        54.21         6.28        60.30 
TCGA-DX-A3LW TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6YQ TCGA-DX-A6YT 
      108.13        14.99        64.18        24.26         3.06        67.20 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       50.50        16.87        64.21        21.30        34.49        75.32 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BV TCGA-DX-AB2E 
        7.04        17.95        14.43         9.34        60.66        12.99 
TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-IF-A4AJ 
       49.18        96.89        50.40         4.57        12.62        25.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W 
       40.08        13.58         5.92        10.85         4.08        11.70 
TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX 
        8.28        19.73        14.99         6.35        18.08        20.94 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SG-A849 
       48.59        35.90        30.90        98.27         3.88         6.58 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C3 
       17.92        27.22        72.72        22.62        26.43        15.95 
TCGA-X9-A971 
       15.58 

$`14Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        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        31.00        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
        9.04        23.08        70.49        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       39.35        28.80        34.88         9.73        19.30        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU 
       17.79        21.63        16.18        34.55        66.31        23.54 
TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       74.10        88.31        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       48.20        14.07        59.87        33.07        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       35.77        14.07       124.37        27.95        35.54        36.69 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       19.43         6.58         1.15         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W 
       40.60        86.10        12.07         9.21        71.57       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        19.20        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       32.15        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       15.91        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37        19.53         3.22         1.38        19.89        37.12 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
       28.21       143.41       116.88        73.28        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        1.05         3.91        71.70        36.39        27.29       123.78 
TCGA-K1-A6RT TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
        9.04        22.03        13.35         8.32         0.49         4.34 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        81.01         5.03         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH 
       46.82        18.08       188.15       130.32        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C 
        0.72        11.18        18.94        19.82         5.06         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22         0.72        10.72        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        38.27        65.46         9.04        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08        36.82        18.35        25.71        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       35.08        17.72        36.43 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.56               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            108.13             188.15 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             19.73              25.08 
[1] "0.6 - 108.1 (19.7)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.7"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    31  24
  14Q GAIN WILD-TYPE 101  90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     31   24
  14Q GAIN WILD-TYPE  101   90
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               31                101
  MALE                 24                 90
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       1                         5    43
  14Q GAIN WILD-TYPE     5                        13   151
D26V4, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   43                151
[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"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  44
  14Q GAIN WILD-TYPE   4 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   44
  14Q GAIN WILD-TYPE    4  147
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               44                147
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    38  23
  15Q GAIN WILD-TYPE 124  59
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                61                183 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                23                 59 
$`15Q GAIN MUTATED`
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-DX-A1KX 
       68.55        88.57        44.91        42.84        31.00        38.24 
TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3U7 TCGA-DX-A3U9 
       42.54        76.41         6.28         8.58        42.77        14.99 
TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BA TCGA-DX-A6YS TCGA-DX-A6YT 
       39.35        64.18        24.26        66.05        66.31        67.20 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A8BG TCGA-DX-A8BO TCGA-DX-A8BU 
       16.87        64.21        34.49        17.95        35.77        36.69 
TCGA-DX-A8BX TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2X TCGA-HB-A43Z TCGA-HB-A5W3 
       19.43        12.07        49.18        13.28        15.91        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       41.33        19.53         3.22        19.89        25.22        40.08 
TCGA-IS-A3KA TCGA-JV-A75J TCGA-K1-A42W TCGA-LI-A67I TCGA-MJ-A68H TCGA-PC-A5DL 
       13.58         3.91        27.29        22.03        14.99        37.55 
TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF 
       18.08        46.82        18.08        35.90        30.90        98.27 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q 
       11.18        18.94         3.88         6.58        19.82        27.22 
TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8XS TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X6-A8C4 
        5.06         0.72        72.72        26.43        15.95        16.83 
TCGA-X9-A971 
       15.58 

$`15Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY 
       36.30        19.69        53.49        54.74        25.25        10.32 
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        36.69        18.54        54.21        59.24        33.53 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 
       74.66         5.26        66.87        27.81        60.30         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       17.10        20.05        34.68        15.06        17.75         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       10.68        44.45        28.80        34.88         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.15        15.95        11.47        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU 
       17.79        21.63        16.18         3.06        34.55        23.54 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EM 
       50.50        74.10        88.31        21.30        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       14.43         9.34        59.87        33.07        44.68        38.17 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ 
       14.07       124.37        27.95        35.54        60.66         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        12.99         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z 
       86.10         9.21        71.57        96.89       106.45        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
        0.07         0.07         2.07        48.30        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK 
       23.97         0.10         9.80        80.48        21.37         1.38 
TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 
       37.12        28.21       143.41       116.88        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       22.62        16.41         1.05        71.70        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 
        9.04        10.85         4.08        11.70        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
        8.28         0.49         4.34        19.73        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
        7.46        10.45         4.08       120.20         6.35        38.63 
TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB 
       81.01        20.94         5.03         9.83         1.84        48.59 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SI-A71O 
      188.15       130.32        62.20        10.52         0.72        17.92 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
        9.93        13.22        10.72        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       41.49        38.27        65.46        22.62         9.04        57.80 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 
       29.92        18.08        36.82        18.35        25.71        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       35.08        17.72        36.43 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.72               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             98.27             188.15 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             25.22              22.85 
[1] "0.7 - 98.3 (25.2)"  "0.1 - 188.2 (22.9)"
[1] "hr=" "1.2"
D27V2, continuous
D27V3, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   39 22
  15Q GAIN WILD-TYPE 93 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     39   22
  15Q GAIN WILD-TYPE   93   92
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               39                 93
  MALE                 22                 92
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       2                         3    49
  15Q GAIN WILD-TYPE     4                        15   145
D27V4, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                3                 15
  WHITE                                   49                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"
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3  47
  15Q GAIN WILD-TYPE   2 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   47
  15Q GAIN WILD-TYPE    2  144
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               47                144
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    18  21
  16P GAIN WILD-TYPE 144  61
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                39                205 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                 61 
$`16P GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HX TCGA-DX-A1KU TCGA-DX-A1KW 
       19.69        44.91        54.74        42.84        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A2J0 TCGA-DX-A3U5 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A6YS 
       38.24         9.70        15.06        14.99        24.26        66.31 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BH TCGA-DX-A8BK 
       23.54        50.50        21.30        34.49        14.43        59.87 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2P 
       33.07        44.68        27.95        12.99        86.10        12.07 
TCGA-DX-AB2X TCGA-FX-A2QS TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IF-A4AJ TCGA-IF-A4AK 
       13.28         0.46        80.48        21.37        25.22        40.08 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-K1-A6RU TCGA-LI-A67I TCGA-MO-A47R TCGA-SG-A6Z4 
       13.58         5.92        10.85        22.03        10.45        18.94 
TCGA-SG-A6Z7 TCGA-X2-A95T TCGA-X6-A7W8 
        3.88        57.80        26.43 

$`16P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY 
       36.30        53.49        68.55        88.57        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KY 
       31.00        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 
       36.69        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        34.68        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       14.96        26.47        72.72        25.08        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YX 
       21.63        16.18         3.06        34.55        67.20        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       74.10        64.21        88.31        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
      135.48        29.49        48.20        14.07         7.04        17.95 
TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT 
        9.34        38.17        35.77        14.07       124.37        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F 
       36.69        60.66        19.43         6.58         1.15         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
        4.67        12.39        40.60        49.18         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       96.89       106.45        50.40        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
       60.00        84.66        32.15        50.89        71.31         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.07        20.32         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       41.33         9.80        19.53         3.22         1.38        19.89 
TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       37.12        28.21       143.41       116.88        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       16.41         1.05         3.91        71.70        36.39        27.29 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 
      123.78         9.04         4.08        11.70        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         7.46         4.08       120.20        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
       38.63        81.01        18.08        20.94         5.03         9.83 
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        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
      188.15       130.32        98.27        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       11.18         6.58        17.92        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
        9.93        13.22         0.72        10.72        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        4.80        72.72        41.49        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        9.04        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       15.95        16.83        38.96        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.46               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             86.10             188.15 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             23.54              23.08 
[1] "0.5 - 86.1 (23.5)"  "0.1 - 188.2 (23.1)"
[1] "hr=" "2"  
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    20  19
  16P GAIN WILD-TYPE 112  95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     20   19
  16P GAIN WILD-TYPE  112   95
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               20                112
  MALE                 19                 95
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         1    34
  16P GAIN WILD-TYPE     5                        17   160
D28V4, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                 17
  WHITE                                   34                160
[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"
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  32
  16P GAIN WILD-TYPE   5 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   32
  16P GAIN WILD-TYPE    5  159
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               32                159
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    11   9
  16Q GAIN WILD-TYPE 151  73
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                20                224 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 9                 73 
$`16Q GAIN MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HX TCGA-DX-A1KW TCGA-DX-A3U5 TCGA-DX-A6YU 
       44.91        54.74        42.84        32.71        15.06        23.54 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BS TCGA-DX-AB2E 
       21.30        34.49        17.95        59.87        27.95        12.99 
TCGA-DX-AB2O TCGA-IE-A3OV TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       86.10        80.48       143.41         5.92        18.94         3.88 
TCGA-SI-A71O TCGA-WK-A8Y0 
       17.92        22.62 

$`16Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU 
       36.30        19.69        53.49        68.55        88.57        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       10.32        31.00        36.03        18.64        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        34.68        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       14.96        26.47        72.72        25.08        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
       21.63        16.18         3.06        34.55        66.31        67.20 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL 
       50.50        16.87        74.10        64.21        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
        7.04        14.43         9.34        33.07        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       35.77        14.07       124.37        35.54        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       19.43         6.58         1.15         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       40.60        12.07        49.18         9.21        71.57        96.89 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.10         0.07        20.32         0.07         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       48.30        34.88         4.57        15.91        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10        41.33         9.80        21.37        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38        19.89        37.12        25.22        40.08        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      116.88        13.58        73.28        22.62        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
       10.85         4.08        11.70        22.03        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
        6.35        38.63        81.01        18.08        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        9.83         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       30.90       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
        0.72        11.18         6.58        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
        9.93        13.22         0.72        10.72        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB 
        4.80        72.72        41.49        38.27        65.46         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       57.80        26.43        29.92        18.08        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       25.71        15.95        16.83        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.88               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            143.41             188.15 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            25.745             22.965 
[1] "3.9 - 143.4 (25.7)" "0.1 - 188.2 (23.0)"
[1] "hr=" "1.2"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    12   8
  16Q GAIN WILD-TYPE 120 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12    8
  16Q GAIN WILD-TYPE  120  106
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               12                120
  MALE                  8                106
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         1    18
  16Q GAIN WILD-TYPE     6                        17   176
D29V4, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                1                 17
  WHITE                                   18                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"
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  16
  16Q GAIN WILD-TYPE   5 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   16
  16Q GAIN WILD-TYPE    5  175
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               16                175
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    34  24
  17P GAIN WILD-TYPE 128  58
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                58                186 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                24                 58 
$`17P GAIN MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KW 
       44.91        54.74        42.84        18.64         0.56        32.71 
TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3UF TCGA-DX-A48K 
       12.85        54.21        59.24         6.28        64.18        19.30 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YV 
       26.47        15.95         9.11        16.18        67.20        50.50 
TCGA-DX-A6YZ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BV 
       74.10        33.07        44.68        38.17        35.77        60.66 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB37 TCGA-FX-A3RE 
       71.57        96.89       106.45        13.28        84.66         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-JV-A75J TCGA-K1-A6RU 
       20.32         0.07         4.57        12.62         3.91        10.85 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DP TCGA-QC-A7B5 
       22.03        13.35        10.45         4.08        18.08         5.03 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71P TCGA-UE-A6QU 
       46.82        18.08        18.94         6.58        19.82         0.72 
TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC 
       10.72        72.72        22.62         9.04        26.43        36.82 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C6 TCGA-X9-A971 
       25.71        15.95        35.08        15.58 

$`17P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU 
       36.30        19.69        53.49        68.55        88.57        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KX 
       10.32        31.00        36.03        26.56        14.04        38.24 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       36.69        18.54        33.53        42.54        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 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       17.10        20.05        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        24.26        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        25.15        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       28.96        17.79        21.63         3.06        34.55        66.31 
TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       23.54        16.87        64.21        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       14.07         7.04        17.95        14.43         9.34        59.87 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX 
       14.07       124.37        27.95        35.54        36.69        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
        6.58         1.15        12.99         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2Z 
       40.60        86.10        12.07        49.18         9.21        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85       101.98        19.20        60.00        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       71.31         0.46         0.10         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
       34.88        15.91        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        21.37        19.53         3.22         1.38        19.89 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        40.08        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62        16.41         1.05 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
       71.70        36.39        27.29       123.78         9.04         4.08 
TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       11.70         8.32         8.28         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL 
       14.99        17.98        15.65         7.46       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 
        6.35        38.63        81.01        20.94         9.83         1.84 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
       48.59        35.90        30.90       188.15       130.32        98.27 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O 
       62.20        10.52         0.72        11.18         3.88        17.92 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XO 
       27.22         5.06         9.93        13.22        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA 
        4.80        41.49        38.27        65.46        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       18.08        18.35        16.83        38.96        17.72        36.43 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.07               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            106.45             188.15 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            20.070             24.115 
[1] "0.1 - 106.5 (20.1)" "0.1 - 188.2 (24.1)"
[1] "hr=" "1.4"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    29  29
  17P GAIN WILD-TYPE 103  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29   29
  17P GAIN WILD-TYPE  103   85
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               29                103
  MALE                 29                 85
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       3                         3    46
  17P GAIN WILD-TYPE     3                        15   148
D30V4, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    3                  3
  BLACK OR AFRICAN AMERICAN                3                 15
  WHITE                                   46                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"
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  48
  17P GAIN WILD-TYPE   4 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   48
  17P GAIN WILD-TYPE    4  143
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               48                143
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    37  16
  17Q GAIN WILD-TYPE 125  66
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                53                191 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 66 
$`17Q GAIN MUTATED`
TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1L2 
       54.74        42.84        18.64         0.56        32.71        59.24 
TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU 
       10.68        19.30         9.11        16.18        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       50.50        74.10        33.07        44.68        38.17        35.77 
TCGA-DX-A8BV TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       60.66        49.18        71.57        96.89       106.45        13.28 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A5W3 TCGA-IE-A6BZ TCGA-IW-A3M4 
        0.07        20.32         0.07        12.62        19.89        73.28 
TCGA-JV-A75J TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH TCGA-MO-A47R TCGA-PC-A5DP 
        3.91        10.85        22.03        13.35        10.45        18.08 
TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 
        5.03        18.08        35.90        11.18        18.94         6.58 
TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8Y0 
       19.82         5.06         0.72        10.72        72.72        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X9-A971 
        9.04        26.43        25.71        15.95        15.58 

$`17Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU 
       25.25        10.32        31.00        36.03        26.56        14.04 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
       38.24        12.85        36.69        18.54        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        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        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       34.68        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       25.08        25.15        15.95        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       28.96        17.79        21.63         3.06        34.55        66.31 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       16.87        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BP 
        7.04        17.95        14.43         9.34        59.87        14.07 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ 
      124.37        27.95        35.54        36.69        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        12.99         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
       86.10        12.07         9.21        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       19.20        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.46         0.10         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57        15.91        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
       80.48        21.37        19.53         3.22         1.38        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        40.08        28.21       143.41       116.88        13.58 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62        16.41         1.05        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 
       27.29       123.78         9.04         4.08        11.70         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         7.46         4.08       120.20        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        81.01        20.94         9.83         1.84        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        30.90       188.15       130.32        98.27        62.20 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C 
       10.52         0.72         3.88        17.92        27.22         9.93 
TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
       13.22        26.17        11.93         4.80        41.49        38.27 
TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       65.46        57.80        29.92        18.08        36.82        18.35 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        36.43 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            106.45             188.15 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             19.82              25.15 
[1] "0.1 - 106.5 (19.8)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1"  
D31V2, continuous
D31V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   33 20
  17Q GAIN WILD-TYPE 99 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     33   20
  17Q GAIN WILD-TYPE   99   94
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               33                 99
  MALE                 20                 94
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       3                         2    45
  17Q GAIN WILD-TYPE     3                        16   149
D31V4, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    3                  3
  BLACK OR AFRICAN AMERICAN                2                 16
  WHITE                                   45                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"
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     2  47
  17Q GAIN WILD-TYPE   3 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   47
  17Q GAIN WILD-TYPE    3  144
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               47                144
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    29  19
  18P GAIN WILD-TYPE 133  63
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                48                196 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                19                 63 
$`18P GAIN MUTATED`
TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A23Y 
       53.49        88.57        18.64        32.71        33.53         6.28 
TCGA-DX-A3U7 TCGA-DX-A3UE TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YU TCGA-DX-A6YX 
       42.77        34.88        15.95        66.05        23.54        16.87 
TCGA-DX-A6Z0 TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS 
       64.21        17.95        59.87        44.68        35.77        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2V 
       36.69        60.66         1.15         8.75        86.10        96.89 
TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-FX-A3TO TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EI 
      106.45        50.40        20.32        15.91         0.10        19.53 
TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-K1-A6RV TCGA-LI-A9QH 
       19.89        13.58         5.92        16.41         4.08        13.35 
TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DM TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-RN-AAAQ 
        8.28        10.45         6.35         9.83        46.82        11.18 
TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X9-A971 TCGA-X9-A973 
       18.94        17.92        36.82        15.95        15.58        36.43 

$`18P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        19.69        68.55        44.91        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX 
       42.84        10.32        31.00        36.03        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        42.54        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        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       34.68        15.06        17.75         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        25.15        11.47        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       17.79        21.63        16.18         3.06        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       67.20        50.50        74.10        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BN 
       14.07         7.04        14.43         9.34        33.07        38.17 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E 
       14.07       124.37        35.54        19.43         6.58        12.99 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
        4.67        12.39        40.60        12.07        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       71.57        13.28        22.85       101.98        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.07         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.57        12.62        23.97        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
       21.37         3.22         1.38        37.12        25.22        40.08 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF 
       28.21       143.41       116.88        73.28        22.62         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       10.85        11.70        22.03         8.32         0.49         4.34 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        15.65         7.46         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
      120.20        37.55        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        5.03         1.84        18.08        48.59        35.90        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
      188.15       130.32        98.27        62.20        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        3.88         6.58        19.82        27.22         5.06         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22         0.72        10.72        26.17        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       72.72        41.49        38.27        65.46        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        26.43        29.92        18.08        18.35        25.71 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       16.83        38.96        35.08        17.72 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.10               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            106.45             188.15 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            19.710             24.115 
[1] "0.1 - 106.5 (19.7)" "0.1 - 188.2 (24.1)"
[1] "hr=" "1.3"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    29  20
  18P GAIN WILD-TYPE 103  94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     29   20
  18P GAIN WILD-TYPE  103   94
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               29                103
  MALE                 20                 94
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       2                         5    37
  18P GAIN WILD-TYPE     4                        13   157
D32V4, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   37                157
[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"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  40
  18P GAIN WILD-TYPE   5 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   40
  18P GAIN WILD-TYPE    5  151
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               40                151
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    21  11
  18Q GAIN WILD-TYPE 141  71
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                32                212 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                11                 71 
$`18Q GAIN MUTATED`
TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A3U7 TCGA-DX-A3UE 
       88.57        18.64        59.24        33.53        42.77        34.88 
TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A8BG TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O 
       23.54        74.10        17.95         1.15         8.75        86.10 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A43Z TCGA-HS-A5N8 
       96.89        50.40         0.46        20.32        15.91         0.10 
TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-K1-A6RV 
       19.53        19.89        13.58         5.92        16.41         4.08 
TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-SI-A71O 
        8.28        10.45        37.55         9.83        46.82        17.92 
TCGA-WP-A9GB TCGA-X9-A971 
        9.04        15.58 

