[1] "ofn"        "-oTLUAD-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/LUAD-TP/22506767/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/22531211/transformed.cor.cli.txt"

nPatients in clinical file=522, in cluster file=516, common to both=516
[1]  82 516
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              142               374 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              142               374 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              319               197 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              319               197 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              154               362 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              154               362 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              143               373 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              143               373 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               44               472 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               44               472 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               90               426 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               90               426 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               83               433 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               83               433 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               49               467 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               49               467 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              279               237 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              279               237 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              132               384 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              132               384 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              146               370 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              146               370 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               60               456 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               60               456 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              267               249 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              267               249 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              220               296 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              220               296 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              125               391 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              125               391 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              245               271 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              245               271 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               45               471 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               45               471 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               34               482 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               34               482 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               112                404 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               112                404 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                79                437 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                79                437 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                94                422 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                94                422 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               118                398 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               118                398 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               138                378 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               138                378 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               133                383 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               133                383 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                43                473 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                43                473 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               129                387 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               129                387 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                38                478 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                38                478 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               137                379 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               137                379 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               101                415 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               101                415 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                84                432 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                84                432 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               191                325 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               191                325 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                92                424 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                92                424 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                69                447 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                69                447 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                33                483 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                33                483 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                78                438 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                78                438 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               175                341 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               175                341 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               201                315 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               201                315 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                98                418 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                98                418 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                62                454 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                62                454 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               53               463 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               53               463 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               86               430 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               86               430 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               80               436 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               80               436 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               488 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               488 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               492 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               492 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               25               491 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               25               491 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              211               305 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              211               305 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              144               372 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              144               372 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              119               397 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              119               397 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              136               380 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              136               380 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               45               471 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               45               471 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              143               373 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              143               373 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              101               415 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              101               415 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              217               299 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              217               299 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               34               482 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               34               482 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               41               475 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               41               475 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              200               316 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              200               316 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               56               460 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               56               460 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              269               247 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              269               247 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              249               267 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              249               267 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               110                406 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               110                406 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               132                384 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               132                384 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               111                405 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               111                405 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                87                429 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                87                429 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               109                407 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               109                407 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                94                422 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                94                422 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               251                265 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               251                265 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               114                402 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               114                402 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               244                272 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               244                272 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               107                409 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               107                409 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               137                379 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               137                379 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               219                297 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               219                297 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                60                456 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                60                456 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               180                336 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               180                336 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               215                301 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               215                301 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               245                271 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               245                271 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               159                357 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               159                357 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               113                403 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               113                403 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                67                449 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                67                449 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               166                350 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               166                350 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               221                295 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               221                295 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              106               410 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              106               410 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               61               455 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               61               455 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RESIDUAL_TUMOR"                      