$`18Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        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        31.00        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        38.24        12.85        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       18.54        54.21        42.54        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 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       17.10        20.05        34.68        15.06        17.75         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF 
       14.99        10.68        44.45        39.35        28.80        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47        72.72        25.08        25.15        15.95        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV 
       16.18         3.06        34.55        66.31        67.20        50.50 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       16.87        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
        7.04        14.43         9.34        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        35.77        14.07       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G 
       36.69        60.66        19.43         6.58        12.99         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       12.39        40.60        12.07        49.18         9.21        71.57 
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        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE 
       84.66        32.15        50.89        71.31         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
        0.07         0.07         2.07        48.30        34.88         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97        41.33         9.80        80.48        21.37 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        3.22         1.38        37.12        25.22        40.08        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J 
      143.41       116.88        73.28        22.62         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
       71.70        36.39        27.29       123.78         9.04        10.85 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       11.70        22.03        13.35         8.32         0.49         4.34 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        15.65         7.46         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
      120.20         6.35        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        5.03         1.84        18.08        48.59        35.90        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
      188.15       130.32        98.27        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q 
       11.18        18.94         3.88         6.58        19.82        27.22 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J 
        5.06         9.93        13.22         0.72        10.72        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62        57.80        26.43        29.92        18.08        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.35        25.71        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A973 
       17.72        36.43 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.10               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             96.89             188.15 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            18.295             25.115 
[1] "0.1 - 96.9 (18.3)"  "0.1 - 188.2 (25.1)"
[1] "hr=" "1.2"
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    21  12
  18Q GAIN WILD-TYPE 111 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     21   12
  18Q GAIN WILD-TYPE  111  102
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               21                111
  MALE                 12                102
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       1                         4    25
  18Q GAIN WILD-TYPE     5                        14   169
D33V4, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   25                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"
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  29
  18Q GAIN WILD-TYPE   5 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   29
  18Q GAIN WILD-TYPE    5  162
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               29                162
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    47  34
  19P GAIN WILD-TYPE 115  48
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                81                163 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                34                 48 
$`19P GAIN MUTATED`
TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       88.57        18.64         0.56        14.04        32.71        38.24 
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y 
       12.85        18.54        54.21        59.24        74.66         6.28 
TCGA-DX-A2J0 TCGA-DX-A3M2 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48N 
        9.70        34.68        42.77        14.99        64.18        12.26 
TCGA-DX-A6B8 TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YZ 
       15.95        34.55        66.31        67.20        50.50        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7ES 
       64.21        88.31        21.30        34.49        48.36        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM 
        7.04        17.95        14.43         9.34        33.07        44.68 
TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS 
       35.77        27.95        35.54        36.69        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB35 
       12.99        86.10        49.18        96.89        13.28        19.20 
TCGA-DX-AB3A TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HS-A5NA 
       32.15         0.07        20.32         0.07         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-LI-A9QH TCGA-MB-A8JK TCGA-QC-A6FX TCGA-QQ-A5V9 
        3.91        27.29        13.35         4.34        20.94        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-SG-A849 TCGA-SI-A71O 
       18.08        35.90       188.15        98.27         6.58        17.92 
TCGA-SI-A71P TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB 
       19.82        13.22         0.72        72.72        38.27         9.04 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X9-A973 
       18.08        36.82        36.43 

$`19P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        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        31.00        36.03        26.56 
TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       36.69        33.53        42.54         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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       17.75         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        72.72        25.08        25.15        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO 
        3.06        23.54        16.87        75.32        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR 
       29.49        48.20        59.87        38.17        14.07       124.37 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
       60.66         6.58         8.75         4.67        12.39        40.60 
TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 
       12.07         9.21        71.57       106.45        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
      101.98        60.00        84.66        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z 
        0.10         0.07         2.07        48.30        34.88        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IE-A4EK 
       12.62        23.97         0.10        41.33        21.37         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        40.08        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28        22.62        16.41        71.70        36.39 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I 
      123.78         9.04        10.85         4.08        11.70        22.03 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.32         8.28         0.49        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N 
        6.35        38.63        81.01        18.08         5.03         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH 
        1.84        48.59        30.90       130.32        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8B 
        0.72        11.18        18.94         3.88        27.22         5.06 
TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
        9.93        10.72        26.17        11.93         4.80        41.49 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD 
       65.46        22.62        57.80        26.43        29.92        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       25.71        15.95        16.83        38.96        35.08        17.72 
TCGA-X9-A971 
       15.58 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.07               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            188.15             143.41 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             20.32              23.97 
[1] "0.1 - 188.2 (20.3)" "0.1 - 143.4 (24.0)"
[1] "hr=" "1.4"
D34V2, continuous
D34V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   37 45
  19P GAIN WILD-TYPE 95 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     37   45
  19P GAIN WILD-TYPE   95   69
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               37                 95
  MALE                 45                 69
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       2                         5    64
  19P GAIN WILD-TYPE     4                        13   130
D34V4, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   64                130
[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"
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  61
  19P GAIN WILD-TYPE   2 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   61
  19P GAIN WILD-TYPE    2  130
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               61                130
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    38  23
  19Q GAIN WILD-TYPE 124  59
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                61                183 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                 59 
$`19Q GAIN MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       88.57        44.91        14.04        32.71        38.24        12.85 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3M2 TCGA-DX-A3U9 
       54.21        59.24        74.66         6.28        34.68        14.99 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
       64.18        12.26        15.95        34.55        66.31        67.20 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7ES 
       23.54        50.50        74.10        64.21        21.30        14.07 
TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-A8BU 
       17.95         9.34        33.07        44.68        27.95        36.69 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB35 
       19.43         1.15        12.99        96.89        13.28        19.20 
TCGA-FX-A3TO TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
       20.32         4.57         9.80        19.53         3.22        19.89 
TCGA-JV-A5VF TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JK TCGA-MJ-A68H 
        1.05         4.08        11.70        13.35         4.34        14.99 
TCGA-QC-A6FX TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A849 
       20.94        18.08        48.59        35.90        98.27         6.58 
TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XS TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A8C3 
        0.72        26.17        72.72         9.04        36.82        15.95 
TCGA-X9-A973 
       36.43 

$`19Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        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        31.00        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        36.69        18.54        33.53        42.54         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 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        25.15        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YX 
        9.11        17.79        21.63        16.18         3.06        16.87 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       88.31        34.49        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BN 
       29.49        48.20         7.04        14.43        59.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ 
       35.77        14.07       124.37        35.54        60.66         6.58 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
        8.75         4.67        12.39        40.60        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 
       49.18         9.21        71.57       106.45        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
      101.98        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.46         0.10         0.07         0.07         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       48.30        34.88        15.91        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       41.33        80.48        21.37         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       40.08        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62        16.41         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-MB-A5Y8 
       27.29       123.78         9.04        10.85        22.03         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        8.28         0.49        19.73        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
       10.45         4.08       120.20        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        18.08         5.03         9.83         1.84        46.82 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       30.90       188.15       130.32        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       11.18        18.94         3.88        17.92        19.82        27.22 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ 
        5.06         9.93        13.22        10.72        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 
       41.49        38.27        65.46        22.62        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       29.92        18.08        18.35        25.71        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       35.08        17.72        15.58 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.72               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             98.27             188.15 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             20.32              24.26 
[1] "0.7 - 98.3 (20.3)"  "0.1 - 188.2 (24.3)"
[1] "hr=" "1.2"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    28  34
  19Q GAIN WILD-TYPE 104  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     28   34
  19Q GAIN WILD-TYPE  104   80
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               28                104
  MALE                 34                 80
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       2                         4    48
  19Q GAIN WILD-TYPE     4                        14   146
D35V4, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   48                146
[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"
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  48
  19Q GAIN WILD-TYPE   4 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   48
  19Q GAIN WILD-TYPE    4  143
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               48                143
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    34  27
  20P GAIN WILD-TYPE 128  55
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                183 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                27                 55 
$`20P GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       19.69        26.56         0.56        14.04        32.71        38.24 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3UA 
       18.54        54.21        74.66         6.28        42.77        10.68 
TCGA-DX-A48P TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6Z0 
       14.96        23.44         3.06        34.55        23.54        64.21 
TCGA-DX-A7EI TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX 
       34.49        14.43        33.07        27.95        36.69        19.43 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 
        1.15        12.99        96.89       106.45        22.85        19.20 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A3OV 
        0.10        20.32         0.07        12.62        41.33        80.48 
TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-K1-A42W 
        3.22        25.22        40.08        13.58         5.92        27.29 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DL 
        4.08        11.70        13.35         8.28         4.08        37.55 
TCGA-QC-A7B5 TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-UE-A6QU 
        5.03        11.18         3.88        17.92        19.82         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XX TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C3 
       10.72        26.17        38.27        26.43        36.82        15.95 
TCGA-X6-A8C6 
       35.08 

$`20P GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       12.85        36.69        59.24        33.53        42.54         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 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       17.10        20.05        34.68        15.06        17.75         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R 
        9.73        19.30        24.26        12.26        27.22        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       72.72        25.08        25.15        15.95        11.47        66.05 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YS 
       28.96         9.11        17.79        21.63        16.18        66.31 
TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF 
       67.20        50.50        16.87        74.10        88.31        21.30 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM 
       14.07         7.04        17.95         9.34        59.87        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV 
       38.17        35.77        14.07       124.37        35.54        60.66 
TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
        6.58         8.75         4.67        12.39        40.60        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB2Z 
       12.07        49.18         9.21        71.57        13.28        50.40 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
      101.98        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.46         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH 
        4.57        15.91        23.97         0.10         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 
       19.53         1.38        19.89        37.12        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
      116.88        73.28        22.62        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I 
       71.70        36.39       123.78         9.04        10.85        22.03 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.32         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
       15.65         7.46        10.45       120.20         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        18.08        20.94         9.83         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       18.08        48.59        35.90        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A849 
       98.27        62.20        10.52         0.72        18.94         6.58 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ 
       27.22         5.06         9.93        13.22        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       72.72        41.49        65.46        22.62         9.04        57.80 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       29.92        18.08        18.35        25.71        16.83        38.96 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            106.45             188.15 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             19.69              25.15 
[1] "0.1 - 106.5 (19.7)" "0.1 - 188.2 (25.1)"
[1] "hr=" "2.1"
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    26  35
  20P GAIN WILD-TYPE 106  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     26   35
  20P GAIN WILD-TYPE  106   79
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               26                106
  MALE                 35                 79
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       2                         2    48
  20P GAIN WILD-TYPE     4                        16   146
D36V4, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                2                 16
  WHITE                                   48                146
[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"
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1  48
  20P GAIN WILD-TYPE   4 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1   48
  20P GAIN WILD-TYPE    4  143
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               48                143
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    47  35
  20Q GAIN WILD-TYPE 115  47
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                82                162 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                35                 47 
$`20Q GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       19.69        88.57        44.91        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R 
       32.71        38.24        12.85        18.54        54.21        74.66 
TCGA-DX-A23Y TCGA-DX-A3LW TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A48P TCGA-DX-A6B8 
        6.28       108.13        42.77        10.68        14.96        15.95 
TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z0 
       23.44         3.06        34.55        23.54        74.10        64.21 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BM 
       21.30        34.49         7.04        14.43        33.07        44.68 
TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E 
       35.77        27.95        36.69        19.43         1.15        12.99 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 
       12.07        49.18        96.89       106.45        22.85        19.20 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-IE-A3OV 
        0.10        20.32         0.07         4.57        12.62        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 
       19.53         3.22        40.08       143.41        13.58         5.92 
TCGA-K1-A42W TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
       27.29         4.08        11.70        22.03        13.35         8.28 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        4.08        37.55        20.94         5.03        46.82        18.08 
TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
       30.90        98.27        11.18         3.88         6.58        17.92 
TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XX 
       19.82         5.06         0.72        10.72        26.17        38.27 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C6 
       26.43        36.82        15.95        35.08 

$`20Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        53.49        68.55        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KZ TCGA-DX-A1L2 
       10.32        31.00        36.03        18.64        36.69        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        42.54         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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       23.08        70.49        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       17.75         4.54        14.99        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       27.22        26.47        72.72        25.08        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       66.05        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EL 
       66.31        67.20        50.50        16.87        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR 
       17.95         9.34        59.87        38.17        14.07       124.37 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       35.54        60.66         6.58         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB2Z 
       40.60        86.10         9.21        71.57        13.28        50.40 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
      101.98        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.46         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
       15.91        23.97         0.10        41.33         9.80        21.37 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 
        1.38        19.89        37.12        25.22        28.21       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28        22.62        16.41         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-MB-A5Y8 TCGA-MB-A5YA 
       36.39       123.78         9.04        10.85         8.32         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       10.45       120.20         6.35        38.63        81.01        18.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VD 
        9.83         1.84        48.59        35.90       188.15       130.32 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SI-A71Q TCGA-SI-AA8C 
       62.20        10.52         0.72        18.94        27.22         9.93 
TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY 
       13.22        11.93         4.80        72.72        41.49        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       22.62         9.04        57.80        29.92        18.08        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       25.71        16.83        38.96        17.72        15.58        36.43 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            143.41             188.15 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            20.070             25.235 
[1] "0.1 - 143.4 (20.1)" "0.1 - 188.2 (25.2)"
[1] "hr=" "1.8"
D37V2, continuous
D37V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   34 48
  20Q GAIN WILD-TYPE 98 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     34   48
  20Q GAIN WILD-TYPE   98   66
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               34                 98
  MALE                 48                 66
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         4    67
  20Q GAIN WILD-TYPE     4                        14   127
D37V4, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   67                127
[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"
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     2  66
  20Q GAIN WILD-TYPE   3 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2   66
  20Q GAIN WILD-TYPE    3  125
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               66                125
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    30  25
  21Q GAIN WILD-TYPE 132  57
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                55                189 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                25                 57 
$`21Q GAIN MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 
       44.91        42.84        18.64        32.71        12.85        54.21 
TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U9 TCGA-DX-A48K TCGA-DX-A6B8 
        8.58       108.13        34.68        14.99        19.30        15.95 
TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EM TCGA-DX-A7ET 
       34.55        23.54        50.50        74.10        48.36         7.04 
TCGA-DX-A8BH TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-AB2E TCGA-DX-AB2W TCGA-DX-AB35 
       14.43        27.95        60.66        12.99       106.45        19.20 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ 
        4.57         0.10        41.33        80.48         3.22        19.89 
TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A6RU TCGA-LI-A67I 
       25.22        13.58         5.92         1.05        10.85        22.03 
TCGA-MB-A5Y8 TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QC-A7B5 
        8.32        14.99         4.08        37.55         6.35         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SI-A71Q 
        9.83        46.82        48.59        35.90        98.27        27.22 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 
       13.22         0.72        38.27        22.62         9.04        26.43 
TCGA-X9-A971 
       15.58 

$`21Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX 
       25.25        10.32        31.00        36.03        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        38.24        36.69        18.54        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6Z0 
       16.18         3.06        66.31        67.20        16.87        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO 
       88.31        21.30        34.49        75.32        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK 
       29.49        48.20        14.07        17.95         9.34        59.87 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
       33.07        44.68        38.17        35.77        14.07       124.37 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F 
       35.54        36.69        19.43         6.58         1.15         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        4.67        12.39        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
        9.21        71.57        96.89        13.28        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
      101.98        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        2.07        48.30        34.88        15.91        12.62        23.97 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK 
        9.80        21.37        19.53         1.38        37.12        40.08 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
       28.21       143.41       116.88        73.28        22.62        16.41 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
        4.08        11.70        13.35         8.28         0.49         4.34 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK 
       19.73        17.98        15.65         7.46        10.45       120.20 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       38.63        81.01        18.08        20.94         1.84        18.08 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       30.90       188.15       130.32        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       11.18        18.94         3.88         6.58        17.92        19.82 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
        5.06         9.93        10.72        26.17        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       72.72        41.49        65.46        57.80        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       36.82        18.35        25.71        15.95        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       35.08        17.72        36.43 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.10               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            108.13             188.15 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             19.89              24.26 
[1] "0.1 - 108.1 (19.9)" "0.1 - 188.2 (24.3)"
[1] "hr=" "1.7"
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    26  29
  21Q GAIN WILD-TYPE 106  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     26   29
  21Q GAIN WILD-TYPE  106   85
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               26                106
  MALE                 29                 85
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       2                         8    39
  21Q GAIN WILD-TYPE     4                        10   155
D38V4, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                8                 10
  WHITE                                   39                155
[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"
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  46
  21Q GAIN WILD-TYPE   5 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   46
  21Q GAIN WILD-TYPE    5  145
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               46                145
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    39  19
  22Q GAIN WILD-TYPE 123  63
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                58                186 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                 63 
$`22Q GAIN MUTATED`
TCGA-3B-A9HT TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A3M2 TCGA-DX-A3UA 
       54.74        14.04        38.24        12.85        34.68        10.68 
TCGA-DX-A48K TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YR 
       19.30        27.22        14.96        23.44         9.11        34.55 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BS TCGA-DX-A8BT 
       64.21        88.31        34.49         9.34        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
       36.69        12.99         8.75        12.07        49.18         9.21 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 
       96.89       106.45        13.28        48.30        15.91        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-JV-A5VE TCGA-JV-A75J 
       41.33        19.53         3.22        40.08        16.41         3.91 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM 
       13.35         8.28        14.99         4.08        37.55         6.35 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC 
       18.08        20.94         5.03        46.82        48.59        35.90 
TCGA-QQ-A8VF TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-VT-A80G TCGA-WK-A8Y0 
       98.27        18.94         6.58        17.92        10.72        22.62 
TCGA-X6-A7WA TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C6 
       29.92        15.95        16.83        35.08 

$`22Q GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       26.56         0.56        32.71        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
        9.73        24.26        12.26        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BG 
       25.15        15.95        11.47        66.05        28.96        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
       21.63        16.18         3.06        66.31        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EM 
       50.50        16.87        74.10        21.30        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       17.95        14.43        59.87        33.07        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       35.77        14.07       124.37        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2T 
        1.15         4.67        12.39        40.60        86.10        71.57 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       50.40        22.85       101.98        19.20        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       32.15        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV 
       20.32         0.07         0.07         2.07        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK 
       23.97         0.10         9.80        80.48        21.37         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       19.89        37.12        25.22        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN 
       13.58        73.28         5.92        22.62         1.05        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       36.39        27.29       123.78         9.04        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       11.70        22.03         8.32         0.49         4.34        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN 
       17.98        15.65         7.46        10.45       120.20        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VB 
       81.01         9.83         1.84        18.08        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 
      130.32        62.20        10.52         0.72        11.18         3.88 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       19.82        27.22         5.06         9.93        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
       26.17        11.93         4.80        72.72        41.49        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WC 
       65.46         9.04        57.80        26.43        18.08        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       18.35        25.71        38.96        17.72        15.58        36.43 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              3.22               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            106.45             188.15 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            19.120             25.115 
[1] "3.2 - 106.5 (19.1)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.1"
D39V2, continuous
D39V3, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   34 24
  22Q GAIN WILD-TYPE 98 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     34   24
  22Q GAIN WILD-TYPE   98   90
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               34                 98
  MALE                 24                 90
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       1                         5    49
  22Q GAIN WILD-TYPE     5                        13   145
D39V4, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   49                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"
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  48
  22Q GAIN WILD-TYPE   2 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   48
  22Q GAIN WILD-TYPE    2  143
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               48                143
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    47  24
  XP GAIN WILD-TYPE 115  58
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               71               173 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               24                58 
$`XP GAIN MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-DX-A1KX TCGA-DX-A1KZ 
       19.69        25.25        42.84        31.00        38.24        36.69 
TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A3LW TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UE 
        6.28        60.30       108.13        10.68        39.35        34.88 
TCGA-DX-A3UF TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YS TCGA-DX-A6YT 
       64.18        15.95        66.05        23.44        66.31        67.20 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A8BG 
       23.54        50.50        74.10        64.21        48.36        17.95 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BX 
        9.34        33.07        44.68        27.95        35.54        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2Q 
        6.58         1.15         8.75        12.39        86.10        49.18 
TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-FX-A3TO TCGA-HB-A2OT 
       71.57       106.45        13.28        22.85        20.32        48.30 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA 
       41.33        80.48        19.53        19.89        37.12        13.58 
TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A42W TCGA-LI-A67I TCGA-MJ-A68H TCGA-PC-A5DN 
       22.62         3.91        27.29        22.03        14.99        38.63 
TCGA-QC-A6FX TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z7 
       20.94        18.08        35.90        98.27        10.52         3.88 
TCGA-SG-A849 TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XS TCGA-WP-A9GB TCGA-X6-A7W8 
        6.58         0.72        26.17        72.72         9.04        26.43 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X9-A971 TCGA-X9-A973 
       29.92        36.82        25.71        15.58        36.43 

$`XP GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        36.03        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       32.71        12.85        18.54        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       42.54        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49        17.10        20.05        34.68        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J 
       42.77         4.54        14.99        44.45        28.80         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF 
       72.72        25.08        25.15        11.47        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX 
       17.79        21.63        16.18         3.06        34.55        16.87 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO 
       88.31        21.30        34.49        75.32        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK 
       29.49        48.20        14.07         7.04        14.43        59.87 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-A8BV 
       38.17        35.77        14.07       124.37        36.69        60.66 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2V 
       12.99         4.67        40.60        12.07         9.21        96.89 
TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       50.40       101.98        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       50.89        71.31         0.46         0.10         0.07         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         2.07        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK 
       23.97         0.10         9.80        21.37         3.22         1.38 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       25.22        40.08        28.21       143.41       116.88        73.28 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
        5.92        16.41         1.05        71.70        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 
        9.04        10.85         4.08        11.70        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
        8.28         0.49         4.34        19.73        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
        7.46        10.45         4.08       120.20        37.55         6.35 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        18.08         5.03         9.83         1.84        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q 
       48.59        30.90       188.15       130.32        62.20         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       11.18        18.94        17.92        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
        9.93        13.22        10.72        11.93         4.80        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A7WD 
       38.27        65.46        22.62        57.80        18.08        18.35 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       15.95        16.83        38.96        35.08        17.72 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.72              0.07 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           108.13            188.15 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            27.29             19.82 
[1] "0.7 - 108.1 (27.3)" "0.1 - 188.2 (19.8)"
[1] "hr=" "1.1"
D40V2, continuous
D40V3, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   45 27
  XP GAIN WILD-TYPE 87 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     45   27
  XP GAIN WILD-TYPE   87   87
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              45                87
  MALE                27                87
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       2                         6    59
  XP GAIN WILD-TYPE     4                        12   135
D40V4, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  59               135
[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"
D40V5, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     3  61
  XP GAIN WILD-TYPE   2 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3   61
  XP GAIN WILD-TYPE    2  130
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              61               130
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    17  15
  XQ GAIN WILD-TYPE 145  67
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               32               212 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               15                67 
$`XQ GAIN MUTATED`
TCGA-3R-A8YX TCGA-DX-A1KZ TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A6YS TCGA-DX-A6YV 
        0.56        36.69         6.28        60.30        66.31        50.50 
TCGA-DX-A6Z0 TCGA-DX-A8BJ TCGA-DX-A8BX TCGA-DX-AB2H TCGA-DX-AB2Q TCGA-DX-AB2T 
       64.21         9.34        19.43        12.39        49.18        71.57 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-HB-A2OT TCGA-HS-A5N9 TCGA-IE-A3OV 
      106.45        13.28        22.85        48.30        41.33        80.48 
TCGA-IE-A4EI TCGA-IS-A3KA TCGA-JV-A75J TCGA-K1-A42W TCGA-LI-A67I TCGA-QC-A6FX 
       19.53        13.58         3.91        27.29        22.03        20.94 
TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-VT-A80J 
       18.08        98.27        10.52         3.88         6.58        26.17 
TCGA-WK-A8XS TCGA-X6-A7W8 
       72.72        26.43 

$`XQ GAIN WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
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        38.24        12.85 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       18.54        54.21        59.24        33.53        42.54        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 
        5.26        76.41        66.87        27.81         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       17.10        20.05        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       15.95        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT 
       17.79        21.63        16.18         3.06        34.55        67.20 
TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       23.54        16.87        74.10        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL 
       14.07         7.04        17.95        14.43        59.87        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS 
       44.68        38.17        35.77        14.07       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       35.54        36.69        60.66         6.58         1.15        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S 
        8.75         4.67        40.60        86.10        12.07         9.21 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       96.89        50.40       101.98        19.20        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       32.15        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV 
       20.32         0.07         0.07         2.07        34.88         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH 
       15.91        12.62        23.97         0.10         9.80        21.37 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
        3.22         1.38        19.89        37.12        25.22        40.08 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       143.41       116.88        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
       16.41         1.05        71.70        36.39       123.78         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       10.85         4.08        11.70        13.35         8.32         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49         4.34        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
        7.46        10.45         4.08       120.20        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       38.63        81.01        18.08         5.03         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       46.82        48.59        35.90        30.90       188.15       130.32 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P 
       62.20         0.72        11.18        18.94        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       27.22         5.06         9.93        13.22         0.72        10.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        41.49        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        9.04        57.80        29.92        18.08        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       25.71        15.95        16.83        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.56              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           106.45            188.15 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            24.51             23.26 
[1] "0.6 - 106.5 (24.5)" "0.1 - 188.2 (23.3)"
[1] "hr=" "1.3"
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    19  13
  XQ GAIN WILD-TYPE 113 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     19   13
  XQ GAIN WILD-TYPE  113  101
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              19               113
  MALE                13               101
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         2    25
  XQ GAIN WILD-TYPE     6                        16   169
D41V4, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  25               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"
D41V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3  22
  XQ GAIN WILD-TYPE   2 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   22
  XQ GAIN WILD-TYPE    2  169
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              22               169
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    23   7
  1P LOSS WILD-TYPE 139  75
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               30               214 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                75 
$`1P LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A6B9 
       38.24        36.69        18.54        10.68        64.18        11.47 
TCGA-DX-A6BA TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BV TCGA-DX-AB2V TCGA-DX-AB2Z 
       66.05        66.31        21.30        60.66        96.89        50.40 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
        0.07         0.07        19.89       143.41       116.88        73.28 
TCGA-IW-A3M6 TCGA-K1-A42X TCGA-MO-A47R TCGA-QQ-A8VB TCGA-SG-A6Z4 TCGA-SI-A71P 
       22.62       123.78        10.45       188.15        18.94        19.82 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XT TCGA-WK-A8Y0 TCGA-X6-A7WD TCGA-X9-A971 
       27.22         9.93        41.49        22.62        18.35        15.58 

$`1P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        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-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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        59.47        54.77         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 
      108.13        17.10        20.05        34.68        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        14.99        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       14.96        26.47        72.72        25.08        25.15        15.95 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
        3.06        34.55        67.20        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       74.10        64.21        88.31        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        35.77        14.07       124.37        27.95        35.54 
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        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        4.67        12.39        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 
        9.21        71.57       106.45        13.28        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       19.20        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.46         0.10        20.32         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       34.88         4.57        15.91        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       41.33         9.80        80.48        21.37        19.53         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3KA 
        1.38        37.12        25.22        40.08        28.21        13.58 
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        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I 
       27.29         9.04        10.85         4.08        11.70        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35         8.32         8.28         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        15.65         7.46         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
       37.55         6.35        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.03         9.83         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        30.90       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B 
        0.72        11.18         3.88         6.58        17.92         5.06 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22         0.72        10.72        26.17        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       72.72        38.27        65.46         9.04        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       29.92        18.08        36.82        25.71        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       38.96        35.08        17.72        36.43 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           188.15            135.48 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            24.92             23.26 
[1] "0.1 - 188.2 (24.9)" "0.1 - 135.5 (23.3)"
[1] "hr=" "2.1"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    23   7
  1P LOSS WILD-TYPE 109 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     23    7
  1P LOSS WILD-TYPE  109  107
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              23               109
  MALE                 7               107
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       2                         2    23
  1P LOSS WILD-TYPE     4                        16   171
D42V4, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  23               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"
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  22
  1P LOSS WILD-TYPE   5 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   22
  1P LOSS WILD-TYPE    5  169
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              22               169
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    25  12
  1Q LOSS WILD-TYPE 137  70
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               37               207 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12                70 
$`1Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-DX-A6B8 TCGA-DX-A6BA 
       38.24        36.69        18.54         9.70        15.95        66.05 
TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BH TCGA-DX-A8BV 
        9.11        66.31        16.87        21.30        14.43        60.66 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A2QS 
       86.10        12.07        49.18        96.89        50.40         0.46 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3K8 
        0.07         4.57        12.62        19.89       143.41       116.88 
TCGA-K1-A42X TCGA-LI-A9QH TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DO TCGA-QC-AA9N 
      123.78        13.35         4.34         4.08        81.01         9.83 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-WK-A8Y0 
       11.18        18.94        19.82         5.06         9.93        22.62 
TCGA-X6-A7WD 
       18.35 

$`1Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        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-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       17.10        20.05        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        23.44        28.96        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ 
        3.06        34.55        67.20        23.54        50.50        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       64.21        88.31        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
      135.48        29.49        48.20        14.07         7.04        17.95 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        59.87        33.07        44.68        38.17        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX 
       14.07       124.37        27.95        35.54        36.69        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
        6.58         1.15        12.99         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       40.60         9.21        71.57       106.45        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
      101.98        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO 
       71.31         0.10         0.07        20.32         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
       48.30        34.88        15.91        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37        19.53         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M4 
       37.12        25.22        40.08        28.21        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62        16.41         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W 
       36.39        27.29         9.04        10.85         4.08        11.70 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       22.03         8.32         8.28         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        15.65         7.46        10.45       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 
        6.35        38.63        18.08        20.94         5.03         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
       46.82        18.08        48.59        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
      130.32        98.27        62.20        10.52         0.72         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
        6.58        17.92        27.22        13.22         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
       26.17        11.93         4.80        72.72        41.49        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46         9.04        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       36.82        25.71        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.07              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           143.41            188.15 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            18.54             25.15 
[1] "0.1 - 143.4 (18.5)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    23  14
  1Q LOSS WILD-TYPE 109 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     23   14
  1Q LOSS WILD-TYPE  109  100
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              23               109
  MALE                14               100
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         2    30
  1Q LOSS WILD-TYPE     6                        16   164
D43V4, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  30               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"
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  26
  1Q LOSS WILD-TYPE   4 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   26
  1Q LOSS WILD-TYPE    4  165
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              26               165
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    51  32
  2P LOSS WILD-TYPE 111  50
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               83               161 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32                50 
$`2P LOSS MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1L0 TCGA-DX-A1L2 
       88.57        25.25        18.64        26.56        18.54        59.24 
TCGA-DX-A23Y TCGA-DX-A3M2 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD 
        6.28        34.68        42.77        14.99        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48V 
       34.88        64.18        24.26        14.96        26.47        25.08 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU 
       15.95        66.05         3.06        34.55        67.20        23.54 
TCGA-DX-A6YX TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       16.87        48.36        15.62         7.04        17.95        14.43 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU 
       59.87        44.68        38.17        35.77        27.95        36.69 
TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB2T 
       60.66         1.15         8.75        12.39        12.07        71.57 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A3TO 
       96.89        50.40        19.20        84.66        32.15        20.32 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       48.30        34.88        15.91        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        9.80        80.48         3.22        19.89        37.12        25.22 
TCGA-IF-A4AK TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W TCGA-LI-A9QH TCGA-MJ-A68H 
       40.08        16.41        71.70        27.29        13.35        14.99 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-SG-A6Z4 TCGA-SI-A71O 
       81.01        18.08         9.83        46.82        18.94        17.92 
TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        5.06        10.72        72.72        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X9-A971 
        9.04        26.43        18.08        25.71        15.58 

$`2P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        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        31.00        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        38.24        12.85        36.69        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       42.54        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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48K 
       17.75         4.54        10.68        44.45         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB 
       12.26        27.22        72.72        25.15        11.47        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YS 
       28.96         9.11        17.79        21.63        16.18        66.31 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       50.50        74.10        64.21        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       75.32       135.48        29.49        48.20        14.07         9.34 
TCGA-DX-A8BL TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ 
       33.07        14.07       124.37        35.54        19.43         6.58 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.99         4.67        40.60        86.10        49.18         9.21 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB3B 
      106.45        13.28        22.85       101.98        60.00        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
       71.31         0.46         0.10         0.07         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
        2.07         4.57        41.33        21.37        19.53         1.38 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
       22.62         1.05         3.91        36.39       123.78         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       10.85         4.08        11.70        22.03         8.32         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49         4.34        19.73        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
       10.45         4.08       120.20        37.55         6.35        38.63 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       20.94         5.03         1.84        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       30.90       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q 
        0.72        11.18         3.88         6.58        19.82        27.22 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
        9.93        13.22         0.72        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 
       41.49        57.80        29.92        36.82        18.35        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        36.43 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.10              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            96.89            188.15 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            25.22             21.63 
[1] "0.1 - 96.9 (25.2)"  "0.1 - 188.2 (21.6)"
[1] "hr=" "1.2"
D44V2, continuous
D44V3, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   50 34
  2P LOSS WILD-TYPE 82 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     50   34
  2P LOSS WILD-TYPE   82   80
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              50                82
  MALE                34                80
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                        10    66
  2P LOSS WILD-TYPE     6                         8   128
D44V4, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN              10                 8
  WHITE                                  66               128
[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"
D44V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  74
  2P LOSS WILD-TYPE   5 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   74
  2P LOSS WILD-TYPE    5  117
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              74               117
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    38  28
  2Q LOSS WILD-TYPE 124  54
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               66               178 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               28                54 
$`2Q LOSS MUTATED`
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3M2 
       18.64        26.56        18.54        59.24         6.28        34.68 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V 
       42.77        14.99        28.80        24.26        26.47        25.08 
TCGA-DX-A6B8 TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YX 
       15.95        16.18         3.06        34.55        67.20        16.87 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL 
       48.36        15.62         7.04        14.43        59.87        33.07 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2H TCGA-DX-AB2P 
       38.17        27.95        36.69         1.15        12.39        12.07 
TCGA-DX-AB2V TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3L4 
       96.89        19.20        32.15        20.32        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ 
        4.57        15.91        12.62         0.10         9.80         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A42W 
       19.89        37.12        40.08        16.41         1.05        27.29 
TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-SG-A6Z4 
       14.99         6.35        18.08         5.03         9.83        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX 
        3.88        17.92         5.06        10.72        72.72        38.27 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
       22.62         9.04        26.43        18.08        36.82        25.71 

$`2Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
        0.56        14.04        32.71        38.24        12.85        36.69 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       54.21        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       20.05        15.06        17.75         4.54        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       39.35        34.88        64.18         9.73        19.30        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       27.22        14.96        72.72        25.15        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS 
       23.44        28.96         9.11        17.79        21.63        66.31 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       23.54        50.50        74.10        64.21        88.31        21.30 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       34.49        75.32       135.48        29.49        48.20        14.07 
TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
       17.95         9.34        44.68        35.77        14.07       124.37 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       35.54        60.66        19.43         6.58        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
        4.67        40.60        86.10        49.18         9.21        71.57 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
      106.45        13.28        50.40        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       84.66        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV 
        0.07         0.07         2.07        23.97        41.33        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 
       21.37        19.53         1.38        25.22        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J 
      116.88        13.58        73.28         5.92        22.62         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       71.70        36.39       123.78         9.04        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       11.70        22.03        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        4.34        19.73        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX 
        4.08       120.20        37.55        38.63        81.01        20.94 
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        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
      188.15       130.32        98.27        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT 
       11.18         6.58        19.82        27.22         9.93        13.22 
TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY 
        0.72        26.17        11.93         4.80        41.49        65.46 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       57.80        29.92        18.35        15.95        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       35.08        17.72        15.58        36.43 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            96.89            188.15 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           18.790            25.235 
[1] "0.1 - 96.9 (18.8)"  "0.1 - 188.2 (25.2)"
[1] "hr=" "2.1"
D45V2, continuous
D45V3, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   33 34
  2Q LOSS WILD-TYPE 99 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     33   34
  2Q LOSS WILD-TYPE   99   80
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              33                99
  MALE                34                80
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         8    52
  2Q LOSS WILD-TYPE     6                        10   142
D45V4, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               8                10
  WHITE                                  52               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  57
  2Q LOSS WILD-TYPE   5 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   57
  2Q LOSS WILD-TYPE    5  134
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              57               134
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    31  23
  3P LOSS WILD-TYPE 131  59
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               54               190 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               23                59 
$`3P LOSS MUTATED`
TCGA-3B-A9HL TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y 
       19.69        32.71        38.24        18.54        74.66         6.28 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3UA 
        9.04        23.08        17.10        20.05        34.68        10.68 
TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU 
       12.26        26.47        15.95         3.06        34.55        23.54 
TCGA-DX-A7EF TCGA-DX-A7EO TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BM TCGA-DX-A8BT 
       21.30       135.48        17.95        14.43        44.68        35.54 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2X 
        6.58         1.15        40.60        86.10        71.57        13.28 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3C TCGA-HB-A3YV TCGA-HB-A43Z 
      101.98        19.20        60.00        71.31         4.57        15.91 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-JV-A5VF TCGA-K1-A42X TCGA-K1-A6RU 
        3.22        19.89        37.12         1.05       123.78        10.85 
TCGA-LI-A9QH TCGA-MB-A8JK TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A8VB 
       13.35         4.34        10.45        37.55         6.35       188.15 
TCGA-RN-AAAQ TCGA-WK-A8XT TCGA-X6-A7W8 TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-X9-A971 
       11.18        41.49        26.43        16.83        17.72        15.58 

$`3P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       26.56         0.56        14.04        12.85        36.69        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49       108.13        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
        9.73        19.30        24.26        27.22        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        25.15        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YT 
        9.11        17.79        21.63        16.18        66.31        67.20 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       50.50        16.87        74.10        64.21        88.31        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       75.32        48.36        15.62        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BO 
        7.04         9.34        59.87        33.07        38.17        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
       14.07       124.37        27.95        36.69        60.66        19.43 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB2Q 
       12.99         8.75         4.67        12.39        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB37 
        9.21        96.89       106.45        50.40        22.85        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       32.15        50.89         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A5W3 
        0.07         0.07         2.07        48.30        34.88        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
       19.53         1.38        25.22        40.08        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV 
        3.91        71.70        36.39        27.29         9.04         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       11.70        22.03         8.32         8.28         0.49        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        15.65         7.46         4.08       120.20 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
       38.63        81.01        18.08        20.94         5.03         9.83 
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        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 
      130.32        98.27        62.20        10.52         0.72        18.94 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
        3.88         6.58        17.92        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
        9.93        13.22         0.72        10.72        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
        4.80        72.72        38.27        65.46        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X9-A973 
       15.95        38.96        35.08        36.43 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.05              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           188.15            143.41 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           19.445            25.185 
[1] "1.1 - 188.2 (19.4)" "0.1 - 143.4 (25.2)"
[1] "hr=" "1.5"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    29  27
  3P LOSS WILD-TYPE 103  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     29   27
  3P LOSS WILD-TYPE  103   87
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              29               103
  MALE                27                87
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         3    46
  3P LOSS WILD-TYPE     5                        15   148
D46V4, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  46               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"
D46V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  44
  3P LOSS WILD-TYPE   4 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   44
  3P LOSS WILD-TYPE    4  147
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              44               147
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    26  22
  3Q LOSS WILD-TYPE 136  60
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               48               196 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               22                60 
$`3Q LOSS MUTATED`
TCGA-3B-A9HL TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R 
       19.69        32.71        38.24        18.54        54.21        74.66 
TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
        6.28         9.04        23.08        17.10        20.05        34.68 
TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YR 
       10.68        12.26        26.47        15.95         3.06        34.55 
TCGA-DX-A7EF TCGA-DX-A7EO TCGA-DX-A8BH TCGA-DX-AATS TCGA-DX-AB2J TCGA-DX-AB35 
       21.30       135.48        14.43         1.15        40.60        19.20 
TCGA-DX-AB36 TCGA-DX-AB3C TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IE-A3OV TCGA-IE-A4EJ 
       60.00        71.31         4.57        15.91        80.48         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-JV-A5VF TCGA-K1-A42X TCGA-K1-A6RU TCGA-LI-A9QH 
       19.89        37.12         1.05       123.78        10.85        13.35 
TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM 
        8.32         4.34        14.99        10.45        37.55         6.35 
TCGA-QQ-A8VB TCGA-RN-AAAQ TCGA-VT-A80G TCGA-X6-A7W8 TCGA-X6-A8C4 TCGA-X9-A971 
      188.15        11.18        10.72        26.43        16.83        15.58 

$`3Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 
       26.56         0.56        14.04        12.85        36.69        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        42.54         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        59.47        54.77        70.49 
TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
      108.13        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       19.30        24.26        27.22        14.96        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.15        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
       17.79        21.63        16.18        66.31        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       50.50        16.87        74.10        64.21        88.31        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       75.32        48.36        15.62        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
        7.04        17.95         9.34        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        35.77        14.07       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       36.69        60.66        19.43         6.58        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
        4.67        12.39        86.10        12.07        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
       71.57        96.89       106.45        13.28        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-FX-A2QS TCGA-FX-A3NJ 
      101.98        84.66        32.15        50.89         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.07        20.32         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
       34.88        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       21.37        19.53         1.38        25.22        40.08        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT 
       16.41         3.91        71.70        36.39        27.29         9.04 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
        4.08        11.70        22.03         8.28         0.49        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN 
       17.98        15.65         7.46         4.08       120.20        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       81.01        18.08        20.94         5.03         9.83         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        30.90       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       98.27        62.20        10.52         0.72        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        6.58        17.92        19.82        27.22         5.06         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.22         0.72        26.17        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       41.49        38.27        65.46        22.62         9.04        57.80 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       29.92        18.08        36.82        18.35        25.71        15.95 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       38.96        35.08        17.72        36.43 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.05              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           188.15            143.41 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           17.820            25.235 
[1] "1.1 - 188.2 (17.8)" "0.1 - 143.4 (25.2)"
[1] "hr=" "1.8"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    22  27
  3Q LOSS WILD-TYPE 110  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     22   27
  3Q LOSS WILD-TYPE  110   87
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              22               110
  MALE                27                87
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         2    39
  3Q LOSS WILD-TYPE     5                        16   155
D47V4, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  39               155
[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"
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  37
  3Q LOSS WILD-TYPE   4 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   37
  3Q LOSS WILD-TYPE    4  154
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              37               154
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    24  17
  4P LOSS WILD-TYPE 138  65
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               41               203 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               17                65 
$`4P LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9I3 TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LT 
       19.69        88.57        26.56         8.58         9.04        23.08 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48L TCGA-DX-A48R 
       42.77        10.68        28.80        34.88        24.26        26.47 
TCGA-DX-A6B8 TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BG 
       15.95        66.31        21.30        34.49         7.04        17.95 
TCGA-DX-A8BK TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2O 
       59.87       124.37        60.66         6.58        12.99        86.10 
TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EK TCGA-IW-A3M5 
       50.40       101.98        15.91        12.62         1.38         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A42X TCGA-LI-A67I TCGA-LI-A9QH 
       22.62         1.05        27.29       123.78        22.03        13.35 
TCGA-MO-A47R TCGA-PC-A5DM TCGA-QQ-A5V9 TCGA-SI-AA8C TCGA-X2-A95T 
       10.45         6.35        46.82         9.93        57.80 