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 516 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=174,	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=286,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=94,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 516 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RESIDUAL_TUMOR"               
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
171 278  46  19 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
171 278  46  19 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
171 278  46  19 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
171 278  46  19 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
333  96  74   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  333    96    76 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
333  96  74   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  333    96    76 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=12, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=94, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, 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    88  52
  1P GAIN WILD-TYPE 235 129
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              140               364 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               52               129 
$`1P GAIN MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4427 TCGA-38-6178 TCGA-44-2662 TCGA-44-8119 
       19.96         8.02        26.01        14.73        42.08         9.37 
TCGA-49-4501 TCGA-49-6742 TCGA-49-AAR0 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       46.72        16.04       156.66        21.47        41.69        23.05 
TCGA-55-6979 TCGA-55-7573 TCGA-55-A48X TCGA-55-A4DF TCGA-67-6217 TCGA-95-7562 
        7.79        16.01        22.65        20.19        13.87         2.86 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-05-4389 TCGA-05-4420 TCGA-05-4424 
       21.83        27.19         2.43        45.01        29.98        30.02 
TCGA-05-4432 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-38-4632 TCGA-44-2659 
       25.02         4.96        22.03         9.04        44.61        44.94 
TCGA-44-3917 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 
       38.89        23.18        61.28        16.44         7.17        18.87 
TCGA-44-7672 TCGA-44-A47B TCGA-44-A4SU TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 
       23.64         9.44        13.45        12.66        14.07        29.46 
TCGA-49-6744 TCGA-49-AAQV TCGA-49-AARQ TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       55.33        22.26       221.33        20.52        71.47       101.72 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 
       49.28         8.22        14.27        78.67        48.46        57.53 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 
       53.16         3.91        11.05         5.62        40.73        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-7281 TCGA-55-7576 TCGA-55-7907 TCGA-55-7911 
       45.34        32.71        28.67        22.03        11.28        17.65 
TCGA-55-8089 TCGA-55-8096 TCGA-55-8206 TCGA-55-8514 TCGA-55-A494 TCGA-55-A4DG 
       23.08        23.64        29.19        17.10        15.81        19.99 
TCGA-55-A57B TCGA-62-8399 TCGA-62-A46O TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
       17.95        88.64        47.80        56.81        81.80        38.37 
TCGA-64-5781 TCGA-67-3772 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
       51.25        18.84        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-75-5147 
       19.43         8.42        15.35         4.31         9.24        43.82 
TCGA-75-6206 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 
       85.15       108.66        27.16        19.27        19.50        38.50 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7535 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 
        9.57       104.19        31.20        10.55       232.18        77.59 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
       32.78        37.74         4.08         0.79        22.82        31.20 
TCGA-86-8280 TCGA-86-8585 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6828 
       23.05        11.61        28.34        29.46        13.64        10.62 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       10.19        12.23        27.68        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7944 TCGA-95-8494 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 
       41.82        12.39         2.76        42.25        61.48        18.54 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 
       15.39        16.41        20.58        19.76        20.84        24.56 
TCGA-J2-A4AG TCGA-L9-A7SV TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4TF TCGA-MP-A5C7 
       32.48        18.58        58.45        58.85        11.05        73.91 
TCGA-NJ-A55O TCGA-O1-A52J 
        0.43        59.11 

$`1P GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 
       14.01         9.96        20.05         9.01        15.02        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       28.41        35.28        11.64        26.30        43.53        38.10 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 
       23.93        27.78        86.01        18.31        29.00        29.23 
TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-55-1595 
       11.08        17.16        11.64        37.32        40.60        48.62 
TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        5.79         7.99        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       19.66        19.73        17.98        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 
       18.15        13.68        16.93        20.58        19.59        20.65 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
       16.54        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 
        6.35        10.09         5.29        31.23        10.09        50.07 
TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
        3.98        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
        2.99        14.96        12.00        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
       24.00        29.00         2.04         0.46         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F 
        8.68        97.74       120.79        37.71        49.05         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       46.98        44.42        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 
       28.01        23.77        19.56        23.15        21.63        32.45 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       22.72        19.46        36.07        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       15.32        11.54        13.64        76.21        28.11        28.57 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       35.54        32.84         8.81        29.75        55.89        53.29 
TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
      123.58       164.12         9.86        15.72        60.16        47.41 
TCGA-50-5930 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 
        9.27         8.45        15.12        60.72        42.35        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6970 
       67.89        30.58        14.30        80.52        42.51        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       46.03        53.65         3.88        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 
      107.21        70.26        20.02        27.09        32.71         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 
       23.15        25.41        18.64        34.19        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
       29.23        29.72        15.19         5.06        17.79        15.65 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       13.74        20.28        17.72        19.96        26.01        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
        0.92         4.57        39.98        42.38        14.60        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
       39.25        40.96        29.92        39.09        37.02        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        2.04        42.90        28.41        28.47        20.05        20.05 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 
        4.41        13.41        26.73        23.38        26.30        30.31 
TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-6212 
        1.25        50.33        11.18        66.64        77.85        49.84 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       36.66       100.57       163.10         5.69        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       21.90        39.95       119.51        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
       22.92       238.29        88.14        26.53         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
       26.01        39.35        39.75       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
       19.89        35.24         4.57        24.33        32.65        31.04 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       21.47        14.60        13.91        30.84        27.58         0.62 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       26.50         3.81        24.23        26.47        41.36         1.97 
TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        2.60         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7567 TCGA-95-8039 TCGA-95-A4VP 
       19.82        22.45        17.46        18.67        27.29        19.89 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        25.48         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M6 
        5.39        18.12        14.30        21.60        21.44        18.67 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       34.85        36.76         1.45        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 
       35.47        19.00        14.30        14.53         1.91        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63         2.76        86.14        49.35        37.35        86.04 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
        5.49        41.59        29.46        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.49        19.82        20.28        16.87 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.43              0.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           232.18            238.29 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           22.145            21.455 
[1] "0.4 - 232.2 (22.1)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         3       36       35        1        22        19
  1P GAIN WILD-TYPE       2       97      104        0        28        53
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1P GAIN MUTATED           15          2        7
  1P GAIN WILD-TYPE         57          9       18
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                36                97
  STAGE IB                35               104
  STAGE II                 1                 0
  STAGE IIA               22                28
  STAGE IIB               19                53
  STAGE IIIA              15                57
  STAGE IIIB               2                 9
  STAGE IV                 7                18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED    50  78   9   4
  1P GAIN WILD-TYPE 121 200  37  15
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              50               121
  T2              78               200
  T3               9                37
  T4               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  1P GAIN MUTATED    85  40    14
  1P GAIN WILD-TYPE 248  56    62
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                 85               248
  N1                 40                56
  N2+N3              14                62
[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"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   100   7
  1P GAIN WILD-TYPE 249  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    100    7
  1P GAIN WILD-TYPE  249   18