$`4P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       42.84        10.32        31.00        36.03        18.64         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04        32.71        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 
       76.41        66.87         6.28        27.81        60.30         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       59.47        54.77        70.49       108.13        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       34.68        15.06        17.75         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       39.35        64.18         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        72.72        25.08        25.15        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
        3.06        34.55        67.20        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       74.10        64.21        88.31        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BJ 
      135.48        29.49        48.20        14.07        14.43         9.34 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS 
       33.07        44.68        38.17        35.77        14.07        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G 
       35.54        36.69        19.43         1.15         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       12.39        40.60        12.07        49.18         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
       96.89       106.45        13.28        22.85        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.07        20.32         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
       34.88         4.57        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48        21.37        19.53         3.22        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        40.08        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT 
       73.28        16.41         3.91        71.70        36.39         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       10.85         4.08        11.70         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08       120.20        37.55        38.63        81.01        18.08 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       20.94         5.03         9.83         1.84        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 
       10.52         0.72        11.18        18.94         3.88         6.58 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
       17.92        19.82        27.22         5.06        13.22         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       10.72        26.17        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA 
       38.27        65.46        22.62         9.04        26.43        29.92 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       18.08        36.82        18.35        25.71        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       38.96        35.08        17.72        15.58        36.43 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.05              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           124.37            188.15 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            22.62             23.54 
[1] "1.1 - 124.4 (22.6)" "0.1 - 188.2 (23.5)"
[1] "hr=" "1.3"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    25  16
  4P LOSS WILD-TYPE 107  98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25   16
  4P LOSS WILD-TYPE  107   98
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              25               107
  MALE                16                98
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         4    34
  4P LOSS WILD-TYPE     4                        14   160
D48V4, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  34               160
[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"
D48V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     0  32
  4P LOSS WILD-TYPE   5 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0   32
  4P LOSS WILD-TYPE    5  159
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              32               159
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    33  17
  4Q LOSS WILD-TYPE 129  65
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               50               194 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               17                65 
$`4Q LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A23R TCGA-DX-A2IZ 
       19.69        88.57        26.56         0.56        74.66         8.58 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A48L 
        9.04        23.08        42.77        10.68        28.80        24.26 
TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YX 
       26.47        66.05         3.06        66.31        23.54        16.87 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN 
       21.30        34.49        17.95        59.87        44.68        38.17 
TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Z 
      124.37        60.66         6.58        12.99        86.10        50.40 
TCGA-DX-AB32 TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IW-A3M5 
      101.98        15.91         0.10        21.37         1.38         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I 
       22.62         1.05        27.29         4.08        11.70        22.03 
TCGA-MO-A47R TCGA-PC-A5DM TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-SI-AA8C TCGA-WK-A8XS 
       10.45         6.35         9.83        46.82         9.93        72.72 
TCGA-X6-A7WD TCGA-X6-A8C4 
       18.35        16.83 

$`4Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KU 
       42.84        10.32        31.00        36.03        18.64        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        27.81        60.30         9.70        59.47        54.77 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       70.49       108.13        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       17.75         4.54        14.99        44.45        39.35        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        19.30        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB 
       72.72        25.08        25.15        15.95        11.47        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YR 
       28.96         9.11        17.79        21.63        16.18        34.55 
TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL 
       67.20        50.50        74.10        64.21        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BP 
        7.04        14.43         9.34        33.07        35.77        14.07 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F 
       27.95        35.54        36.69        19.43         1.15         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
        4.67        12.39        40.60        12.07        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 
       71.57        96.89       106.45        13.28        22.85        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.10         0.07        20.32         0.07         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
       48.30        34.88         4.57        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
        9.80        80.48        19.53         3.22        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        40.08        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       73.28        16.41         3.91        71.70        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        9.04        10.85        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08       120.20        37.55        38.63        81.01        18.08 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       20.94         5.03         1.84        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       30.90       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
        0.72        11.18        18.94         3.88         6.58        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       19.82        27.22         5.06        13.22         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       26.17        11.93         4.80        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       22.62         9.04        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       36.82        25.71        15.95        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           124.37            188.15 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           21.700            25.115 
[1] "0.1 - 124.4 (21.7)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.1"
D49V2, continuous
D49V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   33 17
  4Q LOSS WILD-TYPE 99 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     33   17
  4Q LOSS WILD-TYPE   99   97
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              33                99
  MALE                17                97
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       2                         4    38
  4Q LOSS WILD-TYPE     4                        14   156
D49V4, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               4                14
  WHITE                                  38               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"
D49V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     0  40
  4Q LOSS WILD-TYPE   5 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      0   40
  4Q LOSS WILD-TYPE    5  151
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              40               151
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    11   9
  5P LOSS WILD-TYPE 151  73
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               20               224 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                73 
$`5P LOSS MUTATED`
TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3M1 
        0.56        32.71        36.69        74.66        23.08        20.05 
TCGA-DX-A3UA TCGA-DX-A6YQ TCGA-DX-A6Z0 TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BO 
       10.68         3.06        64.21        17.95         9.34        35.77 
TCGA-IS-A3K7 TCGA-K1-A42X TCGA-K1-A6RU TCGA-MB-A8JL TCGA-QQ-A5VB TCGA-WK-A8Y0 
      143.41       123.78        10.85        19.73        48.59        22.62 
TCGA-X6-A8C3 TCGA-X6-A8C6 
       15.95        35.08 

$`5P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 
       18.64        26.56        14.04        38.24        12.85        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       54.21        59.24        33.53        42.54         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 
       59.47        54.77         9.04        70.49       108.13        17.10 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       34.68        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       72.72        25.08        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
       34.55        66.31        67.20        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       74.10        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP 
       14.43        59.87        33.07        44.68        38.17        14.07 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      124.37        27.95        35.54        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
        6.58         1.15        12.99         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       40.60        86.10        12.07        49.18         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
       96.89       106.45        13.28        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       19.20        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        2.07        48.30        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
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-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       40.08        28.21       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62        16.41         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       27.29         9.04         4.08        11.70        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J 
        8.32         8.28         0.49         4.34        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
        6.35        38.63        81.01        18.08        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
        9.83         1.84        46.82        18.08        35.90        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
      188.15       130.32        98.27        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       11.18        18.94         3.88         6.58        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       27.22         5.06         9.93        13.22         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
       26.17        11.93         4.80        72.72        41.49        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46         9.04        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       36.82        18.35        25.71        16.83        38.96        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.56              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           143.41            188.15 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            22.85             23.49 
[1] "0.6 - 143.4 (22.9)" "0.1 - 188.2 (23.5)"
[1] "hr=" "1.3"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    13   7
  5P LOSS WILD-TYPE 119 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     13    7
  5P LOSS WILD-TYPE  119  107
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              13               119
  MALE                 7               107
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       1                         0    14
  5P LOSS WILD-TYPE     5                        18   180
D50V4, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                18
  WHITE                                  14               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"
D50V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  11
  5P LOSS WILD-TYPE   5 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   11
  5P LOSS WILD-TYPE    5  180
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              11               180
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    22  12
  5Q LOSS WILD-TYPE 140  70
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               34               210 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12                70 
$`5Q LOSS MUTATED`
TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3M1 
        0.56        32.71        36.69        74.66        23.08        20.05 
TCGA-DX-A3UA TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ 
       10.68        64.21        21.30         7.04        17.95         9.34 
TCGA-DX-A8BO TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2Z TCGA-FX-A2QS 
       35.77         1.15        12.99         8.75        50.40         0.46 
TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-K1-A42X TCGA-K1-A6RU TCGA-LI-A9QH 
       21.37        19.89        25.22       123.78        10.85        13.35 
TCGA-MB-A8JL TCGA-QQ-A5VB TCGA-SG-A6Z4 TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-WP-A9GB 
       19.73        48.59        18.94        10.72        22.62         9.04 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C6 
       36.82        18.35        15.95        35.08 

$`5Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 
       18.64        26.56        14.04        38.24        12.85        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       54.21        59.24        33.53        42.54         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 
       59.47        54.77         9.04        70.49       108.13        17.10 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       34.68        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       72.72        25.08        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV 
        3.06        34.55        66.31        67.20        23.54        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       16.87        74.10        88.31        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH 
       15.62       135.48        29.49        48.20        14.07        14.43 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR 
       59.87        33.07        44.68        38.17        14.07       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        35.54        36.69        60.66        19.43         6.58 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        4.67        12.39        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
        9.21        71.57        96.89       106.45        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
      101.98        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       71.31         0.10         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        2.07        48.30        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       23.97         0.10        41.33         9.80        80.48        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        3.22         1.38        37.12        40.08        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT 
        1.05         3.91        71.70        36.39        27.29         9.04 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        4.08        11.70        22.03         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        4.34        14.99        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08       120.20        37.55         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       18.08        20.94         5.03         9.83         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        35.90        30.90       188.15       130.32        98.27 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 
       62.20        10.52         0.72        11.18         3.88         6.58 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       17.92        19.82        27.22         5.06         9.93        13.22 
TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
        0.72        26.17        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46        57.80        26.43        29.92        18.08 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       25.71        16.83        38.96        17.72        15.58        36.43 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.46              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           123.78            188.15 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            19.81             25.20 
[1] "0.5 - 123.8 (19.8)" "0.1 - 188.2 (25.2)"
[1] "hr=" "1.4"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    20  14
  5Q LOSS WILD-TYPE 112 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     20   14
  5Q LOSS WILD-TYPE  112  100
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              20               112
  MALE                14               100
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       1                         1    28
  5Q LOSS WILD-TYPE     5                        17   166
D51V4, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               1                17
  WHITE                                  28               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"
D51V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  26
  5Q LOSS WILD-TYPE   5 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   26
  5Q LOSS WILD-TYPE    5  165
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              26               165
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    46  11
  6P LOSS WILD-TYPE 116  71
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               57               187 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11                71 
$`6P LOSS MUTATED`
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I3 TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT 
       42.84        10.32        26.56        36.69        74.66        23.08 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48K 
       17.10        20.05        10.68        39.35        64.18        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB 
       24.26        27.22        14.96        25.08        66.05        23.44 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6Z2 
        9.11        16.18        66.31        67.20        16.87        88.31 
TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BL TCGA-DX-A8BR TCGA-DX-AB2F TCGA-DX-AB2Q 
       34.49        48.36        33.07       124.37         8.75        49.18 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A3OV 
       71.57        96.89         0.07        15.91        12.62        80.48 
TCGA-IW-A3M6 TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A8JL TCGA-PC-A5DL TCGA-QC-A7B5 
       22.62        71.70        36.39        19.73        37.55         5.03 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-A71Q 
       30.90       188.15        11.18        18.94        19.82        27.22 
TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-X6-A7W8 TCGA-X6-A7WC 
       10.72        11.93        72.72        65.46        26.43        36.82 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       15.95        16.83        38.96 

$`6P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       54.74        25.25        31.00        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        38.24        12.85        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U5 
       54.77         9.04        70.49       108.13        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UD 
       17.75        42.77         4.54        14.99        44.45        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 
       34.88         9.73        12.26        26.47        72.72        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       15.95        11.47        28.96        17.79        21.63         3.06 
TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
       34.55        23.54        50.50        74.10        64.21        21.30 
TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       75.32        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM 
        7.04        17.95        14.43         9.34        59.87        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       38.17        35.77        14.07        27.95        35.54        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        12.99         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2W 
       12.39        40.60        86.10        12.07         9.21       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       13.28        50.40        22.85       101.98        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.07        20.32         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        4.57        23.97         0.10        41.33         9.80        21.37 
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-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       40.08        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A42X 
        5.92        16.41         1.05         3.91        27.29       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
        9.04        10.85         4.08        11.70        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J 
        8.32         8.28         0.49         4.34        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM 
       15.65         7.46        10.45         4.08       120.20         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 
       38.63        81.01        18.08        20.94         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VF 
       46.82        18.08        48.59        35.90       130.32        98.27 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
       62.20        10.52         0.72         3.88         6.58        17.92 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XQ 
        5.06         9.93        13.22         0.72        26.17         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        38.27        22.62         9.04        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       18.08        18.35        25.71        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.07              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           188.15            143.41 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            26.56             21.37 
[1] "0.1 - 188.2 (26.6)" "0.1 - 143.4 (21.4)"
[1] "hr=" "2.4"
D52V2, continuous
D52V3, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   33 24
  6P LOSS WILD-TYPE 99 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     33   24
  6P LOSS WILD-TYPE   99   90
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              33                99
  MALE                24                90
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       2                         3    49
  6P LOSS WILD-TYPE     4                        15   145
D52V4, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  49               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"
D52V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  48
  6P LOSS WILD-TYPE   4 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   48
  6P LOSS WILD-TYPE    4  143
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              48               143
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    36  14
  6Q LOSS WILD-TYPE 126  68
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               50               194 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14                68 
$`6Q LOSS MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-DX-A23R TCGA-DX-A3U7 
       88.57        25.25        42.84        26.56        74.66        42.77 
TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6BA 
       10.68        64.18        24.26        14.96        25.08        66.05 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM 
       66.31        67.20        16.87        21.30        34.49        48.36 
TCGA-DX-A8BL TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2V 
       33.07        14.07       124.37         8.75        49.18        96.89 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-K1-A6RV 
       20.32         0.07        15.91         0.10        80.48         4.08 
TCGA-MB-A8JL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF 
       19.73        81.01         5.03        30.90       188.15        98.27 
TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-VT-A80G 
       10.52        11.18        18.94         3.88        19.82        10.72 
TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC 
       11.93        72.72        65.46        22.62        26.43        36.82 
TCGA-X6-A8C3 TCGA-X6-A8C5 
       15.95        38.96 

$`6Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       20.05        34.68        15.06        17.75         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        34.88         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 
       12.26        27.22        26.47        72.72        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ 
       16.18         3.06        34.55        23.54        50.50        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       64.21        88.31        75.32        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ 
       48.20        14.07         7.04        17.95        14.43         9.34 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT 
       59.87        44.68        38.17        35.77        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       36.69        60.66        19.43         6.58         1.15        12.99 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S 
        4.67        12.39        40.60        86.10        12.07         9.21 
TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
       71.57       106.45        13.28        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       19.20        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.46         0.10         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
       34.88         4.57        12.62        23.97        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        40.08        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
       71.70        36.39        27.29       123.78         9.04        10.85 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       11.70        22.03        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        4.34        14.99        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP 
        4.08       120.20        37.55         6.35        38.63        18.08 
TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       20.94         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-A71O 
       35.90       130.32        62.20         0.72         6.58        17.92 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J 
       27.22         5.06         9.93        13.22         0.72        26.17 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
        4.80        41.49        38.27         9.04        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 
       18.08        18.35        25.71        16.83        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           188.15            143.41 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           25.840            22.325 
[1] "0.1 - 188.2 (25.8)" "0.1 - 143.4 (22.3)"
[1] "hr=" "1.6"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    30  20
  6Q LOSS WILD-TYPE 102  94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     30   20
  6Q LOSS WILD-TYPE  102   94
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              30               102
  MALE                20                94
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       1                         3    43
  6Q LOSS WILD-TYPE     5                        15   151
D53V4, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               3                15
  WHITE                                  43               151
[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"
D53V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  42
  6Q LOSS WILD-TYPE   4 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   42
  6Q LOSS WILD-TYPE    4  149
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              42               149
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    21   9
  7P LOSS WILD-TYPE 141  73
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               30               214 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                9                73 
$`7P LOSS MUTATED`
TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48P TCGA-DX-A48U 
        6.28        17.10        42.77        28.80        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A8BP 
       25.08         9.11        21.63        21.30        15.62        14.07 
TCGA-DX-A8BV TCGA-DX-AB2P TCGA-FX-A3TO TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IW-A3M6 
       60.66        12.07        20.32        23.97        80.48        22.62 
TCGA-K1-A42W TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5YA TCGA-PC-A5DM TCGA-PC-A5DO 
       27.29         4.08        11.70         0.49         6.35        81.01 
TCGA-SG-A6Z4 TCGA-SI-AA8C TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A8C6 TCGA-X9-A971 
       18.94         9.93        72.72        38.27        35.08        15.58 

$`7P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       18.64        26.56         0.56        14.04        32.71        38.24 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        36.69        18.54        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       42.54        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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       23.08        70.49       108.13        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       27.22        26.47        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
       23.44        28.96        17.79        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       66.31        67.20        23.54        50.50        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EO 
       64.21        88.31        34.49        75.32        48.36       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       29.49        48.20        14.07         7.04        17.95        14.43 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        59.87        33.07        44.68        38.17        35.77 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ 
      124.37        27.95        35.54        36.69        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        12.99         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
       86.10        49.18         9.21        71.57        96.89       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       13.28        50.40        22.85       101.98        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.07         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57        15.91        12.62         0.10        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        40.08        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28         5.92        16.41         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH 
       36.39       123.78         9.04        10.85        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.32         8.28         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       38.63        18.08        20.94         5.03         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
       46.82        18.08        48.59        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32        98.27        62.20        10.52         0.72        11.18 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
        3.88         6.58        17.92        19.82        27.22         5.06 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22         0.72        10.72        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       41.49        65.46        22.62         9.04        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       29.92        18.08        36.82        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       16.83        38.96        17.72        36.43 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.49              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            81.01            188.15 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           20.810            24.705 
[1] "0.5 - 81.0 (20.8)"  "0.1 - 188.2 (24.7)"
[1] "hr=" "1"  
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    12  19
  7P LOSS WILD-TYPE 120  95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     12   19
  7P LOSS WILD-TYPE  120   95
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE              12               120
  MALE                19                95
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         0    28
  7P LOSS WILD-TYPE     5                        18   166
D54V4, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 5
  BLACK OR AFRICAN AMERICAN               0                18
  WHITE                                  28               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"
D54V5, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  28
  7P LOSS WILD-TYPE   5 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   28
  7P LOSS WILD-TYPE    5  163
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              28               163
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    20  12
  7Q LOSS WILD-TYPE 142  70
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               32               212 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               12                70 
$`7Q LOSS MUTATED`
TCGA-3B-A9HQ TCGA-3B-A9HY TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48J 
       68.55        10.32        17.10        42.77        28.80         9.73 
TCGA-DX-A48P TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YU TCGA-DX-A7EN TCGA-DX-A7ET 
       14.96         9.11        21.63        23.54        15.62         7.04 
TCGA-DX-A8BG TCGA-DX-A8BP TCGA-DX-A8BV TCGA-DX-AB2P TCGA-FX-A3TO TCGA-HB-A3L4 
       17.95        14.07        60.66        12.07        20.32        34.88 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-K1-A42W TCGA-MB-A5YA TCGA-PC-A5DM 
       37.12        25.22         5.92        27.29         0.49         6.35 
TCGA-PC-A5DP TCGA-QQ-A5VA TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-SI-AA8C 
       18.08        18.08        10.52        18.94         5.06         9.93 
TCGA-WK-A8XS TCGA-WK-A8XX 
       72.72        38.27 