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0             100               249
  1               7                18
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    76  66
  1P GAIN WILD-TYPE 200 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     76   66
  1P GAIN WILD-TYPE  200  174
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              76               200
  MALE                66               174
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   116  18
  1P GAIN WILD-TYPE 294  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    116   18
  1P GAIN WILD-TYPE  294   42
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO              116               294
  YES              18                42
[1] 2 2
[1] FALSE
D1V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1P GAIN MUTATED                            5
  1P GAIN WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1P GAIN MUTATED                                  25
  1P GAIN WILD-TYPE                                82
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                   96
  1P GAIN WILD-TYPE                                                225
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1P GAIN MUTATED                                            0
  1P GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1P GAIN MUTATED                                               6
  1P GAIN WILD-TYPE                                            13
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1P GAIN MUTATED                                0
  1P GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  1P GAIN MUTATED                                    2
  1P GAIN WILD-TYPE                                  1
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  1P GAIN MUTATED                              0                             4
  1P GAIN WILD-TYPE                            2                            19
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  1P GAIN MUTATED                                 0
  1P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  1P GAIN MUTATED                                               2
  1P GAIN WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  1P GAIN MUTATED                              2
  1P GAIN WILD-TYPE                            8
D1V10, multiclass
                                                    clus
vv                                                   1P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              96
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    6
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   1P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               225
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     13
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     19
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
D1V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    89   5   1   7
  1P GAIN WILD-TYPE 255   8   3  19
D1V13, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              89               255
  R1               5                 8
  R2               1                 3
  RX               7                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  1     3
  1P GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          17   104
  1P GAIN WILD-TYPE                        35   286
D1V14, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                     17                35
  WHITE                                        104               286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2 102
  1P GAIN WILD-TYPE   5 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2  102
  1P GAIN WILD-TYPE    5  282
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             102               282
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   205 109
  1Q GAIN WILD-TYPE 118  72
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              314               190 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              109                72 
$`1Q GAIN MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-5420 TCGA-38-4629 
       19.96        14.01         8.02        20.05        15.02        28.41 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2662 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 
       14.73        26.30        42.08        27.78        86.01        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-AAR0 
       29.23         9.37        11.08        46.72        16.04       156.66 
TCGA-49-AARN TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6979 
       37.32        21.47        41.69        23.05        48.62         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 TCGA-55-8203 TCGA-55-8511 
        7.99        16.01        14.53         6.15        17.98        18.15 
TCGA-55-8619 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 
       13.68        22.65        20.58        19.59        20.19        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7633 TCGA-80-5611 TCGA-91-7771 
       52.60        82.68        39.09        50.24        85.32        16.18 
TCGA-93-8067 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        6.12         2.86        15.68        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       20.19        17.75        20.68        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       21.83        27.19         5.29         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 TCGA-05-4417 
        3.98        45.01        37.02         0.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 
       29.98        30.02        25.02        25.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 TCGA-38-4628 
       22.03         9.04         2.04         0.46        97.74        49.05 
TCGA-38-4632 TCGA-44-2656 TCGA-44-2659 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 
       44.61        46.98        44.94        25.02        38.89        34.06 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       26.56        28.01        23.77        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       16.44        22.72         7.17        18.87        23.64        12.66 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       15.32         9.44        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
       28.57        12.66        35.54        14.07        32.84        29.46 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR9 
       53.29        55.33        22.26        22.26        62.24         8.55 
TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      123.58       221.33         9.86        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
       15.72        49.28         8.22        14.27        78.67        48.46 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-8457 TCGA-50-8460 
       57.53        53.16         3.91        11.05        36.99        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       30.54        13.94        67.89        80.52         5.62        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       15.25        53.65        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 
       24.99        70.26        28.67        20.02        32.71        22.03 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        3.91        25.41        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       18.44        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 TCGA-55-8506 TCGA-55-8508 
       17.79        23.64        29.19        17.56         0.36        20.28 
TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z 
       17.72        17.10        14.66         1.58        20.71        21.40 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O 
       15.81        19.99        17.95        14.60        88.64        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A470 TCGA-64-1676 TCGA-64-1679 
       19.53        56.71        54.35        39.25        56.81        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 
       37.02        38.37        28.41        51.25        20.05        18.84 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
       12.66        14.73         5.72         6.64         6.12        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        5.42         7.56        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 
        4.24        19.43         8.42        23.38        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5147 TCGA-75-6206 
       30.31         9.24         1.25        11.18        43.82        85.15 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      108.66        27.16        19.27        20.58       129.53        21.90 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 
       22.92         9.57       104.19        88.14        31.20        53.33 
TCGA-78-7539 TCGA-78-8640 TCGA-78-8655 TCGA-80-5608 TCGA-86-6562 TCGA-86-7701 
       26.01       232.18        77.59        93.11        12.36        31.13 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 
       38.04        32.78        19.89        37.74         4.08         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       22.82        32.65        31.20        23.05        14.60        11.61 
TCGA-86-8669 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       30.84        28.34        26.50        29.46         3.81        24.23 
TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       13.64        10.62        10.19         2.60        12.23        27.68 
TCGA-91-6849 TCGA-91-8496 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        1.15        16.60        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       42.25        64.60        61.48        25.48        18.54         0.59 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        16.41        14.30        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       20.84        18.67        24.56         1.45        21.57        18.08 
TCGA-J2-A4AG TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       32.48        18.58        38.63         2.76        86.14        58.45 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG 
       58.85         5.49        29.46        24.36        73.91        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.13         1.64        47.08         0.43        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

$`1Q GAIN WILD-TYPE`
TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 TCGA-38-4630 TCGA-38-4631 
        9.96         9.01        26.01        15.02        35.28        11.64 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-7661 TCGA-49-6745 TCGA-49-6761 
       43.53        38.10        23.93        18.31        17.16        11.64 
TCGA-50-5932 TCGA-55-6978 TCGA-55-7724 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 
       40.60         5.79        23.18        21.44        19.66        19.73 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8621 TCGA-64-1677 TCGA-78-7166 
       16.93        19.69        32.12        16.93        20.65         8.48 
TCGA-78-8660 TCGA-91-6836 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7948 
       10.55        13.71         1.45        17.29        16.54        15.65 
TCGA-97-A4M2 TCGA-J2-8192 TCGA-MP-A4TA TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       20.52        24.30        31.23        24.03        47.05        19.00 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-35-4122 TCGA-35-4123 
       12.00        21.99        26.01        24.00         7.40         5.98 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 
        8.68       120.79        37.71         4.37        44.42        42.77 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 
        3.19        37.15        38.24        33.73        33.30        28.37 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-7660 TCGA-44-7667 TCGA-44-8120 
       19.56        23.15        21.63        19.46        36.07         8.55 
TCGA-44-A479 TCGA-44-A47G TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-AAR2 
       15.98        11.54         8.81        29.75        55.89        73.12 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARR TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 
       28.90        40.41       164.12        60.16        47.41         9.27 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 
        8.45        15.12        60.72        42.35        25.55        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-53-7624 TCGA-53-A4EZ 
        6.21         0.72        10.13        36.79        34.29        35.21 
TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6968 TCGA-55-6971 TCGA-55-6975 
       38.73        30.58        14.30        42.51        46.03         3.88 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7570 TCGA-55-7728 TCGA-55-7994 TCGA-55-8097 
       40.54       107.21        27.09        23.15        19.82        15.65 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8512 
       22.16        15.42        15.72        14.47        13.74        19.96 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-62-8394 
       26.01        17.62        12.33         3.25         0.92         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       39.98        42.38        49.25        67.96        72.30        13.61 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       40.96        29.92        39.09        87.98         2.04        42.90 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-6216 TCGA-69-7763 TCGA-69-7974 