$`7Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        53.49        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       25.25        42.84        31.00        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        38.24        12.85        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       18.54        54.21        59.24        33.53        42.54        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        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        20.05        34.68        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
        4.54        14.99        10.68        44.45        39.35        34.88 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R 
       64.18        19.30        24.26        12.26        27.22        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       72.72        25.08        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
       23.44        28.96        17.79        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       66.31        67.20        50.50        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EO 
       88.31        21.30        34.49        75.32        48.36       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       29.49        48.20        14.07        14.43         9.34        59.87 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       33.07        44.68        38.17        35.77       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       35.54        36.69        19.43         6.58         1.15        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2Q 
        8.75         4.67        12.39        40.60        86.10        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
        9.21        71.57        96.89       106.45        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       50.89        71.31         0.46         0.10         0.07         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         2.07        48.30         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K6 
       19.53         3.22         1.38        19.89        40.08        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
      143.41       116.88        13.58        73.28        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91        71.70        36.39       123.78         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
       10.85         4.08        11.70        22.03        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        8.28         4.34        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
        7.46        10.45         4.08       120.20        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        20.94         5.03         9.83         1.84        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
       48.59        35.90        30.90       188.15       130.32        98.27 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
       62.20         0.72        11.18         3.88         6.58        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J 
       19.82        27.22        13.22         0.72        10.72        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       11.93         4.80        41.49        65.46        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       57.80        26.43        29.92        18.08        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       25.71        15.95        16.83        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.49              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            72.72            188.15 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           18.015            25.200 
[1] "0.5 - 72.7 (18.0)"  "0.1 - 188.2 (25.2)"
[1] "hr=" "1.7"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    16  17
  7Q LOSS WILD-TYPE 116  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     16   17
  7Q LOSS WILD-TYPE  116   97
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              16               116
  MALE                17                97
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         2    31
  7Q LOSS WILD-TYPE     6                        16   163
D55V4, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               2                16
  WHITE                                  31               163
[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"
D55V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  32
  7Q LOSS WILD-TYPE   5 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   32
  7Q LOSS WILD-TYPE    5  159
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              32               159
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    36  21
  8P LOSS WILD-TYPE 126  61
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               57               187 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               21                61 
$`8P LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KW 
       19.69        88.57        44.91        18.64         0.56        32.71 
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3U7 
       38.24        36.69        59.24         6.28         9.04        42.77 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48R TCGA-DX-A6BK 
       10.68        44.45         9.73        19.30        26.47        16.18 
TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BG 
       67.20        16.87        21.30        34.49         7.04        17.95 
TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       14.43        33.07        60.66         1.15        12.99         8.75 
TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-FX-A2QS TCGA-FX-A3RE 
       86.10        71.57        96.89        13.28         0.46         0.07 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A6BZ TCGA-IS-A3K7 
       34.88        15.91         0.10        41.33        19.89       143.41 
TCGA-JV-A5VE TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JK TCGA-MB-A8JL 
       16.41         4.08        11.70        13.35         4.34        19.73 
TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-VT-A80G TCGA-WK-A8XS 
       48.59         3.88        17.92        27.22        10.72        72.72 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X9-A971 
       25.71        16.83        15.58 

$`8P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        53.49        68.55        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY 
       10.32        31.00        36.03        26.56        14.04        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        42.54        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 
       59.47        54.77        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       20.05        34.68        15.06        17.75         4.54        14.99 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48N 
       39.35        28.80        34.88        64.18        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       27.22        14.96        72.72        25.08        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV 
       21.63         3.06        34.55        66.31        23.54        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       74.10        64.21        88.31        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK 
      135.48        29.49        48.20        14.07         9.34        59.87 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS 
       44.68        38.17        35.77        14.07       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-DX-AB2H 
       35.54        36.69        19.43         6.58         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2Z 
       40.60        12.07        49.18         9.21       106.45        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       50.89        71.31         0.10        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA 
        2.07        48.30         4.57        12.62        23.97         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
       80.48        21.37        19.53         3.22         1.38        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        40.08        28.21       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-MB-A5Y8 
       27.29       123.78         9.04        10.85        22.03         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        8.28         0.49        14.99        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
       10.45         4.08       120.20        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       81.01        18.08        20.94         5.03         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       46.82        18.08        35.90        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
       98.27        62.20        10.52         0.72        11.18        18.94 
TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        6.58        19.82         5.06         9.93        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       26.17        11.93         4.80        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       22.62         9.04        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       36.82        18.35        15.95        38.96        35.08        17.72 
TCGA-X9-A973 
       36.43 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.07              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           143.41            188.15 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            18.64             25.15 
[1] "0.1 - 143.4 (18.6)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.3"
D56V2, continuous
D56V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   33 25
  8P LOSS WILD-TYPE 99 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     33   25
  8P LOSS WILD-TYPE   99   89
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              33                99
  MALE                25                89
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       0                         7    42
  8P LOSS WILD-TYPE     6                        11   152
D56V4, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               7                11
  WHITE                                  42               152
[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"
D56V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     0  42
  8P LOSS WILD-TYPE   5 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   42
  8P LOSS WILD-TYPE    5  149
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              42               149
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    27  15
  8Q LOSS WILD-TYPE 135  67
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               42               202 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15                67 
$`8Q LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9I1 TCGA-DX-A1KX TCGA-DX-A1KZ 
       19.69        88.57        44.91        18.64        38.24        36.69 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3U7 TCGA-DX-A48J TCGA-DX-A48L 
       59.24         6.28         9.04        42.77         9.73        24.26 
TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI 
        3.06        67.20        16.87        74.10        21.30        34.49 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BV TCGA-DX-AATS 
        7.04        17.95        33.07        38.17        60.66         1.15 
TCGA-DX-AB2F TCGA-DX-AB2V TCGA-HB-A43Z TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 
        8.75        96.89        15.91         3.22        19.89       143.41 
TCGA-JV-A5VE TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JK TCGA-PC-A5DO 
       16.41         4.08        11.70        13.35         4.34        81.01 
TCGA-QC-AA9N TCGA-SI-AA8B TCGA-WK-A8XS TCGA-X2-A95T TCGA-X6-A8C2 TCGA-X9-A971 
        9.83         5.06        72.72        57.80        25.71        15.58 

$`8Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        53.49        68.55        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        31.00        36.03        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       32.71        12.85        18.54        54.21        33.53        42.54 
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        59.47        54.77        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 
      108.13        17.10        20.05        34.68        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88        64.18        19.30        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47        72.72        25.08        25.15        15.95        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6Z0 
       16.18        34.55        66.31        23.54        50.50        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       88.31        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM 
       48.20        14.07        14.43         9.34        59.87        44.68 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       35.77        14.07       124.37        27.95        35.54        36.69 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
       19.43         6.58        12.99         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W 
       86.10        12.07        49.18         9.21        71.57       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       13.28        50.40        22.85       101.98        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.07        20.32         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
       34.88         4.57        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ 
        9.80        80.48        21.37        19.53         1.38        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        40.08        28.21       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-MB-A5Y8 
       27.29       123.78         9.04        10.85        22.03         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        8.28         0.49        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
        7.46        10.45         4.08       120.20        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        18.08        20.94         5.03         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       18.08        48.59        35.90        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
       98.27        62.20        10.52         0.72        11.18        18.94 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
        3.88         6.58        17.92        19.82        27.22         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22         0.72        10.72        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 
       41.49        38.27        65.46        22.62         9.04        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       29.92        18.08        36.82        18.35        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       38.96        35.08        17.72        36.43 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.15              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           143.41            188.15 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           19.790            23.755 
[1] "1.1 - 143.4 (19.8)" "0.1 - 188.2 (23.8)"
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    26  17
  8Q LOSS WILD-TYPE 106  97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     26   17
  8Q LOSS WILD-TYPE  106   97
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              26               106
  MALE                17                97
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         6    31
  8Q LOSS WILD-TYPE     6                        12   163
D57V4, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  31               163
[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"
D57V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  35
  8Q LOSS WILD-TYPE   5 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   35
  8Q LOSS WILD-TYPE    5  156
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              35               156
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    50  31
  9P LOSS WILD-TYPE 112  51
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               81               163 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               31                51 
$`9P LOSS MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       88.57        44.91        31.00        18.64        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LW 
       14.04        12.85        66.87         6.28         9.04       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A3UF 
       17.10        20.05        34.68        42.77        28.80        64.18 
TCGA-DX-A48J TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BF 
        9.73        26.47        25.08        25.15        66.05         9.11 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        34.55        66.31        16.87        74.10        64.21 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EQ TCGA-DX-A8BJ TCGA-DX-A8BN 
       21.30        34.49        75.32        29.49         9.34        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       35.77        14.07       124.37         6.58        12.99         8.75 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3RE 
       40.60        12.07       101.98        32.15         0.46         0.07 
TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 
       48.30         0.10        80.48        19.53         3.22       143.41 
TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A6RU TCGA-LI-A9QH TCGA-MB-A5Y8 
        5.92         3.91        27.29        10.85        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO 
        8.28        19.73        10.45         4.08        38.63        81.01 
TCGA-QC-A7B5 TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71Q 
        5.03        35.90       188.15        10.52        11.18        27.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        0.72        10.72        26.17        38.27        65.46        22.62 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A971 
       15.95        16.83        15.58 

$`9P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        19.69        53.49        68.55        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ 
       42.84        10.32        36.03        32.71        38.24        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       18.54        54.21        59.24        33.53        42.54        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
        5.26        76.41        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3U5 TCGA-DX-A3U6 
       59.47        54.77        23.08        70.49        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
        4.54        14.99        10.68        44.45        39.35        34.88 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       15.95        11.47        23.44        28.96        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EM 
       16.18        67.20        23.54        50.50        88.31        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
       15.62       135.48        48.20        14.07         7.04        17.95 
TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-A8BT 
       14.43        59.87        33.07        44.68        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2G TCGA-DX-AB2H 
       36.69        60.66        19.43         1.15         4.67        12.39 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
       86.10        49.18         9.21        71.57        96.89       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       13.28        50.40        22.85        19.20        60.00        84.66 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       50.89        71.31         0.10        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        2.07        34.88         4.57        15.91        12.62        23.97 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       41.33         9.80        21.37         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        40.08        28.21       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       22.62        16.41         1.05        71.70        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK 
        9.04         4.08        11.70        22.03         0.49         4.34 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL 
       14.99        17.98        15.65         7.46       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
        6.35        18.08        20.94         9.83         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       18.08        48.59        30.90       130.32        98.27        62.20 
TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        18.94         3.88         6.58        17.92        19.82 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
        5.06         9.93        13.22        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       41.49         9.04        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       36.82        18.35        25.71        38.96        35.08        17.72 
TCGA-X9-A973 
       36.43 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           188.15            135.48 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            21.30             23.54 
[1] "0.1 - 188.2 (21.3)" "0.1 - 135.5 (23.5)"
[1] "hr=" "1.3"
D58V2, continuous
D58V3, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   48 33
  9P LOSS WILD-TYPE 84 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     48   33
  9P LOSS WILD-TYPE   84   81
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              48                84
  MALE                33                81
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       3                         7    64
  9P LOSS WILD-TYPE     3                        11   130
D58V4, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   3                 3
  BLACK OR AFRICAN AMERICAN               7                11
  WHITE                                  64               130
[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"
D58V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     1  63
  9P LOSS WILD-TYPE   4 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   63
  9P LOSS WILD-TYPE    4  128
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              63               128
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    26  23
  9Q LOSS WILD-TYPE 136  59
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               49               195 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23                59 
$`9Q LOSS MUTATED`
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23Y 
       18.64        26.56         0.56        14.04        12.85         6.28 
TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48R 
        9.04       108.13        34.68        28.80         9.73        26.47 
TCGA-DX-A48V TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       25.08         9.11        66.31        16.87        74.10        64.21 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-AB2E 
       21.30        34.49         9.34        38.17       124.37        12.99 
TCGA-DX-AB2T TCGA-DX-AB3A TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IS-A3K7 
       71.57        32.15        48.30         0.10        80.48       143.41 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A6RV TCGA-MB-A5Y8 TCGA-MB-A8JL 
       13.58         5.92         3.91         4.08         8.32        19.73 
TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DO TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ 
       14.99        10.45        81.01       188.15        10.52        11.18 
TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XX TCGA-WP-A9GB 
        3.88        27.22         0.72        10.72        38.27         9.04 
TCGA-X6-A8C4 
       16.83 

$`9Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       32.71        38.24        36.69        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        72.72        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       23.44        28.96        17.79        21.63        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EL 
       34.55        67.20        23.54        50.50        88.31        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
        7.04        17.95        14.43        59.87        33.07        44.68 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       35.77        14.07        27.95        35.54        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       19.43         6.58         1.15         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V 
       40.60        86.10        12.07        49.18         9.21        96.89 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
      106.45        13.28        50.40        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       60.00        84.66        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
        0.07        20.32         0.07         0.07         2.07        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57        15.91        12.62        23.97        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       25.22        40.08        28.21       116.88        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       16.41         1.05        71.70        36.39        27.29       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
        9.04        10.85        11.70        22.03        13.35         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
        0.49         4.34        17.98        15.65         7.46         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX 
      120.20        37.55         6.35        38.63        18.08        20.94 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.03         9.83         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        30.90       130.32        98.27        62.20         0.72 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C 
       18.94         6.58        17.92        19.82         5.06         9.93 
TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       13.22        26.17        11.93         4.80        72.72        41.49 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       65.46        22.62        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 
       36.82        18.35        25.71        15.95        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.10              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           188.15            135.48 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            16.87             24.26 
[1] "0.1 - 188.2 (16.9)" "0.1 - 135.5 (24.3)"
[1] "hr=" "1.7"
D59V2, continuous
D59V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    28  21
  9Q LOSS WILD-TYPE 104  93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     28   21
  9Q LOSS WILD-TYPE  104   93
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              28               104
  MALE                21                93
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       2                         6    36
  9Q LOSS WILD-TYPE     4                        12   158
D59V4, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  36               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"
D59V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  35
  9Q LOSS WILD-TYPE   4 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   35
  9Q LOSS WILD-TYPE    4  156
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              35               156
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   79 36
  10P LOSS WILD-TYPE 83 46
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               115                129 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                 46 
$`10P LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HY 
       19.69        53.49        68.55        88.57        44.91        10.32 
TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R 
       36.03        26.56        32.71        38.24        18.54        74.66 
TCGA-DX-A23Y TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K 
        6.28        14.99        10.68        34.88        64.18        19.30 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU 
       23.44         9.11        16.18         3.06        34.55        23.54 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7ET 
       16.87        64.21        88.31        75.32        48.36         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR 
       17.95        14.43         9.34        44.68        35.77       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2O 
       27.95        35.54        60.66         6.58         8.75        86.10 
TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB3C TCGA-FX-A2QS 
       12.07        96.89        22.85       101.98        71.31         0.46 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
        0.07        20.32         0.07         0.07        48.30         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI 
       15.91        12.62        23.97         0.10        80.48        19.53 
TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 
        3.22        25.22        40.08       143.41         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU TCGA-KF-A41W 
       16.41         3.91        71.70        27.29        10.85        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       13.35         8.32         0.49         4.34        19.73        14.99 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A6FX 
       10.45         4.08       120.20        37.55        81.01        20.94 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        5.03         9.83        46.82        48.59        35.90        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
      188.15        10.52        11.18         6.58        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO 
       27.22         5.06         9.93         0.72        26.17        11.93 
TCGA-WK-A8XS TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 
       72.72        26.43        29.92        18.35        15.95        38.96 
TCGA-X9-A971 
       15.58 

$`10P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I1 
       36.30        54.74        25.25        42.84        31.00        18.64 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
        0.56        14.04        12.85        36.69        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        42.54         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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
       23.08        70.49       108.13        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77         4.54        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U 
       28.80         9.73        24.26        12.26        27.22        72.72 
TCGA-DX-A48V TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YT 
       25.08        28.96        17.79        21.63        66.31        67.20 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO 
       50.50        74.10        21.30        34.49        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN 
       29.49        48.20        14.07        59.87        33.07        38.17 
TCGA-DX-A8BP TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G 
       14.07        36.69        19.43         1.15        12.99         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W 
       12.39        40.60        49.18         9.21        71.57       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       13.28        50.40        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-FX-A3NJ TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N9 TCGA-HS-A5NA 
       50.89         0.10         2.07        34.88        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K8 
       21.37         1.38        19.89        37.12        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
       13.58        73.28         1.05        36.39       123.78         9.04 
TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.08        22.03         8.28        17.98        15.65         7.46 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD 
        6.35        38.63        18.08         1.84        18.08       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-UE-A6QT 
       98.27        62.20         0.72        18.94         3.88        13.22 
TCGA-VT-A80G TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       10.72         4.80        41.49        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 
        9.04        57.80        18.08        36.82        25.71        16.83 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       35.08        17.72        36.43 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            188.15             135.48 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             19.82              27.22 
[1] "0.1 - 188.2 (19.8)" "0.1 - 135.5 (27.2)"
[1] "hr=" "1"  
D60V2, continuous
D60V3, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   73 43
  10P LOSS WILD-TYPE 59 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     73   43
  10P LOSS WILD-TYPE   59   71
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               73                 59
  MALE                 43                 71
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       4                        12    91
  10P LOSS WILD-TYPE     2                         6   103
D60V4, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    4                  2
  BLACK OR AFRICAN AMERICAN               12                  6
  WHITE                                   91                103
[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"
D60V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1 97
  10P LOSS WILD-TYPE  4 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   97
  10P LOSS WILD-TYPE    4   94
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               97                 94
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   84 41
  10Q LOSS WILD-TYPE 78 41
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               125                119 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                41                 41 
$`10Q LOSS MUTATED`
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HY 
       53.49        68.55        88.57        44.91        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23Y 
       31.00        36.03        26.56        38.24        18.54         6.28 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
       42.77        14.99        10.68        39.35        34.88        64.18 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF 
       25.15        15.95        11.47        66.05        23.44         9.11 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18         3.06        34.55        23.54        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BG 
       64.21        88.31        75.32        48.36         7.04        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       14.43         9.34        35.77       124.37        27.95        35.54 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O 
       60.66         6.58         1.15        12.99         8.75        86.10 
TCGA-DX-AB2P TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       12.07        71.57        96.89         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
       20.32         0.07         0.07        48.30         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       12.62        23.97         0.10        80.48        21.37        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        3.22         1.38        19.89        25.22        40.08        28.21 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
      143.41        13.58        22.62        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 
       71.70        27.29        10.85        11.70        13.35         8.32 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
        0.49         4.34        14.99        10.45         4.08        37.55 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V9 
        6.35        81.01        18.08        20.94         5.03        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ 
       48.59        35.90        30.90       188.15        10.52        11.18 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G 
       18.94         6.58        17.92         5.06         0.72        10.72 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       72.72        65.46        22.62        26.43        29.92        18.08 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X9-A971 
       18.35        25.71        15.95        38.96        15.58 

$`10Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX 
       36.30        19.69        54.74        42.84        18.64         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        32.71        12.85        36.69        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD 
       34.68        15.06        17.75         4.54        44.45        28.80 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48V TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
        9.73        12.26        25.08        28.96        17.79        21.63 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN 
       66.31        67.20        50.50        21.30        34.49        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL 
      135.48        29.49        48.20        14.07        59.87        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AB2G 
       44.68        38.17        14.07        36.69        19.43         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2X 
       12.39        40.60        49.18         9.21       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       50.40        22.85       101.98        19.20        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N9 
       32.15        50.89        71.31         2.07        34.88        41.33 
TCGA-HS-A5NA TCGA-IF-A3RQ TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-K1-A3PO 
        9.80        37.12       116.88        73.28         5.92        36.39 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A8JL 
      123.78         9.04         4.08        22.03         8.28        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QC-AA9N 
       17.98        15.65         7.46       120.20        38.63         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
        1.84        18.08       130.32        98.27        62.20         0.72 
TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J 
        3.88        19.82        27.22         9.93        13.22        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T 
       11.93         4.80        41.49        38.27         9.04        57.80 
TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       36.82        16.83        35.08        17.72        36.43 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.56 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            188.15             135.48 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             19.89              28.96 
[1] "0.1 - 188.2 (19.9)" "0.6 - 135.5 (29.0)"
[1] "hr=" "1.2"
D61V2, continuous
D61V3, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   78 48
  10Q LOSS WILD-TYPE 54 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     78   48
  10Q LOSS WILD-TYPE   54   66
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               78                 54
  MALE                 48                 66
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       4                        13   102
  10Q LOSS WILD-TYPE     2                         5    92
D61V4, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    4                  2
  BLACK OR AFRICAN AMERICAN               13                  5
  WHITE                                  102                 92
[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"
D61V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1 110
  10Q LOSS WILD-TYPE   4  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1  110
  10Q LOSS WILD-TYPE    4   81
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO              110                 81
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    56  34
  11P LOSS WILD-TYPE 106  48
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                90                154 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                34                 48 
$`11P LOSS MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KW 
       88.57        44.91        42.84        18.64         0.56        32.71 
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y 
       38.24        36.69        18.54        59.24        74.66         6.28 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.70        59.47        23.08       108.13        17.10        20.05 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       14.99        28.80        64.18        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YT 
       14.96        15.95         9.11         3.06        66.31        67.20 
TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BG 
       23.54        74.10        34.49        48.36         7.04        17.95 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV 
       59.87        44.68        35.77        27.95        36.69        60.66 
TCGA-DX-AB2G TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3B 
        4.67        71.57        96.89        19.20        84.66        50.89 
TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        48.30         4.57        15.91        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
        0.10        41.33        19.89        37.12        25.22        40.08 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42W TCGA-LI-A9QH 
        5.92        22.62         1.05        71.70        27.29        13.35 
TCGA-MB-A8JK TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QQ-A8VB 
        4.34        10.45        37.55         6.35        81.01       188.15 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B 
       11.18        18.94         3.88        17.92        19.82         5.06 
TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        9.93        10.72        72.72        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X9-A971 
        9.04        18.08        36.82        16.83        35.08        15.58 