       28.47        20.05        14.04         4.64        22.68         6.05 
TCGA-69-7978 TCGA-69-8453 TCGA-73-4666 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
        4.41        26.73        26.30        50.33        66.64        77.85 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7152 
       49.84        36.66       100.57       163.10         5.69        39.95 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
      238.29        26.53         8.02        39.35        10.55        39.75 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 
      110.50        27.09         5.88        34.39        20.55        35.24 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8278 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 
        4.57        24.33        31.04        21.47        13.91        27.58 
TCGA-86-8672 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6848 TCGA-91-8497 
        0.62        26.47        41.36         1.97         7.36        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 
        1.18        19.82        22.45        63.52        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R 
        5.39        18.12        21.60        34.85        36.76        21.63 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 
       35.47        19.00        14.30        14.53         1.91        15.65 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TI 
       49.35        37.35        86.04        41.59        11.05        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A55A 
       11.15        19.13        71.05         0.49 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.00              0.49 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           232.18            238.29 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           21.455            21.810 
[1] "0.0 - 232.2 (21.5)" "0.5 - 238.3 (21.8)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         3       90       84        1        34        41
  1Q GAIN WILD-TYPE       2       43       55        0        16        31
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1Q GAIN MUTATED           38          8       15
  1Q GAIN WILD-TYPE         34          3       10
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                90                43
  STAGE IB                84                55
  STAGE II                 1                 0
  STAGE IIA               34                16
  STAGE IIB               41                31
  STAGE IIIA              38                34
  STAGE IIIB               8                 3
  STAGE IV                15                10
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q GAIN MUTATED   110 166  28  13
  1Q GAIN WILD-TYPE  61 112  18   6
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1             110                61
  T2             166               112
  T3              28                18
  T4              13                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  1Q GAIN MUTATED   208  61    40
  1Q GAIN WILD-TYPE 125  35    36
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                208               125
  N1                 61                35
  N2+N3              40                36
[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"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   218  15
  1Q GAIN WILD-TYPE 131  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    218   15
  1Q GAIN WILD-TYPE  131   10
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             218               131
  1              15                10
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   165 154
  1Q GAIN WILD-TYPE 111  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    165  154
  1Q GAIN WILD-TYPE  111   86
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE             165               111
  MALE               154                86
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   257  37
  1Q GAIN WILD-TYPE 153  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    257   37
  1Q GAIN WILD-TYPE  153   23
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              257               153
  YES              37                23
[1] 2 2
[1] FALSE
D2V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1Q GAIN MUTATED                           13
  1Q GAIN WILD-TYPE                          5
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1Q GAIN MUTATED                                  65
  1Q GAIN WILD-TYPE                                42
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                  197
  1Q GAIN WILD-TYPE                                                124
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1Q GAIN MUTATED                                            1
  1Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1Q GAIN MUTATED                                              13
  1Q GAIN WILD-TYPE                                             6
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1Q GAIN MUTATED                                2
  1Q GAIN WILD-TYPE                              0
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  1Q GAIN MUTATED                                    2
  1Q GAIN WILD-TYPE                                  1
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  1Q GAIN MUTATED                              0                            17
  1Q GAIN WILD-TYPE                            2                             6
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  1Q GAIN MUTATED                                 0
  1Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  1Q GAIN MUTATED                                               4
  1Q GAIN WILD-TYPE                                             1
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  1Q GAIN MUTATED                              5
  1Q GAIN WILD-TYPE                            5
D2V10, multiclass
                                                    clus
vv                                                   1Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             197
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   13
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                   17
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     5
                                                    clus
vv                                                   1Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               124
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      6
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                      6
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      1
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
D2V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   206   9   2  19
  1Q GAIN WILD-TYPE 138   4   2   7
D2V13, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             206               138
  R1               9                 4
  R2               2                 2
  RX              19                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1     6
  1Q GAIN WILD-TYPE                                0     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          34   241
  1Q GAIN WILD-TYPE                        18   149
D2V14, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          6                 1
  BLACK OR AFRICAN AMERICAN                     34                18
  WHITE                                        241               149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     3 238
  1Q GAIN WILD-TYPE   4 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3  238
  1Q GAIN WILD-TYPE    4  146
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             238               146
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    94  57
  2P GAIN WILD-TYPE 229 124
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              151               353 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               57               124 
$`2P GAIN MUTATED`
TCGA-05-4382 TCGA-05-4418 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-7670 
       19.96         9.01        35.28        11.64        14.73        29.00 
TCGA-49-6742 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-7573 TCGA-55-8203 
       16.04        41.69        23.05        48.62        16.01        17.98 
TCGA-55-8205 TCGA-55-8511 TCGA-67-6217 TCGA-73-4662 TCGA-78-7633 TCGA-91-6836 
       19.69        18.15        13.87        82.68        50.24        13.71 
TCGA-95-7043 TCGA-95-A4VK TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       16.54        21.40        23.80         6.35        10.09        27.19 
TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 
        2.43         3.98        45.01        37.02         0.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 
       14.96        29.98        30.02        29.00        22.03         7.40 
TCGA-35-4123 TCGA-38-4632 TCGA-44-2657 TCGA-44-2668 TCGA-44-3918 TCGA-44-6779 
        5.98        44.61        44.42        25.02        34.06        16.44 
TCGA-44-7667 TCGA-44-A47A TCGA-44-A47G TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       36.07        15.32        11.54        28.11        28.57        12.66 
TCGA-49-4507 TCGA-49-4510 TCGA-49-6743 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ 
        8.81        29.46        53.29         8.55       123.58       221.33 
TCGA-50-5072 TCGA-50-5946 TCGA-50-6592 TCGA-50-6593 TCGA-50-6673 TCGA-53-7624 
        8.22        53.16        25.55        11.05         0.72        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-6970 TCGA-55-6981 
       13.94        35.21        38.73        67.89        15.25        45.34 
TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 TCGA-55-7907 TCGA-55-7910 
       92.81        28.67        20.02        22.03        11.28        34.19 
TCGA-55-7911 TCGA-55-7995 TCGA-55-8096 TCGA-55-8208 TCGA-55-8507 TCGA-55-8510 
       17.65        29.23        23.64        22.16        13.74        17.72 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       14.66         1.58        12.33         0.92        15.81        19.99 
TCGA-55-A57B TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-64-1678 TCGA-64-1680 
       17.95        49.25        47.80        56.71        39.09        37.02 
TCGA-64-5774 TCGA-67-3770 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       87.98        20.05        13.61         7.56         6.05         4.41 
TCGA-69-7980 TCGA-69-8255 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS 
       13.51         4.24        15.35        30.31         9.24        11.18 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 
       77.85        43.82        36.66       108.66       100.57        27.16 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
      129.53        21.90        38.50        64.90        22.92         9.57 
TCGA-78-7163 TCGA-78-7539 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
      238.29        26.01       232.18        77.59       110.50        93.11 
TCGA-86-6562 TCGA-86-7711 TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       12.36        34.39        38.04        35.24        37.74         4.08 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 TCGA-91-6829 TCGA-91-6831 
       14.60        11.61        30.84        28.34        41.36        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7567 
        2.60        12.23        27.68        23.61         1.08        18.67 
TCGA-95-7944 TCGA-97-7547 TCGA-97-7938 TCGA-97-8179 TCGA-99-8025 TCGA-99-8032 
       12.39        64.60         0.59        14.30        34.85         1.45 
TCGA-99-8033 TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-NJ-A4YQ 
       21.57         1.91         2.76        41.59        19.13        47.08 
TCGA-O1-A52J 
       59.11 

$`2P GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 
       14.01         9.96         8.02        20.05        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       15.02        28.41        26.30        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 
       23.93        27.78        86.01        18.31        29.23         9.37 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
       11.08        46.72        17.16        11.64       156.66        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 
       40.60        21.47         5.79         7.79         7.99        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 
       14.53        21.44         6.15        19.66        19.73        16.93 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       32.12        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-8660 
       20.19        20.65        52.60        39.09         8.48        10.55 
TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 
       85.32        16.18         1.45         6.12        17.29         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.68        15.65        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA 
       17.75        20.68        24.30        21.83         5.29        31.23 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4422 
       10.09        50.07        24.03        47.05        19.00        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         0.46         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 
       37.71        49.05         4.37        46.98        44.94        42.77 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 