$`11P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        19.69        53.49        68.55        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY 
       10.32        31.00        36.03        26.56        14.04        12.85 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       54.21        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       27.81        60.30         8.58        54.77         9.04        70.49 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       34.68        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48R 
       44.45        39.35        34.88         9.73        19.30        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        25.15        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YV 
       28.96        17.79        21.63        16.18        34.55        50.50 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EN 
       16.87        64.21        88.31        21.30        75.32        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BJ 
      135.48        29.49        48.20        14.07        14.43         9.34 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX 
       33.07        38.17        14.07       124.37        35.54        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2J 
        6.58         1.15        12.99         8.75        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2X 
       86.10        12.07        49.18         9.21       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3C 
       50.40        22.85       101.98        60.00        32.15        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.46         0.10        20.32         0.07         0.07         2.07 
TCGA-HB-A3L4 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       34.88         9.80        80.48        21.37        19.53         3.22 
TCGA-IE-A4EK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        28.21       143.41       116.88        13.58        73.28 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
       16.41         3.91        36.39       123.78         9.04        10.85 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        4.08        11.70        22.03         8.32         8.28         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        15.65         7.46         4.08 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
      120.20        38.63        18.08        20.94         5.03         9.83 
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        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 
      130.32        98.27        62.20        10.52         0.72         6.58 
TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       27.22        13.22         0.72        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 
       41.49        57.80        26.43        29.92        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       15.95        38.96        17.72        36.43 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            188.15             143.41 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            23.755             22.440 
[1] "0.1 - 188.2 (23.8)" "0.1 - 143.4 (22.4)"
[1] "hr=" "1.2"
D62V2, continuous
D62V3, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   50 41
  11P LOSS WILD-TYPE 82 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     50   41
  11P LOSS WILD-TYPE   82   73
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               50                 82
  MALE                 41                 73
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       2                         7    68
  11P LOSS WILD-TYPE     4                        11   126
D62V4, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                7                 11
  WHITE                                   68                126
[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"
D62V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  72
  11P LOSS WILD-TYPE   5 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   72
  11P LOSS WILD-TYPE    5  119
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               72                119
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    60  26
  11Q LOSS WILD-TYPE 102  56
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                86                158 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                 56 
$`11Q LOSS MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3R-A8YX TCGA-DX-A1KW 
       88.57        44.91        42.84        31.00         0.56        32.71 
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y 
       38.24        36.69        18.54        59.24        74.66         6.28 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UD 
        9.70        59.47        23.08        20.05        14.99        28.80 
TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF 
       12.26        26.47        72.72        15.95        66.05         9.11 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A7EI 
       16.18        66.31        67.20        23.54        74.10        34.49 
TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO 
       48.36         7.04        17.95        59.87        44.68        35.77 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2G TCGA-DX-AB2O 
       27.95        35.54        36.69        60.66         4.67        86.10 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3B 
       71.57        96.89       101.98        19.20        84.66        50.89 
TCGA-FX-A2QS TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 
        0.46        48.30         4.57        12.62         0.10        41.33 
TCGA-IE-A3OV TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IW-A3M5 TCGA-IW-A3M6 
       80.48        19.89        37.12        40.08         5.92        22.62 
TCGA-JV-A5VF TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JK 
        1.05        27.29        22.03        13.35         8.32         4.34 
TCGA-QC-AA9N TCGA-QQ-A8VB TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
        9.83       188.15        11.18        18.94         3.88        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XS 
       19.82        27.22         5.06         9.93        10.72        72.72 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A8C3 
       38.27        65.46        22.62         9.04        36.82        15.95 
TCGA-X6-A8C4 TCGA-X9-A971 
       16.83        15.58 

$`11Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        19.69        53.49        68.55        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY 
       10.32        36.03        18.64        26.56        14.04        12.85 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       54.21        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       27.81        60.30         8.58        54.77         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
        4.54        10.68        44.45        39.35        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V 
        9.73        19.30        24.26        27.22        14.96        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       25.15        11.47        23.44        28.96        17.79        21.63 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
        3.06        34.55        50.50        16.87        64.21        88.31 
TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        75.32        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BP 
       14.07        14.43         9.34        33.07        38.17        14.07 
TCGA-DX-A8BR TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
      124.37        19.43         6.58         1.15        12.99         8.75 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2W 
       12.39        40.60        12.07        49.18         9.21       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3C 
       13.28        50.40        22.85        60.00        32.15        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.10         0.07        20.32         0.07         0.07         2.07 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI 
       34.88        15.91        23.97         9.80        21.37        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        3.22         1.38        25.22        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28        16.41         3.91        71.70        36.39 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y9 
      123.78         9.04        10.85         4.08        11.70         8.28 
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        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
       10.45         4.08       120.20        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        18.08        20.94         5.03         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        30.90       130.32        98.27 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU 
       62.20        10.52         0.72         6.58        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X2-A95T TCGA-X6-A7W8 
       26.17        11.93         4.80        41.49        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C6 
       29.92        18.08        18.35        25.71        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A973 
       17.72        36.43 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.10               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            188.15             143.41 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            26.845             21.500 
[1] "0.1 - 188.2 (26.8)" "0.1 - 143.4 (21.5)"
[1] "hr=" "1.3"
D63V2, continuous
D63V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   47 40
  11Q LOSS WILD-TYPE 85 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     47   40
  11Q LOSS WILD-TYPE   85   74
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               47                 85
  MALE                 40                 74
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         8    65
  11Q LOSS WILD-TYPE     4                        10   129
D63V4, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN                8                 10
  WHITE                                   65                129
[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"
D63V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  65
  11Q LOSS WILD-TYPE   5 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   65
  11Q LOSS WILD-TYPE    5  126
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               65                126
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    45  18
  12P LOSS WILD-TYPE 117  64
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                63                181 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                18                 64 
$`12P LOSS MUTATED`
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-A3M2 TCGA-DX-A3U9 TCGA-DX-A3UD 
        8.58         9.70        17.10        34.68        14.99        28.80 
TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6BF 
       64.18        26.47        25.08        25.15        15.95         9.11 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6Z2 
        3.06        34.55        67.20        23.54        50.50        88.31 
TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BL 
       21.30        48.36        15.62         7.04        59.87        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU 
       44.68        38.17        35.77       124.37        27.95        36.69 
TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2T TCGA-DX-AB35 TCGA-FX-A3NJ 
       60.66         8.75        12.39        71.57        19.20         0.10 
TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-JV-A5VF 
       23.97        21.37         3.22        19.89        16.41         1.05 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MJ-A68H TCGA-PC-A5DM TCGA-QC-A6FX 
        4.08        11.70        13.35        14.99         6.35        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-WK-A8XS 
        5.03        48.59        18.94         3.88        17.92        72.72 
TCGA-WK-A8XX TCGA-X2-A95T TCGA-X6-A7WD 
       38.27        57.80        18.35 

$`12P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX 
       25.25        42.84        10.32        31.00        36.03         0.56 
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04        38.24        12.85        36.69        18.54        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       27.81        60.30        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       70.49       108.13        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        10.68        44.45        39.35        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        66.05        23.44        28.96        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI 
       16.18        66.31        16.87        74.10        64.21        34.49 
TCGA-DX-A7EL TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG 
       75.32       135.48        29.49        48.20        14.07        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BP TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ 
       14.43         9.34        14.07        35.54        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
        1.15        12.99         4.67        40.60        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
       49.18         9.21        96.89       106.45        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85       101.98        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       71.31         0.46         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        2.07        48.30        34.88         4.57        15.91        12.62 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK 
        0.10        41.33         9.80        80.48        19.53         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        40.08        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A3PN 
       13.58        73.28         5.92        22.62         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I 
       36.39        27.29       123.78         9.04        10.85        22.03 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
        8.32         8.28         0.49         4.34        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        81.01        18.08         9.83         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
       18.08        35.90        30.90       188.15       130.32        98.27 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-A71P 
       62.20        10.52         0.72        11.18         6.58        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       27.22         5.06         9.93        13.22         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 
       26.17        11.93         4.80        41.49        65.46        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
        9.04        26.43        29.92        18.08        36.82        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       15.95        16.83        38.96        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.10               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            124.37             188.15 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             21.37              23.44 
[1] "0.1 - 124.4 (21.4)" "0.1 - 188.2 (23.4)"
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    32  31
  12P LOSS WILD-TYPE 100  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     32   31
  12P LOSS WILD-TYPE  100   83
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               32                100
  MALE                 31                 83
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         7    49
  12P LOSS WILD-TYPE     6                        11   145
D64V4, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                7                 11
  WHITE                                   49                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"
D64V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  52
  12P LOSS WILD-TYPE   5 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   52
  12P LOSS WILD-TYPE    5  139
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               52                139
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    36  16
  12Q LOSS WILD-TYPE 126  66
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                52                192 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                16                 66 
$`12Q LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HU TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1L1 
       19.69        25.25        31.00        26.56        32.71        54.21 
TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LY TCGA-DX-A3UF 
       74.66         8.58         9.70         9.04        17.10        64.18 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YU TCGA-DX-A6YV 
       26.47        15.95        66.05         9.11        23.54        50.50 
TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET TCGA-DX-A8BK 
       16.87        21.30        48.36        15.62         7.04        59.87 
TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2P 
       38.17       124.37        12.99         8.75        12.39        12.07 
TCGA-DX-AB2T TCGA-DX-AB35 TCGA-FX-A3NJ TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IE-A4EJ 
       71.57        19.20         0.10        23.97        21.37         3.22 
TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KF-A41W TCGA-MB-A8JK TCGA-MJ-A68H 
       19.89        16.41         1.05        11.70         4.34        14.99 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-WK-A8XS 
        6.35        81.01         5.03        48.59         3.88        72.72 
TCGA-WK-A8XX TCGA-X2-A95T TCGA-X6-A7WD TCGA-X9-A971 
       38.27        57.80        18.35        15.58 

$`12Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU 
       42.84        10.32        36.03        18.64         0.56        14.04 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
       38.24        12.85        36.69        18.54        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       42.54         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       60.30        59.47        54.77        23.08        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       20.05        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        25.15        11.47        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       17.79        21.63        16.18         3.06        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL 
       67.20        74.10        64.21        88.31        34.49        75.32 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BH 
      135.48        29.49        48.20        14.07        17.95        14.43 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS 
        9.34        33.07        44.68        35.77        14.07        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.54        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V 
        4.67        40.60        86.10        49.18         9.21        96.89 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
      106.45        13.28        50.40        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE 
       84.66        32.15        50.89        71.31         0.46         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57        15.91        12.62         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
       80.48        19.53         1.38        37.12        25.22        40.08 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       22.62         3.91        71.70        36.39        27.29       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
        9.04        10.85         4.08        22.03        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        8.28         0.49        19.73        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP 
       10.45         4.08       120.20        37.55        38.63        18.08 
TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       20.94         9.83         1.84        46.82        18.08        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       30.90       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        11.18        18.94         6.58        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G 
       27.22         5.06         9.93        13.22         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 
       26.17        11.93         4.80        41.49        65.46        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
        9.04        26.43        29.92        18.08        36.82        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       15.95        16.83        38.96        35.08        17.72        36.43 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.10               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            124.37             188.15 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            19.445             25.185 
[1] "0.1 - 124.4 (19.4)" "0.1 - 188.2 (25.2)"
[1] "hr=" "1.1"
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    31  21
  12Q LOSS WILD-TYPE 101  93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     31   21
  12Q LOSS WILD-TYPE  101   93
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               31                101
  MALE                 21                 93
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         6    39
  12Q LOSS WILD-TYPE     6                        12   155
D65V4, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                6                 12
  WHITE                                   39                155
[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"
D65V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  41
  12Q LOSS WILD-TYPE   5 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   41
  12Q LOSS WILD-TYPE    5  150
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               41                150
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   86 44
  13Q LOSS WILD-TYPE 76 38
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               130                114 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                44                 38 
$`13Q LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       19.69        68.55        88.57        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        31.00        18.64        26.56         0.56        14.04 
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y 
       38.24        36.69        18.54        54.21        74.66         6.28 
TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 
        9.70         9.04        23.08        17.10        20.05        14.99 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       39.35        28.80        64.18         9.73        19.30        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB 
       27.22        14.96        25.08        15.95        66.05        23.44 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
        9.11        16.18         3.06        66.31        67.20        23.54 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL 
       16.87        74.10        64.21        88.31        21.30        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       48.36        15.62         7.04        14.43         9.34        59.87 
TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-AATS 
       33.07        35.77        14.07        35.54        36.69         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W 
       12.99         8.75        86.10        49.18        96.89       106.45 
TCGA-DX-AB2Z TCGA-DX-AB35 TCGA-DX-AB3B TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       50.40        19.20        50.89         0.07        20.32         0.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       48.30        34.88         4.57        15.91        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 
        0.10         9.80         3.22        19.89        37.12       143.41 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W 
       73.28        22.62         1.05         3.91        71.70        27.29 
TCGA-K1-A6RU TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MO-A47R 
       10.85        11.70         8.32         8.28        19.73        10.45 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 
        4.08        37.55         6.35        81.01        20.94         5.03 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VH 
       46.82        18.08        48.59        35.90       188.15        10.52 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       11.18        18.94         3.88         6.58        17.92        19.82 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XS 
        5.06         9.93        10.72        26.17        11.93        72.72 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC 
       38.27        65.46        22.62        26.43        29.92        36.82 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       15.95        16.83        38.96        35.08 

$`13Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HS TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KY 
       36.30        53.49        44.91        36.03        32.71        12.85 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU 
       27.81        60.30         8.58        59.47        54.77        70.49 
TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
      108.13        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U 
       10.68        44.45        34.88        12.26        26.47        72.72 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR 
       25.15        11.47        28.96        17.79        21.63        34.55 
TCGA-DX-A6YV TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       50.50        34.49       135.48        29.49        48.20        14.07 
TCGA-DX-A8BG TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BV 
       17.95        44.68        38.17       124.37        27.95        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       19.43         6.58         4.67        12.39        40.60        12.07 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
        9.21        71.57        13.28        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y 
       84.66        32.15        71.31         0.46         0.10         0.07 
TCGA-FX-A8OO TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
        2.07        41.33        80.48        21.37        19.53         1.38 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 
       25.22        40.08        28.21       116.88        13.58         5.92 
TCGA-JV-A5VE TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I 
       16.41        36.39       123.78         9.04         4.08        22.03 
TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       13.35         0.49         4.34        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 
        7.46       120.20        38.63        18.08         9.83         1.84 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SI-A71Q 
       30.90       130.32        98.27        62.20         0.72        27.22 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WP-A9GB TCGA-X2-A95T 
       13.22         0.72         4.80        41.49         9.04        57.80 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       18.08        18.35        25.71        17.72        15.58        36.43 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            188.15             135.48 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            21.120             26.845 
[1] "0.1 - 188.2 (21.1)" "0.1 - 135.5 (26.8)"
[1] "hr=" "1.1"
D66V2, continuous
D66V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   77 53
  13Q LOSS WILD-TYPE 55 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     77   53
  13Q LOSS WILD-TYPE   55   61
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               77                 55
  MALE                 53                 61
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       3                         9   105
  13Q LOSS WILD-TYPE     3                         9    89
D66V4, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    3                  3
  BLACK OR AFRICAN AMERICAN                9                  9
  WHITE                                  105                 89
[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"
D66V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     2 107
  13Q LOSS WILD-TYPE   3  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2  107
  13Q LOSS WILD-TYPE    3   84
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              107                 84
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    45  14
  14Q LOSS WILD-TYPE 117  68
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                59                185 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                14                 68 
$`14Q LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       19.69        42.84        26.56        14.04        32.71        38.24 
TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
       36.69        59.24        74.66        23.08        70.49        17.10 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       34.68        15.06        12.26        27.22        14.96        72.72 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A8BM 
       25.15        15.95        23.54        74.10        88.31        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2O 
       38.17        35.77        35.54        36.69         6.58        86.10 
TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB35 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G 
       12.07       101.98        19.20         0.46         0.10         0.07 
TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IF-A3RQ 
        0.07        34.88         0.10         9.80         3.22        37.12 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF 
       28.21       143.41       116.88        73.28        16.41         1.05 
TCGA-K1-A42X TCGA-MB-A5Y8 TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-RN-AAAQ TCGA-SI-A71P 
      123.78         8.32         5.03        46.82        11.18        19.82 
TCGA-SI-AA8B TCGA-VT-A80G TCGA-WP-A9GB TCGA-X6-A7WB TCGA-X6-A8C2 
        5.06        10.72         9.04        18.08        25.71 

$`14Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       25.25        10.32        31.00        36.03        18.64         0.56 
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       12.85        18.54        54.21        33.53        42.54         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-A3LW TCGA-DX-A3M1 
        9.70        59.47        54.77         9.04       108.13        20.05 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       24.26        26.47        25.08        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         9.11        17.79        21.63        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 
       34.55        66.31        67.20        50.50        16.87        64.21 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       21.30        34.49        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       29.49        48.20        14.07         7.04        17.95        14.43 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS 
        9.34        59.87        33.07        14.07       124.37        27.95 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       60.66        19.43         1.15        12.99         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       12.39        40.60        49.18         9.21        71.57        96.89 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 
      106.45        13.28        50.40        22.85        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A8OO 
       32.15        50.89        71.31         0.07        20.32         2.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
       48.30         4.57        15.91        12.62        23.97        41.33 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
       80.48        21.37        19.53         1.38        19.89        25.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A3PN 
       40.08        13.58         5.92        22.62         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W 
       36.39        27.29         9.04        10.85         4.08        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       22.03        13.35         8.28         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        15.65         7.46        10.45         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
      120.20        37.55         6.35        38.63        81.01        18.08 
TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       20.94         9.83         1.84        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       30.90       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71Q 
        0.72        18.94         3.88         6.58        17.92        27.22 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
        9.93        13.22         0.72        26.17        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
       72.72        41.49        38.27        65.46        22.62        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       26.43        29.92        36.82        18.35        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       38.96        35.08        17.72        15.58        36.43 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            143.41             188.15 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             25.15              22.62 
[1] "0.1 - 143.4 (25.1)" "0.1 - 188.2 (22.6)"
[1] "hr=" "1.6"
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    31  28
  14Q LOSS WILD-TYPE 101  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     31   28
  14Q LOSS WILD-TYPE  101   86
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               31                101
  MALE                 28                 86
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       0                         3    49
  14Q LOSS WILD-TYPE     6                        15   145
D67V4, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                3                 15
  WHITE                                   49                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"
D67V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     0  44
  14Q LOSS WILD-TYPE   5 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0   44
  14Q LOSS WILD-TYPE    5  147
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               44                147
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    17  23
  15Q LOSS WILD-TYPE 145  59
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                40                204 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                23                 59 
$`15Q LOSS MUTATED`
TCGA-3B-A9HL TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3UA 
       19.69        14.04        32.71         9.04        23.08        10.68 
TCGA-DX-A3UB TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YZ 
       44.45        26.47        15.95         9.11         3.06        74.10 
TCGA-DX-A7EF TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       21.30         7.04        14.43        59.87        33.07        44.68 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB37 TCGA-DX-AB3A 
       27.95        35.54        60.66         6.58        84.66        32.15 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 
       20.32         0.07         4.57        37.12       143.41         5.92 
TCGA-JV-A5VE TCGA-KF-A41W TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A8VH 
       16.41        11.70         6.35         5.03         9.83        10.52 
TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X6-A7WB TCGA-X6-A8C6 
       38.27        22.62        18.08        35.08 

$`15Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        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        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
        9.70        59.47        54.77        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       20.05        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       14.99        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        25.15        11.47        66.05        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
       17.79        21.63        16.18        34.55        66.31        67.20 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       23.54        50.50        16.87        64.21        88.31        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP 
       14.07        17.95         9.34        38.17        35.77        14.07 
TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
      124.37        36.69        19.43         1.15        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        4.67        12.39        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
        9.21        71.57        96.89       106.45        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3B TCGA-DX-AB3C 
       22.85       101.98        19.20        60.00        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.46         0.10         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
       34.88        15.91        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
       19.89        25.22        40.08        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       73.28        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I 
       27.29       123.78         9.04        10.85         4.08        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35         8.32         8.28         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        15.65         7.46        10.45         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
      120.20        37.55        38.63        81.01        18.08        20.94 
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        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
      188.15       130.32        98.27        62.20         0.72        11.18 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       18.94         3.88         6.58        17.92        19.82        27.22 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J 
        5.06         9.93        13.22         0.72        10.72        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WP-A9GB 
       11.93         4.80        72.72        41.49        65.46         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        26.43        29.92        36.82        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       15.95        16.83        38.96        17.72        15.58        36.43 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            143.41             188.15 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            20.005             24.670 
[1] "0.1 - 143.4 (20.0)" "0.1 - 188.2 (24.7)"
[1] "hr=" "2.5"
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20  22
  15Q LOSS WILD-TYPE 112  92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20   22
  15Q LOSS WILD-TYPE  112   92
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               20                112
  MALE                 22                 92
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         5    35
  15Q LOSS WILD-TYPE     6                        13   159
D68V4, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   35                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"
D68V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0  36
  15Q LOSS WILD-TYPE   5 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   36
  15Q LOSS WILD-TYPE    5  155
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               36                155
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    47  24
  16P LOSS WILD-TYPE 115  58
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                71                173 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                24                 58 
$`16P LOSS MUTATED`
TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R 
       88.57        18.64         0.56        18.54        59.24        74.66 
TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF 
        6.28        23.08        42.77        10.68        28.80        64.18 
TCGA-DX-A48O TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YT TCGA-DX-A6YZ TCGA-DX-A8BJ 
       27.22        15.95        66.05        67.20        74.10         9.34 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ 
       35.77        14.07       124.37        36.69        60.66         6.58 
TCGA-DX-AATS TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB3A 
        1.15        49.18        71.57       106.45        50.40        32.15 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 
       20.32         0.07         4.57        15.91        12.62         0.10 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-JV-A5VF 
        3.22        19.89        37.12       143.41        16.41         1.05 
TCGA-K1-A3PN TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A8JL TCGA-MJ-A68H TCGA-N1-A6IA 
       71.70         4.08        11.70        19.73        14.99         4.08 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD 
       20.94         5.03         9.83        46.82        35.90        30.90 
TCGA-QQ-A8VH TCGA-SG-A849 TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G 
       10.52         6.58         5.06         9.93         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WB 
       26.17        72.72        38.27        22.62         9.04        18.08 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X9-A973 
       18.35        25.71        16.83        35.08        36.43 