        3.19        37.15        38.24        38.89        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        32.45        61.28        22.72        19.46 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47B TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 
        9.44        13.64        13.45        76.21        35.54        14.07 
TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV 
       32.84        29.75        55.89        55.33        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARR TCGA-4B-A93V 
       73.12        62.24        28.90        40.41       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
       49.28         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 
       48.46        60.72        57.53        42.35         3.91        12.16 
TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        6.21        10.13        36.99        36.79        27.25        30.54 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6982 TCGA-55-6984 
       46.03        53.65         3.88        69.34        32.71        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 
       40.54       107.21        70.26        27.09        32.71         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 
       23.15        25.41        18.64        18.44        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 
       15.19        23.08         5.06        17.79        15.65        29.19 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42        17.56        15.72        14.47         0.36        20.28 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48Y TCGA-55-A48Z 
       19.96        26.01        17.10        17.62        20.71        21.40 
TCGA-55-A490 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
        3.25         4.57        39.98        42.38        14.60        88.64 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
       40.96        29.92        56.81        81.80        38.37         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        6.12        22.68         5.42        13.41        14.01        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 
       26.73        19.43         8.42        23.38        26.30         4.31 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-6206 TCGA-75-6212 TCGA-78-7143 
        1.25        50.33        66.64        85.15        49.84       163.10 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        5.69        19.27        20.58        39.95       119.51        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       32.09         5.88       104.19        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-83-5908 
        8.02        53.33        39.35        10.55        39.75        27.09 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8056 
        5.88        31.13        20.55        32.78        19.89         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
       23.05        21.47        13.91        27.58         0.62        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       29.46         3.81        24.23        13.64        26.47        10.62 
TCGA-91-6830 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        1.97         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 
       19.82        22.45        17.46        19.00        41.82        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
        2.76        19.89        42.25        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
       18.54        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       16.41        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       18.67        24.56        36.76        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 
       32.48        19.00        14.30        14.53        18.58        15.65 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       58.85         5.49        29.46        11.05        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       11.15        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.49         0.43        19.82        20.28        16.87 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.00              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           238.29            164.12 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            22.03             21.47 
[1] "0.0 - 238.3 (22.0)" "0.1 - 164.1 (21.5)"
[1] "hr=" "1"  
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         3       41       39        0        16        17
  2P GAIN WILD-TYPE       2       92      100        1        34        55
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2P GAIN MUTATED           23          4       10
  2P GAIN WILD-TYPE         49          7       15
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                41                92
  STAGE IB                39               100
  STAGE II                 0                 1
  STAGE IIA               16                34
  STAGE IIB               17                55
  STAGE IIIA              23                49
  STAGE IIIB               4                 7
  STAGE IV                10                15
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED    50  80  17   6
  2P GAIN WILD-TYPE 121 198  29  13
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              50               121
  T2              80               198
  T3              17                29
  T4               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  2P GAIN MUTATED    96  29    26
  2P GAIN WILD-TYPE 237  67    50
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                 96               237
  N1                 29                67
  N2+N3              26                50
[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"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   105  10
  2P GAIN WILD-TYPE 244  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    105   10
  2P GAIN WILD-TYPE  244   15
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0             105               244
  1              10                15
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    86  68
  2P GAIN WILD-TYPE 190 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     86   68
  2P GAIN WILD-TYPE  190  172
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              86               190
  MALE                68               172
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   114  27
  2P GAIN WILD-TYPE 296  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    114   27
  2P GAIN WILD-TYPE  296   33
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO              114               296
  YES              27                33
[1] 2 2
[1] FALSE
D3V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2P GAIN MUTATED                            4
  2P GAIN WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2P GAIN MUTATED                                  33
  2P GAIN WILD-TYPE                                74
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                  100
  2P GAIN WILD-TYPE                                                221
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2P GAIN MUTATED                                            0
  2P GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  2P GAIN MUTATED                                               5
  2P GAIN WILD-TYPE                                            14
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  2P GAIN MUTATED                                2
  2P GAIN WILD-TYPE                              0
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  2P GAIN MUTATED                                    1
  2P GAIN WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  2P GAIN MUTATED                              0                             5
  2P GAIN WILD-TYPE                            2                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  2P GAIN MUTATED                                 0
  2P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  2P GAIN MUTATED                                               2
  2P GAIN WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  2P GAIN MUTATED                              2
  2P GAIN WILD-TYPE                            8
D3V10, multiclass
                                                    clus
vv                                                   2P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             100
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    5
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   2P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               221
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     14
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
D3V12, continuous
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED   108   7   2   9
  2P GAIN WILD-TYPE 236   6   2  17
D3V13, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0             108               236
  R1               7                 6
  R2               2                 2
  RX               9                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  1     2
  2P GAIN WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          12   114
  2P GAIN WILD-TYPE                        40   276
D3V14, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                     12                40
  WHITE                                        114               276
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     5 108
  2P GAIN WILD-TYPE   2 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5  108
  2P GAIN WILD-TYPE    2  276
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             108               276
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    88  52
  2Q GAIN WILD-TYPE 235 129
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              140               364 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               52               129 
$`2Q GAIN MUTATED`
TCGA-05-4382 TCGA-05-4405 TCGA-05-4418 TCGA-38-4630 TCGA-38-6178 TCGA-44-7670 
       19.96        20.05         9.01        35.28        14.73        29.00 
TCGA-49-6742 TCGA-50-6597 TCGA-55-1592 TCGA-55-7573 TCGA-55-7726 TCGA-55-8203 
       16.04        41.69        23.05        16.01        21.44        17.98 
TCGA-55-8205 TCGA-55-8207 TCGA-67-6217 TCGA-73-4662 TCGA-78-7633 TCGA-91-6836 
       19.69        32.12        13.87        82.68        50.24        13.71 
TCGA-95-7043 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4TC 
       16.54        17.75        23.80        10.09        27.19         2.43 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 TCGA-05-4417 
        3.98        45.01        37.02         0.00         2.99        14.96 
TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 
       30.02        25.02        29.00        22.03         7.40         8.68 
TCGA-38-4632 TCGA-44-2657 TCGA-44-2668 TCGA-44-3918 TCGA-44-7662 TCGA-44-A47A 
       44.61        44.42        25.02        34.06         7.17        15.32 
TCGA-44-A47G TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 
       11.54        28.11        28.57        12.66        14.07         8.81 
TCGA-49-4510 TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5072 TCGA-50-6592 TCGA-50-6593 
       29.46       221.33         9.86         8.22        25.55        11.05 
TCGA-50-6673 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 
        0.72        34.29        13.94        35.21        38.73        67.89 
TCGA-55-6970 TCGA-55-6975 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 
       15.25         3.88        92.81        28.67        20.02        22.03 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8096 TCGA-55-8208 
       11.28        34.19        17.65        29.23        23.64        22.16 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 TCGA-55-A493 
       13.74        17.72        17.10        14.66        12.33         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8402 TCGA-62-A46R TCGA-62-A471 
       15.81        19.99        17.95        49.25        56.71        40.96 
TCGA-64-1680 TCGA-67-3770 TCGA-67-3771 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
       37.02        20.05        20.05        13.61         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 TCGA-73-4675 TCGA-73-A9RS TCGA-75-5146 
        4.41        13.51         4.24        30.31        11.18        77.85 
TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7149 TCGA-78-7150 
       85.15        36.66       108.66       100.57       129.53        21.90 
TCGA-78-7155 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       38.50        22.92       104.19       238.29        88.14        26.53 
TCGA-78-7539 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 
       26.01       232.18        77.59       110.50        93.11        12.36 
TCGA-86-6851 TCGA-86-7713 TCGA-86-8055 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
        5.88        38.04         4.08        14.60        11.61        30.84 
TCGA-86-8673 TCGA-91-6829 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JN 
       28.34        41.36         2.60        12.23        27.68        23.61 
TCGA-93-A4JO TCGA-95-7567 TCGA-95-7944 TCGA-97-7547 TCGA-97-7937 TCGA-97-7938 
        1.08        18.67        12.39        64.60        18.54         0.59 
TCGA-97-8179 TCGA-99-8025 TCGA-99-8033 TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4T9 
       14.30        34.85        21.57         1.91         2.76        41.59 
TCGA-NJ-A4YQ TCGA-O1-A52J 
       47.08        59.11 

$`2Q GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 
       14.01         9.96         8.02        26.01        15.02        15.02 
TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       28.41        11.64        26.30        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 
       23.93        27.78        86.01        18.31        29.23         9.37 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
       11.08        46.72        17.16        11.64       156.66        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       40.60        21.47        48.62         5.79         7.79         7.99 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 
       23.18        14.53         6.15        19.66        19.73        16.93 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       18.15        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-8660 
       20.19        20.65        52.60        39.09         8.48        10.55 
TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 
       85.32        16.18         1.45         6.12        17.29         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A743 TCGA-MP-A4T8 
       20.52        20.68        24.30         6.35        21.83         5.29 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       31.23        10.09        50.07        24.03        47.05        19.00 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 
       29.98        12.00        21.99        26.01        25.02        24.00 
TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 
        4.96         9.04         2.04         0.46         5.98        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F TCGA-44-2656 TCGA-44-2659 
      120.79        37.71        49.05         4.37        46.98        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 
       42.77         3.19        37.15        38.24        38.89        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       22.72        19.46        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        8.55        15.98         9.44        13.64        13.45        76.21 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
       35.54        32.84        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       40.41       123.58       164.12        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
       15.72        60.16        47.41        49.28         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 
       53.16        42.35         3.91        12.16         6.21        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-5899 TCGA-55-6543 
       36.99        36.79        27.25        30.54        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
       80.52         5.62        42.51        40.73        46.03        53.65 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       69.34        45.34        32.71        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       70.26        27.09        32.71         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.64        18.44        19.82        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 
        5.06        17.79        15.65        29.19        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
       15.72        14.47         0.36        20.28        19.96        26.01 
TCGA-55-8614 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-62-8394 
       17.62         1.58        20.71        21.40         3.25         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        14.60        88.64        47.80        19.53 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 
       54.35        67.96        72.30        13.61        39.25        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        39.09        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       42.90        28.41        51.25        28.47        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
       22.68         5.42        13.41        14.01        13.45        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       19.43         8.42        23.38        26.30        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6212 
        9.24         1.25        50.33        66.64        43.82        49.84 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 
      163.10        27.16         5.69        19.27        20.58        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
      119.51        19.50        32.09         5.88        64.90         9.57 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
       31.20         8.02        53.33        39.35        10.55        39.75 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       27.09        31.13        34.39        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       35.24        37.74         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 
       32.65        31.04        31.20        23.05        21.47        13.91 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       27.58         0.62        26.50        29.46         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6848 
       13.64        26.47        10.62         1.97        10.19         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       17.46        19.00        41.82        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 
       42.25        63.52        61.48        25.48        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
        5.39        18.12        15.39        16.41        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       21.44        19.76        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.63        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
       14.30        14.53        18.58        15.65        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       29.46        11.05        24.36        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05        74.33         0.13         1.64         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.43        19.82        20.28        16.87 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.00              0.13 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           238.29            164.12 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           21.505            21.630 
[1] "0.0 - 238.3 (21.5)" "0.1 - 164.1 (21.6)"
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         3       39       37        0        15        14
  2Q GAIN WILD-TYPE       2       94      102        1        35        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2Q GAIN MUTATED           22          4        9
  2Q GAIN WILD-TYPE         50          7       16
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                39                94
  STAGE IB                37               102
  STAGE II                 0                 1
  STAGE IIA               15                35
  STAGE IIB               14                58
  STAGE IIIA              22                50
  STAGE IIIB               4                 7
  STAGE IV                 9                16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED    47  76  14   5
  2Q GAIN WILD-TYPE 124 202  32  14
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              47               124
  T2              76               202
  T3              14                32
  T4               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  2Q GAIN MUTATED    90  27    24
  2Q GAIN WILD-TYPE 243  69    52
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                 90               243
  N1                 27                69
  N2+N3              24                52
[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"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED   100   9
  2Q GAIN WILD-TYPE 249  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED    100    9
  2Q GAIN WILD-TYPE  249   16
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0             100               249
  1               9                16
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    76  67
  2Q GAIN WILD-TYPE 200 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     76   67
  2Q GAIN WILD-TYPE  200  173
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              76               200
  MALE                67               173
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED   106  24
  2Q GAIN WILD-TYPE 304  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED    106   24
  2Q GAIN WILD-TYPE  304   36
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO              106               304
  YES              24                36
[1] 2 2
[1] FALSE
D4V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2Q GAIN MUTATED                            4
  2Q GAIN WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2Q GAIN MUTATED                                  37
  2Q GAIN WILD-TYPE                                70
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                   87
  2Q GAIN WILD-TYPE                                                234
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2Q GAIN MUTATED                                            0
  2Q GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  2Q GAIN MUTATED                                               5
  2Q GAIN WILD-TYPE                                            14
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  2Q GAIN MUTATED                                0
  2Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  2Q GAIN MUTATED                                    1
  2Q GAIN WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  2Q GAIN MUTATED                              0                             5
  2Q GAIN WILD-TYPE                            2                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  2Q GAIN MUTATED                                 0
  2Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  2Q GAIN MUTATED                                               2
  2Q GAIN WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  2Q GAIN MUTATED                              2
  2Q GAIN WILD-TYPE                            8
D4V10, multiclass
                                                    clus
vv                                                   2Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              87
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    5
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   2Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               234
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     14
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
D4V12, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED   102   5   2   7
  2Q GAIN WILD-TYPE 242   8   2  19
D4V13, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0             102               242
  R1               5                 8
  R2               2                 2
  RX               7                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     1
  2Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          13   104
  2Q GAIN WILD-TYPE                        39   286
D4V14, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                     13                39
  WHITE                                        104               286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4 101
  2Q GAIN WILD-TYPE   3 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4  101
  2Q GAIN WILD-TYPE    3  283
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             101               283
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    26  17
  3P GAIN WILD-TYPE 297 164
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               43               461 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17               164 
$`3P GAIN MUTATED`
TCGA-05-4427 TCGA-05-4434 TCGA-64-1677 TCGA-91-7771 TCGA-93-A4JQ TCGA-J2-8194 
       26.01        15.02        20.65        16.18        17.29        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-05-4420 TCGA-05-4424 TCGA-05-5428 TCGA-35-5375 
        6.35        10.09        29.98        30.02        22.03         8.68 
TCGA-44-5643 TCGA-44-A47B TCGA-49-4487 TCGA-49-4488 TCGA-49-4507 TCGA-49-6743 
       33.30         9.44        28.11        28.57         8.81        53.29 
TCGA-49-AARQ TCGA-50-5946 TCGA-53-A4EZ TCGA-55-6972 TCGA-55-7903 TCGA-55-7995 
      221.33        53.16        35.21        53.65        18.64        29.23 
TCGA-64-5775 TCGA-69-7760 TCGA-69-7974 TCGA-69-7978 TCGA-69-A59K TCGA-73-4676 
        2.04         6.64         6.05         4.41        19.43         9.24 
TCGA-75-5125 TCGA-78-7143 TCGA-78-7145 TCGA-78-8662 TCGA-86-7711 TCGA-86-7953 
       66.64       163.10        27.16       110.50        34.39        32.78 
TCGA-86-8074 TCGA-86-8075 TCGA-91-6828 TCGA-95-8494 TCGA-97-8176 TCGA-J2-A4AD 
        0.79        22.82        10.62         2.76        15.39        18.08 
TCGA-MN-A4N4 
       38.63 

$`3P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       43.53        38.10        42.08        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       16.04        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       21.47        41.69        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       19.66        19.73        17.98        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       18.15        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.19        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 