$`16P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        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        31.00        36.03        26.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04        32.71        38.24        12.85        36.69        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        42.54         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        59.47        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       70.49       108.13        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       17.75         4.54        14.99        44.45        39.35        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        24.26        12.26        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        25.15        11.47        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       66.31        23.54        50.50        16.87        64.21        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       21.30        34.49        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       29.49        48.20        14.07         7.04        17.95        14.43 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT 
       59.87        33.07        44.68        38.17        27.95        35.54 
TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
       19.43        12.99         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB30 
       86.10        12.07         9.21        96.89        13.28        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C 
      101.98        19.20        60.00        84.66        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.46         0.10         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       34.88        23.97        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       19.53         1.38        25.22        40.08        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A3PO 
       13.58        73.28         5.92        22.62         3.91        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH 
       27.29       123.78         9.04        10.85        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 
        8.32         8.28         0.49         4.34        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        7.46        10.45       120.20        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VB 
       81.01        18.08         1.84        18.08        48.59       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32        98.27        62.20         0.72        11.18        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-WK-A8XO 
        3.88        17.92        19.82        27.22        13.22        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
        4.80        41.49        65.46        57.80        26.43        29.92 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       36.82        15.95        38.96        17.72        15.58 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            143.41             188.15 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             19.89              25.08 
[1] "0.1 - 143.4 (19.9)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.1"
D69V2, continuous
D69V3, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   43 29
  16P LOSS WILD-TYPE 89 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     43   29
  16P LOSS WILD-TYPE   89   85
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               43                 89
  MALE                 29                 85
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         9    56
  16P LOSS WILD-TYPE     5                         9   138
D69V4, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                9                  9
  WHITE                                   56                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"
D69V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1  61
  16P LOSS WILD-TYPE   4 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   61
  16P LOSS WILD-TYPE    4  130
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               61                130
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   78 41
  16Q LOSS WILD-TYPE 84 41
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               119                125 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                41                 41 
$`16Q LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 
       19.69        88.57        25.25        10.32        31.00        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R 
       26.56         0.56        14.04        18.54        59.24        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3U9 
        6.28         9.70        23.08        17.10        42.77        14.99 
TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       10.68        39.35        28.80        64.18        19.30        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BA 
       27.22        14.96        26.47        25.08        15.95        66.05 
TCGA-DX-A6BB TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM 
       23.44        67.20        16.87        74.10        64.21        48.36 
TCGA-DX-A7EO TCGA-DX-A7ET TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
      135.48         7.04         9.34        35.77        14.07       124.37 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F 
       35.54        36.69        60.66         6.58         1.15         8.75 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB2Z 
       40.60        12.07        49.18        71.57        13.28        50.40 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
        0.10         0.07        20.32         0.07         0.07        48.30 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        4.57        15.91        12.62        23.97         0.10         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF 
       25.22        40.08        13.58        73.28        16.41         1.05 
TCGA-K1-A3PN TCGA-K1-A42X TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH 
       71.70       123.78        10.85         4.08        11.70        13.35 
TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
        8.32        19.73        14.99        10.45         4.08        37.55 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 
       81.01        18.08        20.94         5.03         9.83        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VH TCGA-SG-A849 TCGA-SI-AA8B 
       48.59        35.90        30.90        10.52         6.58         5.06 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX 
        9.93         0.72        10.72        26.17        72.72        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       65.46         9.04        26.43        29.92        18.08        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X9-A973 
       25.71        16.83        38.96        35.08        36.43 

$`16Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HX 
       36.30        53.49        68.55        44.91        54.74        42.84 
TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       36.03        32.71        38.24        12.85        36.69        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        42.54         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        59.47        54.77         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
      108.13        20.05        34.68        15.06        17.75         4.54 
TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48U TCGA-DX-A6B7 
       44.45        34.88         9.73        12.26        72.72        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6Z2 
        3.06        34.55        66.31        23.54        50.50        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        34.49        75.32        15.62        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       14.07        17.95        14.43        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2H 
       38.17        27.95        19.43        12.99         4.67        12.39 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 
       86.10         9.21        96.89       106.45        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       19.20        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IS-A3K6 
        0.46         2.07        34.88        41.33        80.48        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A3PO 
      143.41       116.88         5.92        22.62         3.91        36.39 
TCGA-K1-A42W TCGA-K1-A6RT TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
       27.29         9.04        22.03         8.28         0.49         4.34 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
       17.98        15.65         7.46       120.20         6.35        38.63 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
        1.84        18.08       188.15       130.32        98.27        62.20 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        11.18        18.94         3.88        17.92        19.82 
TCGA-SI-A71Q TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8Y0 
       27.22        13.22        11.93         4.80        41.49        22.62 
TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A971 
       57.80        36.82        15.95        17.72        15.58 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.46 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            135.48             188.15 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             19.73              27.95 
[1] "0.1 - 135.5 (19.7)" "0.5 - 188.2 (27.9)"
[1] "hr=" "1.3"
D70V2, continuous
D70V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   72 48
  16Q LOSS WILD-TYPE 60 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     72   48
  16Q LOSS WILD-TYPE   60   66
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               72                 60
  MALE                 48                 66
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       2                        13    95
  16Q LOSS WILD-TYPE     4                         5    99
D70V4, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    2                  4
  BLACK OR AFRICAN AMERICAN               13                  5
  WHITE                                   95                 99
[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"
D70V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     2 100
  16Q LOSS WILD-TYPE   3  91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2  100
  16Q LOSS WILD-TYPE    3   91
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              100                 91
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    34  21
  17P LOSS WILD-TYPE 128  61
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                55                189 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                21                 61 
$`17P LOSS MUTATED`
TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9I3 TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT 
       53.49        88.57        26.56        36.69        74.66        23.08 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A6BB TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EF 
       14.99        10.68        23.44        16.87        88.31        21.30 
TCGA-DX-A7EI TCGA-DX-A7EO TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ 
       34.49       135.48         7.04        17.95        14.43         9.34 
TCGA-DX-A8BP TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2H 
       14.07        36.69         6.58         1.15        12.99        12.39 
TCGA-DX-AB2O TCGA-DX-AB32 TCGA-DX-AB35 TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A2OT 
       86.10       101.98        19.20         0.10         0.07        48.30 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ 
        0.10        41.33        80.48         3.22         1.38        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-K1-A42W TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-MB-A5YA 
       28.21       143.41        27.29        11.70         8.32         0.49 
TCGA-MB-A8JK TCGA-PC-A5DL TCGA-QC-A6FX TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-SG-A6Z7 
        4.34        37.55        20.94        35.90        10.52         3.88 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-WK-A8XO TCGA-WK-A8XX 
       17.92        27.22         5.06         9.93        11.93        38.27 
TCGA-WK-A8XY 
       65.46 

$`17P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        19.69        68.55        44.91        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       42.84        10.32        31.00        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        38.24        12.85        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       54.77         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB 
       34.68        15.06        17.75        42.77         4.54        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE 
       25.08        25.15        15.95        11.47        66.05        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 
       66.31        67.20        23.54        50.50        74.10        64.21 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       75.32        48.36        15.62        29.49        48.20        14.07 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       59.87        33.07        44.68        38.17        35.77       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F TCGA-DX-AB2G 
       27.95        35.54        60.66        19.43         8.75         4.67 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       40.60        12.07        49.18         9.21        71.57        96.89 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 
      106.45        13.28        50.40        22.85        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO 
       32.15        50.89        71.31         0.46         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         2.07        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A3RQ 
       23.97         9.80        21.37        19.53        19.89        37.12 
TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       40.08       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       16.41         1.05         3.91        71.70        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
        9.04        10.85         4.08        22.03        13.35         8.28 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08       120.20         6.35        38.63        81.01        18.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.03         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       30.90       188.15       130.32        98.27        62.20         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71P TCGA-UE-A6QT TCGA-UE-A6QU 
       11.18        18.94         6.58        19.82        13.22         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8Y0 
       10.72        26.17         4.80        72.72        41.49        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
        9.04        57.80        26.43        29.92        18.08        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.35        25.71        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.07               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            143.41             188.15 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             19.20              25.08 
[1] "0.1 - 143.4 (19.2)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.3"
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    31  24
  17P LOSS WILD-TYPE 101  90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     31   24
  17P LOSS WILD-TYPE  101   90
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               31                101
  MALE                 24                 90
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         5    45
  17P LOSS WILD-TYPE     6                        13   149
D71V4, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   45                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"
D71V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  44
  17P LOSS WILD-TYPE   4 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   44
  17P LOSS WILD-TYPE    4  147
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               44                147
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    26  20
  17Q LOSS WILD-TYPE 136  62
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                46                198 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                20                 62 
$`17Q LOSS MUTATED`
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        23.08        14.99 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6B8 TCGA-DX-A6BA 
       28.80        34.88        64.18        24.26        15.95        66.05 
TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ 
       16.87        21.30        34.49         7.04        17.95         9.34 
TCGA-DX-A8BP TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2H TCGA-DX-AB2O 
       14.07        36.69         6.58         1.15        12.39        86.10 
TCGA-DX-AB35 TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV 
       19.20         0.10        48.30         0.10        41.33        80.48 
TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-K1-A42W TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A8JK 
        3.22        25.22        27.29         4.08        11.70         4.34 
TCGA-PC-A5DL TCGA-QC-A6FX TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q 
       37.55        20.94        10.52         3.88        17.92        27.22 
TCGA-SI-AA8C TCGA-WK-A8XX TCGA-X6-A7WC TCGA-X6-A8C6 
        9.93        38.27        36.82        35.08 

$`17Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        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-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
        0.56        14.04        32.71        38.24        12.85        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       18.54        54.21        59.24        33.53        42.54         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-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       59.47        54.77         9.04        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       20.05        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       10.68        44.45        39.35         9.73        19.30        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
       16.18         3.06        34.55        66.31        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM 
       50.50        74.10        64.21        88.31        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH 
       15.62       135.48        29.49        48.20        14.07        14.43 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       59.87        33.07        44.68        38.17        35.77       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2F 
       27.95        35.54        60.66        19.43        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
        4.67        40.60        12.07        49.18         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
       96.89       106.45        13.28        50.40        22.85       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
        0.07        20.32         0.07         0.07         2.07        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH 
        4.57        15.91        12.62        23.97         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 
       19.53         1.38        19.89        37.12        40.08        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       16.41         1.05         3.91        71.70        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
        9.04        10.85        22.03        13.35         8.32         8.28 
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        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
       10.45         4.08       120.20         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08         5.03         9.83         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
       48.59        35.90        30.90       188.15       130.32        98.27 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71P 
       62.20         0.72        11.18        18.94         6.58        19.82 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
        5.06        13.22         0.72        10.72        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
        4.80        72.72        41.49        65.46        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        26.43        29.92        18.08        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       15.95        16.83        38.96        17.72        15.58        36.43 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             88.57             188.15 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            21.120             23.755 
[1] "0.1 - 88.6 (21.1)"  "0.1 - 188.2 (23.8)"
[1] "hr=" "1.7"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    23  23
  17Q LOSS WILD-TYPE 109  91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     23   23
  17Q LOSS WILD-TYPE  109   91
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               23                109
  MALE                 23                 91
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         5    36
  17Q LOSS WILD-TYPE     6                        13   158
D72V4, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   36                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"
D72V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  38
  17Q LOSS WILD-TYPE   5 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   38
  17Q LOSS WILD-TYPE    5  153
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               38                153
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    35  25
  18P LOSS WILD-TYPE 127  57
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                60                184 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                25                 57 
$`18P LOSS MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 
       44.91        42.84         0.56        38.24        12.85        18.54 
TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UF 
        9.70        23.08        14.99        10.68        39.35        64.18 
TCGA-DX-A48P TCGA-DX-A6BF TCGA-DX-A6YT TCGA-DX-A6YZ TCGA-DX-A7EI TCGA-DX-A7EM 
       14.96         9.11        67.20        74.10        34.49        48.36 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E 
        7.04        14.43         9.34        35.54         6.58        12.99 
TCGA-DX-AB2G TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB3A 
        4.67        12.07        49.18       101.98        60.00        32.15 
TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IS-A3K7 
       48.30        23.97        80.48        21.37         3.22       143.41 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-PC-A5DL 
       73.28        22.62         1.05        11.70         8.32        37.55 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-A71P 
       18.08        20.94         5.03        10.52         3.88        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS 
       27.22         5.06         9.93        10.72        26.17        72.72 
TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A8C4 TCGA-X6-A8C6 
       38.27        22.62        26.43        18.08        16.83        35.08 

$`18P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       25.25        10.32        31.00        36.03        18.64        26.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        32.71        36.69        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        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        59.47        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       70.49       108.13        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE 
       17.75        42.77         4.54        44.45        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R 
        9.73        19.30        24.26        12.26        27.22        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       72.72        25.08        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       23.44        28.96        17.79        21.63        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 
       34.55        66.31        23.54        50.50        16.87        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       88.31        21.30        75.32        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.20        14.07        17.95        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU 
       38.17        35.77        14.07       124.37        27.95        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2J 
       60.66        19.43         1.15         8.75        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       86.10         9.21        71.57        96.89       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C 
       50.40        22.85        19.20        84.66        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 
        2.07        34.88         4.57        15.91        12.62         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       41.33         9.80        19.53         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 
       25.22        40.08        28.21       116.88        13.58         5.92 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
       16.41         3.91        71.70        36.39        27.29       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
        9.04        10.85         4.08        22.03        13.35         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49         4.34        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
        7.46        10.45         4.08       120.20         6.35        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       81.01         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-UE-A6QT 
        0.72        11.18        18.94         6.58        17.92        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WP-A9GB 
        0.72        11.93         4.80        41.49        65.46         9.04 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       57.80        29.92        36.82        18.35        25.71        15.95 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       38.96        17.72        15.58        36.43 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.56               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            143.41             188.15 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            21.155             25.115 
[1] "0.6 - 143.4 (21.2)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.6"
D73V2, continuous
D73V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   33 27
  18P LOSS WILD-TYPE 99 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     33   27
  18P LOSS WILD-TYPE   99   87
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               33                 99
  MALE                 27                 87
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       1                         5    48
  18P LOSS WILD-TYPE     5                        13   146
D73V4, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   48                146
[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"
D73V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1  50
  18P LOSS WILD-TYPE   4 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   50
  18P LOSS WILD-TYPE    4  141
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               50                141
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    39  30
  18Q LOSS WILD-TYPE 123  52
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                69                175 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                30                 52 
$`18Q LOSS MUTATED`
TCGA-3B-A9HP TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY 
       53.49        44.91        42.84         0.56        38.24        12.85 
TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UA 
       18.54         6.28         9.70        23.08        14.99        10.68 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48P TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YQ 
       64.18        19.30        14.96        66.05         9.11         3.06 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A7ET 
       66.31        67.20        16.87        64.21        48.36         7.04 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BU TCGA-DX-A8BZ 
       14.43         9.34        59.87        35.77        36.69         6.58 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2X TCGA-DX-AB32 
       12.99         4.67        12.07        49.18        13.28       101.98 
TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A48G TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-IE-A3OV 
       60.00        32.15         0.07        48.30        23.97        80.48 
TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-KF-A41W 
        3.22        25.22       143.41        22.62         1.05        11.70 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A7B5 
       22.03         8.32         4.34         6.35        18.08         5.03 
TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P 
      188.15        10.52        11.18        18.94         3.88        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS 
       27.22         5.06         9.93        10.72        26.17        72.72 
TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C6 
       22.62        26.43        35.08 

$`18Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        19.69        68.55        88.57        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       32.71        36.69        54.21        59.24        33.53        42.54 
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-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       17.10        20.05        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        12.26        27.22        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       25.15        15.95        11.47        23.44        28.96        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ 
       21.63        16.18        34.55        23.54        50.50        74.10 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO 
       88.31        21.30        34.49        75.32        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BL TCGA-DX-A8BM 
       29.49        48.20        14.07        17.95        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV 
       38.17        14.07       124.37        27.95        35.54        60.66 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       19.43         1.15         8.75        12.39        40.60        86.10 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 
        9.21        71.57        96.89       106.45        50.40        22.85 
TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       19.20        84.66        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV 
        0.07        20.32         0.07         2.07        34.88         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
       15.91        12.62         0.10        41.33         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 
       19.53         1.38        19.89        37.12        40.08        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        13.58        73.28         5.92        16.41         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
       71.70        36.39        27.29       123.78         9.04        10.85 
TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
        4.08        13.35         8.28         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        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        81.01        20.94         9.83         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        30.90       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-A71O TCGA-UE-A6QT 
       98.27        62.20         0.72         6.58        17.92        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
        0.72        11.93         4.80        41.49        38.27        65.46 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        9.04        57.80        29.92        18.08        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       25.71        15.95        16.83        38.96        17.72        15.58 
TCGA-X9-A973 
       36.43 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            188.15             135.48 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             18.94              25.71 
[1] "0.1 - 188.2 (18.9)" "0.1 - 135.5 (25.7)"
[1] "hr=" "1.8"
D74V2, continuous
D74V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   37 32
  18Q LOSS WILD-TYPE 95 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     37   32
  18Q LOSS WILD-TYPE   95   82
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               37                 95
  MALE                 32                 82
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       1                         5    54
  18Q LOSS WILD-TYPE     5                        13   140
D74V4, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                5                 13
  WHITE                                   54                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1  54
  18Q LOSS WILD-TYPE   4 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1   54
  18Q LOSS WILD-TYPE    4  137
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               54                137
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    15   6
  19P LOSS WILD-TYPE 147  76
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                21                223 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 76 
$`19P LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HX TCGA-DX-A3LT TCGA-DX-AB2W TCGA-IE-A4EH TCGA-IW-A3M6 
       19.69        42.84        23.08       106.45        21.37        22.62 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A7B5 
        4.08        11.70        22.03         6.35        81.01         5.03 
TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8Y0 
       11.18         3.88         5.06         9.93        10.72        22.62 
TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C4 
       26.43        25.71        16.83 

$`19P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       25.25        10.32        31.00        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        38.24        12.85        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       18.54        54.21        59.24        33.53        42.54        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-A3LU 
        8.58         9.70        59.47        54.77         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 
      108.13        17.10        20.05        34.68        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.15        15.95        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       66.31        67.20        23.54        50.50        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        35.77        14.07       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       36.69        60.66        19.43         6.58         1.15        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
        8.75         4.67        12.39        40.60        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z 
       49.18         9.21        71.57        96.89        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
        0.07         0.07         2.07        48.30        34.88         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
       15.91        12.62        23.97         0.10        41.33         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-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        40.08        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28         5.92        16.41         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A9QH 
       36.39        27.29       123.78         9.04        10.85        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
        8.32         8.28         0.49         4.34        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        18.08        20.94         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
       46.82        18.08        48.59        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 
      130.32        98.27        62.20        10.52         0.72        18.94 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU 
        6.58        17.92        19.82        27.22        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
       26.17        11.93         4.80        72.72        41.49        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       65.46         9.04        57.80        29.92        18.08        36.82 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       18.35        15.95        38.96        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3.88               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            106.45             188.15 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             19.69              25.15 
[1] "3.9 - 106.5 (19.7)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.2"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    12   9
  19P LOSS WILD-TYPE 120 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     12    9
  19P LOSS WILD-TYPE  120  105
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               12                120
  MALE                  9                105
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         0    20
  19P LOSS WILD-TYPE     5                        18   174
D75V4, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                0                 18
  WHITE                                   20                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"
D75V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  21
  19P LOSS WILD-TYPE   5 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   21
  19P LOSS WILD-TYPE    5  170
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               21                170
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    26  12
  19Q LOSS WILD-TYPE 136  70
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                38                206 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                 70 
$`19Q LOSS MUTATED`
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-A6Z2 TCGA-DX-A7EI TCGA-DX-A7ET 
       23.08        42.77        28.80        88.31        34.49         7.04 
TCGA-DX-A8BO TCGA-DX-AB2Q TCGA-DX-AB2W TCGA-DX-AB3A TCGA-FX-A48G TCGA-IE-A4EH 
       35.77        49.18       106.45        32.15         0.07        21.37 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-PC-A5DK 
       73.28        22.62         3.91        22.03         8.32       120.20 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
        6.35        81.01         5.03        11.18        18.94         3.88 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WB 
        5.06         9.93        10.72        22.62        26.43        18.08 
TCGA-X6-A8C2 TCGA-X6-A8C4 
       25.71        16.83 