       50.24        10.55        85.32        13.71         1.45         6.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       21.83        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
       47.05        19.00         2.99        14.96        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
        9.04         2.04         0.46         7.40         5.98        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       38.24        38.89        34.06        33.73        26.56        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 
       15.32        11.54        13.64        13.45        76.21        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       35.54        14.07        32.84        29.46        29.75        55.89 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.33        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
        8.55        40.41       123.58       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       48.46        60.72        57.53        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 
       36.79        27.25        34.29        30.54        13.94        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       67.89        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25        46.03         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       23.15        25.41        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       19.82        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       19.99        17.95         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       56.81        39.09        81.80        37.02        38.37        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       42.90        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 
        6.12        22.68        13.61         5.42         7.56        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 
       13.51        14.01        13.45         4.24        26.73         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       23.38        26.30        15.35         4.31        30.31         1.25 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        11.18        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       36.66       108.66       100.57         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 
       93.11        27.09        12.36         5.88        31.13        38.04 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       24.33        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       28.34        26.50        29.46         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       26.47        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 
       41.82        18.67        12.39        27.29        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       15.91        18.67         5.39        18.12        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       24.56        34.85        36.76         1.45        21.57        21.63 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       35.47        32.48        19.00        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       18.58        15.65         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       11.05        24.36        14.10        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82        20.28        59.11        16.87 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.79              0.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           221.33            238.29 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            22.03             21.60 
[1] "0.8 - 221.3 (22.0)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         1       12        7        0         6         8
  3P GAIN WILD-TYPE       4      121      132        1        44        64
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3P GAIN MUTATED            8          0        2
  3P GAIN WILD-TYPE         64         11       23
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                12               121
  STAGE IB                 7               132
  STAGE II                 0                 1
  STAGE IIA                6                44
  STAGE IIB                8                64
  STAGE IIIA               8                64
  STAGE IIIB               0                11
  STAGE IV                 2                23
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED    15  19   7   3
  3P GAIN WILD-TYPE 156 259  39  16
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              15               156
  T2              19               259
  T3               7                39
  T4               3                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  3P GAIN MUTATED    26  13     5
  3P GAIN WILD-TYPE 307  83    71
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                 26               307
  N1                 13                83
  N2+N3               5                71
[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"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    28   2
  3P GAIN WILD-TYPE 321  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     28    2
  3P GAIN WILD-TYPE  321   23
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              28               321
  1               2                23
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    21  23
  3P GAIN WILD-TYPE 255 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     21   23
  3P GAIN WILD-TYPE  255  217
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              21               255
  MALE                23               217
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    30  10
  3P GAIN WILD-TYPE 380  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     30   10
  3P GAIN WILD-TYPE  380   50
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               30               380
  YES              10                50
[1] 2 2
[1] FALSE
D5V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3P GAIN MUTATED                            3
  3P GAIN WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3P GAIN MUTATED                                  12
  3P GAIN WILD-TYPE                                95
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                   26
  3P GAIN WILD-TYPE                                                295
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3P GAIN MUTATED                                            0
  3P GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  3P GAIN MUTATED                                               1
  3P GAIN WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  3P GAIN MUTATED                                1
  3P GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  3P GAIN MUTATED                                    0
  3P GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  3P GAIN MUTATED                              0                             1
  3P GAIN WILD-TYPE                            2                            22
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  3P GAIN MUTATED                                 0
  3P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  3P GAIN MUTATED                                               0
  3P GAIN WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3P GAIN MUTATED                              0
  3P GAIN WILD-TYPE                           10
D5V10, multiclass
                                                    clus
vv                                                   3P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               12
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              26
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   3P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               295
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    26   2   1   5
  3P GAIN WILD-TYPE 318  11   3  21
D5V13, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              26               318
  R1               2                11
  R2               1                 3
  RX               5                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           3    33
  3P GAIN WILD-TYPE                        49   357
D5V14, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      3                49
  WHITE                                         33               357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  30
  3P GAIN WILD-TYPE   5 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   30
  3P GAIN WILD-TYPE    5  354
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              30               354
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    57  32
  3Q GAIN WILD-TYPE 266 149
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               89               415 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               32               149 
$`3Q GAIN MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4427 TCGA-05-4434 TCGA-44-7670 TCGA-49-AAR0 
       19.96         8.02        26.01        15.02        29.00       156.66 
TCGA-49-AARN TCGA-55-7724 TCGA-55-7726 TCGA-55-8205 TCGA-55-A491 TCGA-91-7771 
       37.32        23.18        21.44        19.69        20.58        16.18 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-97-A4LX TCGA-L9-A443 
       17.29        16.54         2.86        15.68        20.19         6.35 
TCGA-L9-A444 TCGA-05-4389 TCGA-05-4420 TCGA-05-4424 TCGA-05-5425 TCGA-05-5428 
       10.09        45.01        29.98        30.02        29.00        22.03 
TCGA-05-5429 TCGA-35-5375 TCGA-38-4626 TCGA-44-2668 TCGA-44-3918 TCGA-44-5643 
        9.04         8.68       120.79        25.02        34.06        33.30 
TCGA-44-6145 TCGA-44-7660 TCGA-44-A47B TCGA-49-4487 TCGA-49-4488 TCGA-49-4507 
       19.56        19.46         9.44        28.11        28.57         8.81 
TCGA-49-6743 TCGA-49-AARQ TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5946 
       53.29       221.33         8.22        14.27        48.46        53.16 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6972 TCGA-55-6984 TCGA-55-7903 TCGA-55-7913 
       35.21        38.73        53.65        24.99        18.64        18.44 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8614 TCGA-55-A490 TCGA-62-A46O TCGA-64-1679 
       29.23        29.72        17.62         3.25        47.80        81.80 
TCGA-64-5815 TCGA-69-7760 TCGA-69-7978 TCGA-69-7980 TCGA-69-A59K TCGA-73-4676 
       28.47         6.64         4.41        13.51        19.43         9.24 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       50.33        66.64        43.82       163.10        27.16         5.69 
TCGA-78-7154 TCGA-78-8662 TCGA-86-7711 TCGA-86-7953 TCGA-86-8074 TCGA-86-8075 
       19.50       110.50        34.39        32.78         0.79        22.82 
TCGA-86-8278 TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 TCGA-91-6828 TCGA-91-6830 
       31.04        21.47        30.84        28.34        10.62         1.97 
TCGA-91-6835 TCGA-93-A4JN TCGA-95-8494 TCGA-97-8176 TCGA-J2-A4AD TCGA-L9-A8F4 
        2.60        23.61         2.76        15.39        18.08        15.65 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4TF TCGA-NJ-A4YF TCGA-S2-AA1A 
       38.63        86.14        11.05        71.05        16.87 

$`3Q GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-5420 TCGA-38-4629 
       14.01         9.96        20.05         9.01        15.02        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       35.28        11.64        14.73        26.30        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 
       42.08        23.93        27.78        86.01        18.31        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
        9.37        11.08        46.72        16.04        17.16        11.64 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
       40.60        21.47        41.69        23.05        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 
        7.79         7.99        16.01        14.53         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       19.73        17.98        16.93        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       16.93        22.65        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7948 TCGA-95-A4VK 
       85.32        13.71         1.45         6.12        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       18.18        17.92        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       23.80        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       10.09        50.07         3.98        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
       47.05        19.00         2.99        14.96        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5715 
       26.01        25.02        25.02        24.00         4.96         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
        0.46         7.40         5.98        97.74        37.71        49.05 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 
       44.61         4.37        46.98        44.42        44.94        42.77 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 
        3.19        37.15        38.24        38.89        33.73        26.56 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.37        28.01        23.77        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 