$`19Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        88.57        44.91        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        31.00        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       32.71        38.24        12.85        36.69        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        27.81        60.30         8.58        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
        9.04        70.49       108.13        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       39.35        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.15        15.95        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       66.31        67.20        23.54        50.50        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       64.21        21.30        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ 
       29.49        48.20        14.07        17.95        14.43         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR 
       59.87        33.07        44.68        38.17        14.07       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       27.95        35.54        36.69        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        12.99         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X 
       86.10        12.07         9.21        71.57        96.89        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 
       50.40        22.85       101.98        19.20        60.00        84.66 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31         0.46         0.10         0.07        20.32 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         2.07        48.30        34.88         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         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-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 
       40.08        28.21       143.41       116.88        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        71.70        36.39        27.29       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
        9.04        10.85         4.08        11.70        13.35         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49         4.34        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP 
        7.46        10.45         4.08        37.55        38.63        18.08 
TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       20.94         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       10.52         0.72         6.58        17.92        19.82        27.22 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.22         0.72        26.17        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        38.27        65.46         9.04        57.80        29.92 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       36.82        18.35        15.95        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            120.20             188.15 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            22.325             24.115 
[1] "0.1 - 120.2 (22.3)" "0.1 - 188.2 (24.1)"
[1] "hr=" "1"  
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    21  17
  19Q LOSS WILD-TYPE 111  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     21   17
  19Q LOSS WILD-TYPE  111   97
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               21                111
  MALE                 17                 97
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         1    34
  19Q LOSS WILD-TYPE     5                        17   160
D76V4, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                1                 17
  WHITE                                   34                160
[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"
D76V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  33
  19Q LOSS WILD-TYPE   3 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   33
  19Q LOSS WILD-TYPE    3  158
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               33                158
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    35  16
  20P LOSS WILD-TYPE 127  66
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                51                193 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                16                 66 
$`20P LOSS MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A3LS TCGA-DX-A3LT 
       44.91        42.84        31.00        36.03         9.04        23.08 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K 
       17.10        20.05        14.99        34.88        64.18        19.30 
TCGA-DX-A48L TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6Z2 
       24.26        25.08        15.95        67.20        16.87        88.31 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BO 
        7.04        17.95         9.34        59.87        38.17        35.77 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2X 
       60.66         6.58        12.07        49.18        71.57        13.28 
TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-FX-A2QS TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-K1-A3PN 
       50.40       101.98         0.46        19.89        16.41        71.70 
TCGA-K1-A6RU TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-PC-A5DK TCGA-PC-A5DO TCGA-QC-A6FX 
       10.85         8.32         4.34       120.20        81.01        20.94 
TCGA-QQ-A5VC TCGA-SG-A849 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY 
       35.90         6.58         5.06        11.93        72.72        65.46 
TCGA-X6-A7WB TCGA-X6-A8C4 TCGA-X9-A971 
       18.08        16.83        15.58 

$`20P LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       25.25        10.32        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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-A3LU TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U5 
       59.47        54.77        70.49       108.13        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       28.80         9.73        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.15        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
       66.31        23.54        50.50        74.10        64.21        21.30 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       34.49        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BP 
       48.20        14.07        14.43        33.07        44.68        14.07 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS 
      124.37        27.95        35.54        36.69        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       12.99         8.75         4.67        12.39        40.60        86.10 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
        9.21        96.89       106.45        22.85        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE 
       84.66        32.15        50.89        71.31         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57        15.91        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37        19.53         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        40.08        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28         5.92        22.62         1.05         3.91 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W 
       36.39        27.29       123.78         9.04         4.08        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       22.03        13.35         8.28         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
       17.98        15.65         7.46        10.45         4.08        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
        6.35        38.63        18.08         5.03         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       46.82        18.08        48.59        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
       98.27        62.20        10.52         0.72        11.18        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT 
        3.88        17.92        19.82        27.22         9.93        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
        0.72        10.72        26.17         4.80        41.49        38.27 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC 
       22.62         9.04        57.80        26.43        29.92        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       18.35        25.71        15.95        38.96        35.08        17.72 
TCGA-X9-A973 
       36.43 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.46               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            120.20             188.15 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             20.94              23.54 
[1] "0.5 - 120.2 (20.9)" "0.1 - 188.2 (23.5)"
[1] "hr=" "1.2"
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    32  20
  20P LOSS WILD-TYPE 100  94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     32   20
  20P LOSS WILD-TYPE  100   94
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               32                100
  MALE                 20                 94
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         4    47
  20P LOSS WILD-TYPE     6                        14   147
D77V4, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   47                147
[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"
D77V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  48
  20P LOSS WILD-TYPE   4 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   48
  20P LOSS WILD-TYPE    4  143
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               48                143
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    15   8
  20Q LOSS WILD-TYPE 147  74
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                23                221 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                 74 
$`20Q LOSS MUTATED`
TCGA-3B-A9HX TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 
       42.84         9.04        23.08        17.10        20.05        14.99 
TCGA-DX-A3UE TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK 
       34.88        16.87        88.31        17.95         9.34        59.87 
TCGA-DX-A8BV TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-IE-A6BZ 
       60.66        71.57        13.28        50.40       101.98        19.89 
TCGA-JV-A5VE TCGA-K1-A6RU TCGA-WK-A8XO TCGA-WK-A8XS TCGA-X9-A971 
       16.41        10.85        11.93        72.72        15.58 

$`20Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       54.74        25.25        10.32        31.00        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        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.69        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-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-A3LU 
       60.30         8.58         9.70        59.47        54.77        70.49 
TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
      108.13        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       72.72        25.08        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV 
        3.06        34.55        66.31        67.20        23.54        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       74.10        64.21        21.30        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP 
       14.43        33.07        44.68        38.17        35.77        14.07 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ 
      124.37        27.95        35.54        36.69        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        12.99         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W 
       86.10        12.07        49.18         9.21        96.89       106.45 
TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         2.07        48.30        34.88         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       21.37        19.53         3.22         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       40.08        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I 
       27.29       123.78         9.04         4.08        11.70        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35         8.32         8.28         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       14.99        17.98        15.65         7.46        10.45         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
      120.20        37.55         6.35        38.63        81.01        18.08 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       20.94         5.03         9.83         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
       48.59        35.90        30.90       188.15       130.32        98.27 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       62.20        10.52         0.72        11.18        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        6.58        17.92        19.82        27.22         5.06         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XQ TCGA-WK-A8XT 
       13.22         0.72        10.72        26.17         4.80        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       38.27        65.46        22.62         9.04        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       29.92        18.08        36.82        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        36.43 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              9.04               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            101.98             188.15 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             19.89              23.97 
[1] "9.0 - 102.0 (19.9)" "0.1 - 188.2 (24.0)"
[1] "hr=" "1"  
D78V2, continuous
D78V3, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    16   8
  20Q LOSS WILD-TYPE 116 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     16    8
  20Q LOSS WILD-TYPE  116  106
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               16                116
  MALE                  8                106
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         2    21
  20Q LOSS WILD-TYPE     6                        16   173
D78V4, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  6
  BLACK OR AFRICAN AMERICAN                2                 16
  WHITE                                   21                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"
D78V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  22
  20Q LOSS WILD-TYPE   5 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   22
  20Q LOSS WILD-TYPE    5  169
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               22                169
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    35  13
  21Q LOSS WILD-TYPE 127  69
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                48                196 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                13                 69 
$`21Q LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R 
       19.69        88.57        38.24        18.54        59.24        74.66 
TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3UF TCGA-DX-A48V 
        6.28        17.10        20.05        15.06        64.18        25.08 
TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BJ TCGA-DX-A8BM 
       23.44         9.11        16.87        21.30         9.34        44.68 
TCGA-DX-A8BO TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2O TCGA-DX-AB2Q 
       35.77        36.69         6.58         1.15        86.10        49.18 
TCGA-DX-AB32 TCGA-FX-A3TO TCGA-HB-A2OT TCGA-IS-A3K7 TCGA-IW-A3M6 TCGA-JV-A5VE 
      101.98        20.32        48.30       143.41        22.62        16.41 
TCGA-K1-A3PN TCGA-K1-A42W TCGA-KF-A41W TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QQ-A8VB 
       71.70        27.29        11.70        81.01        20.94       188.15 
TCGA-QQ-A8VG TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B 
       62.20        11.18        18.94         3.88         6.58         5.06 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 
       10.72        26.17        72.72        25.71        16.83        35.08 

$`21Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        44.91        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        31.00        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
        0.56        14.04        32.71        12.85        36.69        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        42.54         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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U7 
       23.08        70.49       108.13        34.68        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.15        15.95        11.47 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       66.05        28.96        17.79        21.63        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ 
       34.55        66.31        67.20        23.54        50.50        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       64.21        88.31        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
      135.48        29.49        48.20        14.07         7.04        17.95 
TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR 
       14.43        59.87        33.07        38.17        14.07       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2F 
       27.95        35.54        60.66        19.43        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2T 
        4.67        12.39        40.60        12.07         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 
       96.89       106.45        13.28        50.40        22.85        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
        0.10         0.07         0.07         0.07         2.07        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57        15.91        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       19.89        37.12        25.22        40.08        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO 
       13.58        73.28         5.92         1.05         3.91        36.39 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH 
      123.78         9.04        10.85         4.08        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
        8.32         8.28         0.49         4.34        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N 
       37.55         6.35        38.63        18.08         5.03         9.83 
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        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SI-A71O TCGA-SI-A71P 
      130.32        98.27        10.52         0.72        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
       27.22         9.93        13.22         0.72        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       41.49        38.27        65.46        22.62         9.04        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 
       26.43        29.92        18.08        36.82        18.35        15.95 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       38.96        17.72        15.58        36.43 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.15               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            188.15             135.48 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             23.03              23.31 
[1] "1.1 - 188.2 (23.0)" "0.1 - 135.5 (23.3)"
[1] "hr=" "1.5"
D79V2, continuous
D79V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    25  23
  21Q LOSS WILD-TYPE 107  91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     25   23
  21Q LOSS WILD-TYPE  107   91
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               25                107
  MALE                 23                 91
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         4    37
  21Q LOSS WILD-TYPE     5                        14   157
D79V4, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   37                157
[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"
D79V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  37
  21Q LOSS WILD-TYPE   4 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   37
  21Q LOSS WILD-TYPE    4  154
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               37                154
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    42  21
  22Q LOSS WILD-TYPE 120  61
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                63                181 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                21                 61 
$`22Q LOSS MUTATED`
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        59.24 
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        23.08       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA 
       20.05        14.99        24.26        26.47        15.95        66.05 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A8BG 
       16.18        66.31        67.20        23.54        50.50        17.95 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB3A 
       59.87        33.07        12.39        86.10        71.57        32.15 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N8 
        0.07        20.32         0.07        34.88         4.57         0.10 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3K8 
        9.80        21.37        19.89        25.22       143.41       116.88 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A6RU TCGA-K1-A6RV 
        5.92        22.62         1.05        71.70        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-QC-AA9N TCGA-QQ-A8VB TCGA-QQ-A8VH 
       11.70        22.03         8.32         9.83       188.15        10.52 
TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-SI-AA8C TCGA-WK-A8XS TCGA-X2-A95T TCGA-X6-A7W8 
        3.88         5.06         9.93        72.72        57.80        26.43 
TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X9-A971 
       18.08        25.71        15.58 

$`22Q LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       25.25        10.32        31.00        36.03        18.64         0.56 
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 
       14.04        38.24        12.85        36.69        18.54        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z TCGA-DX-A240 
       42.54        74.66         5.26        76.41        27.81        60.30 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M2 
        9.70        59.47        54.77        70.49        17.10        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       12.26        27.22        14.96        72.72        25.08        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
        3.06        34.55        16.87        74.10        64.21        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       21.30        34.49        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ 
       29.49        48.20        14.07         7.04        14.43         9.34 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS 
       44.68        38.17        35.77        14.07       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.54        36.69        60.66        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q 
       12.99         8.75         4.67        40.60        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
        9.21        96.89       106.45        13.28        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C 
      101.98        19.20        60.00        84.66        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A43Z 
        0.46         0.10         0.07         2.07        48.30        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       12.62        23.97        41.33        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        37.12        40.08        28.21        13.58        73.28 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
       16.41         3.91        36.39        27.29       123.78         9.04 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       13.35         8.28         0.49         4.34        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
       37.55         6.35        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        5.03         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 
       30.90       130.32        98.27        62.20         0.72        11.18 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT 
       18.94         6.58        17.92        19.82        27.22        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
        0.72        10.72        26.17        11.93         4.80        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WC 
       38.27        65.46        22.62         9.04        29.92        36.82 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       18.35        15.95        16.83        38.96        35.08        17.72 
TCGA-X9-A973 
       36.43 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.07               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            188.15             135.48 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             22.62              23.97 
[1] "0.1 - 188.2 (22.6)" "0.1 - 135.5 (24.0)"
[1] "hr=" "1"  
D80V2, continuous
D80V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   41 22
  22Q LOSS WILD-TYPE 91 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     41   22
  22Q LOSS WILD-TYPE   91   92
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               41                 91
  MALE                 22                 92
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         4    50
  22Q LOSS WILD-TYPE     5                        14   144
D80V4, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  5
  BLACK OR AFRICAN AMERICAN                4                 14
  WHITE                                   50                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"
D80V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     0  46
  22Q LOSS WILD-TYPE   5 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0   46
  22Q LOSS WILD-TYPE    5  145
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               46                145
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    41  17
  XP LOSS WILD-TYPE 121  65
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               58               186 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               17                65 
$`XP LOSS MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1L0 TCGA-DX-A1L2 
       44.91        10.32        36.03         0.56        18.54        59.24 
TCGA-DX-A2J0 TCGA-DX-A3LY TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P 
        9.70        17.10        28.80         9.73        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6YQ 
       26.47        72.72        25.08        25.15        11.47         3.06 
TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-AB32 
       16.87        21.30        15.62        38.17       124.37       101.98 
TCGA-DX-AB35 TCGA-DX-AB3C TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 
       19.20        71.31         0.07        34.88         4.57        12.62 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IW-A3M4 
        9.80        21.37        25.22        28.21       143.41        73.28 
TCGA-JV-A5VE TCGA-K1-A42X TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y8 
       16.41       123.78        10.85         4.08        13.35         8.32 
TCGA-MB-A8JL TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A8VB TCGA-SI-A71O TCGA-SI-A71Q 
       19.73        81.01         9.83       188.15        17.92        27.22 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
        5.06         9.93        10.72        38.27        65.46        57.80 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08        18.35        16.83        38.96 

$`XP LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       25.25        42.84        31.00        18.64        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
       32.71        38.24        12.85        36.69        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        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        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       23.08        70.49       108.13        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       39.35        34.88        64.18        19.30        24.26        12.26 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       15.95        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
       21.63        16.18        34.55        66.31        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL 
       50.50        74.10        64.21        88.31        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       48.36       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        59.87        33.07        44.68 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       35.77        14.07        27.95        35.54        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       19.43         6.58         1.15        12.99         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.39        40.60        86.10        12.07        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
       71.57        96.89       106.45        13.28        50.40        22.85 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-FX-A2QS TCGA-FX-A3NJ 
       60.00        84.66        32.15        50.89         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A43Z 
        0.07        20.32         0.07         2.07        48.30        15.91 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       23.97         0.10        41.33        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IS-A3KA 
        1.38        19.89        37.12        40.08       116.88        13.58 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A6RT TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       27.29         9.04        11.70        22.03         8.28         0.49 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        4.34        14.99        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP 
        4.08       120.20        37.55         6.35        38.63        18.08 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       20.94         5.03         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        30.90       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P 
        0.72        11.18        18.94         3.88         6.58        19.82 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.22         0.72        26.17        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC 
       41.49        22.62         9.04        26.43        29.92        36.82 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       25.71        15.95        35.08        17.72        15.58        36.43 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.07              0.07 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           188.15            135.48 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           19.465            24.115 
[1] "0.1 - 188.2 (19.5)" "0.1 - 135.5 (24.1)"
[1] "hr=" "1.1"
D81V2, continuous
D81V3, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   35 23
  XP LOSS WILD-TYPE 97 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     35   23
  XP LOSS WILD-TYPE   97   91
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              35                97
  MALE                23                91
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED       0                         6    45
  XP LOSS WILD-TYPE     6                        12   149
D81V4, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               6                12
  WHITE                                  45               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"
D81V5, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0  43
  XP LOSS WILD-TYPE   5 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   43
  XP LOSS WILD-TYPE    5  148
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              43               148
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   68 27
  XQ LOSS WILD-TYPE 94 55
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               95               149 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               27                55 
$`XQ LOSS MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       19.69        44.91        25.25        42.84        10.32        31.00 
TCGA-3B-A9I0 TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A2J0 
       36.03        38.24        12.85        18.54        59.24         9.70 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD 
      108.13        17.10        20.05        10.68        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       34.88        64.18         9.73        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA 
       72.72        25.08        25.15        15.95        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EM 
       23.44        67.20        23.54        16.87        21.30        48.36 
TCGA-DX-A7EN TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS 
       15.62        33.07        44.68        38.17       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB32 
       35.54         6.58         1.15         8.75        86.10       101.98 
TCGA-DX-AB35 TCGA-DX-AB3C TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV 
       19.20        71.31        20.32         0.07        34.88         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IF-A3RQ TCGA-IF-A4AJ 
       12.62        23.97         9.80        21.37        37.12        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A42X 
       28.21       143.41        73.28        22.62        16.41       123.78 
TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-PC-A5DN 
        4.08        13.35         8.32        19.73        14.99        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-RN-AAAQ 
       81.01        18.08         9.83        35.90       188.15        11.18 
TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XX 
       17.92        27.22         9.93         0.72        10.72        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       65.46         9.04        57.80        29.92        18.08        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X9-A971 TCGA-X9-A973 
       25.71        16.83        38.96        15.58        36.43 

$`XQ LOSS WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9I1 
       36.30        53.49        68.55        88.57        54.74        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 
       26.56         0.56        14.04        32.71        36.69        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        27.81        60.30         8.58        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        23.08        70.49        34.68        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A48K TCGA-DX-A48L 
       42.77         4.54        14.99        44.45        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       12.26        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 
        3.06        34.55        66.31        50.50        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       88.31        34.49        75.32       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       14.07         7.04        17.95        14.43         9.34        59.87 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E 
       35.77        14.07        36.69        60.66        19.43        12.99 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
        4.67        12.39        40.60        12.07        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
       71.57        96.89       106.45        13.28        50.40        22.85 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-FX-A2QS TCGA-FX-A3NJ 
       60.00        84.66        32.15        50.89         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 
        0.07         0.07         2.07        48.30        15.91         0.10 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       41.33        80.48        19.53         3.22         1.38        19.89 
TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
       40.08       116.88        13.58         5.92         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KF-A41W 
       71.70        36.39        27.29         9.04        10.85        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 
       22.03         8.28         0.49         4.34        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
        7.46        10.45         4.08       120.20        37.55         6.35 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       20.94         5.03         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 
       30.90       130.32        98.27        62.20        10.52         0.72 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QT 
       18.94         3.88         6.58        19.82         5.06        13.22 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8Y0 
       26.17        11.93         4.80        72.72        41.49        22.62 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C6 TCGA-X6-A8C7 
       26.43        36.82        15.95        35.08        17.72 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           188.15            135.48 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            25.08             22.03 
[1] "0.1 - 188.2 (25.1)" "0.1 - 135.5 (22.0)"
[1] "hr=" "1.3"
D82V2, continuous
D82V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   58 38
  XQ LOSS WILD-TYPE 74 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     58   38
  XQ LOSS WILD-TYPE   74   76
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              58                74
  MALE                38                76
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       2                        10    76
  XQ LOSS WILD-TYPE     4                         8   118
D82V4, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   2                 4
  BLACK OR AFRICAN AMERICAN              10                 8
  WHITE                                  76               118
[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"
D82V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  78
  XQ LOSS WILD-TYPE   5 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   78
  XQ LOSS WILD-TYPE    5  113
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              78               113
[1] 2 2
[1] FALSE