       32.45        61.28        16.44        22.72         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 TCGA-49-4494 
       11.54        13.64        13.45        76.21        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 
       14.07        32.84        29.46        29.75        55.89        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
       40.41       123.58       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
      101.72        15.72        60.16        47.41        49.28         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       78.67         8.45        15.12        60.72        57.53        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        67.89        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 
       42.51        40.73        15.25        46.03         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       45.34        32.71        92.81        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
       23.15        25.41        11.28        34.19        17.65        19.82 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.10        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        19.99        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        39.09        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 
        2.04        42.90        28.41        51.25        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 
       13.41        14.01        13.45         4.24        26.73         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       23.38        26.30        15.35         4.31        30.31         1.25 
TCGA-73-A9RS TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       11.18        77.85        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      100.57        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
      119.51        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       31.13        38.04        20.55        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
        4.08         4.57        24.33        32.65        31.20        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
       14.60        11.61        13.91        27.58         0.62        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       29.46         3.81        24.23        13.64        26.47        41.36 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.19        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO 
       14.27         1.18        19.82        22.45        17.46         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP 
       19.00        41.82        18.67        12.39        27.29        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        0.59        15.91        18.67         5.39        18.12        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
       21.63        35.47        32.48        19.00        14.30        14.53 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
        1.91        18.58         2.76        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH 
       86.04        58.85         5.49        41.59        29.46        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        11.15        19.13        73.91        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        47.08         0.49         0.43        19.82        20.28 
TCGA-O1-A52J 
       59.11 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.79              0.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           221.33            238.29 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            22.03             21.60 
[1] "0.8 - 221.3 (22.0)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         2       27       21        0        12        11
  3Q GAIN WILD-TYPE       3      106      118        1        38        61
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3Q GAIN MUTATED           12          0        4
  3Q GAIN WILD-TYPE         60         11       21
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                27               106
  STAGE IB                21               118
  STAGE II                 0                 1
  STAGE IIA               12                38
  STAGE IIB               11                61
  STAGE IIIA              12                60
  STAGE IIIB               0                11
  STAGE IV                 4                21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q GAIN MUTATED    34  46   8   2
  3Q GAIN WILD-TYPE 137 232  38  17
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              34               137
  T2              46               232
  T3               8                38
  T4               2                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  3Q GAIN MUTATED    59  20    10
  3Q GAIN WILD-TYPE 274  76    66
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                 59               274
  N1                 20                76
  N2+N3              10                66
[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"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    62   4
  3Q GAIN WILD-TYPE 287  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     62    4
  3Q GAIN WILD-TYPE  287   21
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              62               287
  1               4                21
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    46  44
  3Q GAIN WILD-TYPE 230 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     46   44
  3Q GAIN WILD-TYPE  230  196
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              46               230
  MALE                44               196
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    71  12
  3Q GAIN WILD-TYPE 339  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     71   12
  3Q GAIN WILD-TYPE  339   48
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               71               339
  YES              12                48
[1] 2 2
[1] FALSE
D6V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3Q GAIN MUTATED                            4
  3Q GAIN WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3Q GAIN MUTATED                                  21
  3Q GAIN WILD-TYPE                                86
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                   59
  3Q GAIN WILD-TYPE                                                262
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3Q GAIN MUTATED                                            1
  3Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  3Q GAIN MUTATED                                               2
  3Q GAIN WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  3Q GAIN MUTATED                                1
  3Q GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  3Q GAIN MUTATED                                    0
  3Q GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  3Q GAIN MUTATED                              0                             2
  3Q GAIN WILD-TYPE                            2                            21
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  3Q GAIN MUTATED                                 0
  3Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  3Q GAIN MUTATED                                               0
  3Q GAIN WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3Q GAIN MUTATED                              0
  3Q GAIN WILD-TYPE                           10
D6V10, multiclass
                                                    clus
vv                                                   3Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              59
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   3Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               262
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
D6V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    60   2   2   7
  3Q GAIN WILD-TYPE 284  11   2  19
D6V13, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              60               284
  R1               2                11
  R2               2                 2
  RX               7                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  0     0
  3Q GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          10    65
  3Q GAIN WILD-TYPE                        42   325
D6V14, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                     10                42
  WHITE                                         65               325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3  65
  3Q GAIN WILD-TYPE   4 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   65
  3Q GAIN WILD-TYPE    4  319
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              65               319
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    46  35
  4P GAIN WILD-TYPE 277 146
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               81               423 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               35               146 
$`4P GAIN MUTATED`
TCGA-38-4629 TCGA-38-4631 TCGA-44-2662 TCGA-44-7661 TCGA-55-1595 TCGA-55-7573 
       28.41        11.64        42.08        18.31        48.62        16.01 
TCGA-55-8091 TCGA-55-A492 TCGA-80-5611 TCGA-91-6836 TCGA-95-7948 TCGA-05-4432 
       19.73        19.59        85.32        13.71        15.65        25.02 
TCGA-05-5423 TCGA-38-4628 TCGA-44-2656 TCGA-44-4112 TCGA-44-5645 TCGA-44-6775 
        4.96        49.05        46.98        26.56        28.01        23.18 
TCGA-44-A4SU TCGA-49-4488 TCGA-49-6767 TCGA-49-AARQ TCGA-50-6591 TCGA-50-6592 
       13.45        28.57        22.26       221.33         3.91        25.55 
TCGA-50-6594 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-6712 
       12.16        10.13        34.29        13.94        38.73         5.62 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8302 TCGA-55-A490 TCGA-55-A493 
       23.08        17.79        23.64        15.72         3.25         0.92 
TCGA-55-A57B TCGA-62-8402 TCGA-62-A46O TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 
       17.95        49.25        47.80        40.96        56.81        37.02 
TCGA-64-1681 TCGA-69-7980 TCGA-69-8253 TCGA-75-5146 TCGA-75-5147 TCGA-75-6214 
       38.37        13.51        14.01        77.85        43.82        36.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 
      100.57       163.10        27.16        21.90       119.51        19.50 
TCGA-78-7155 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7539 
       38.50       238.29        88.14        26.53        31.20        26.01 
TCGA-78-7542 TCGA-86-7953 TCGA-86-7955 TCGA-86-8278 TCGA-86-8279 TCGA-86-A456 
       10.55        32.78        35.24        31.04        31.20        29.46 
TCGA-91-6848 TCGA-93-A4JP TCGA-95-8494 TCGA-95-A4VP TCGA-97-7937 TCGA-97-8179 
        7.36        19.00         2.76        19.89        18.54        14.30 
TCGA-97-8552 TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 
       20.58         1.91         2.76        58.45        49.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4TF TCGA-NJ-A4YF 
       58.85        11.05        71.05 

$`4P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       26.01        15.02        15.02        35.28        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 
       43.53        38.10        23.93        27.78        86.01        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       11.64       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 
       23.05         5.79         7.79         7.99        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
       21.44         6.15        19.66        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 
       20.19        20.65        13.87        52.60        82.68        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
        8.48        50.24        10.55        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN 
       17.29        16.54         2.86        15.68        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       23.80         6.35        10.09        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       25.02        24.00        29.00        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        0.46         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 
       37.71        44.61         4.37        44.42        44.94        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
        3.19        25.02        37.15        38.24        38.89        34.06 
TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.73        33.30        28.37        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       21.63        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       15.98        15.32         9.44        11.54        13.64        76.21 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.11        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       73.12        62.24        28.90         8.55        40.41       123.58 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
       53.16        42.35        11.05         6.21         0.72        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 
       36.79        27.25        30.54        35.21        67.89        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       14.30        80.52        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
       24.99        40.54       107.21        70.26        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8097 TCGA-55-8206 
       29.23        29.72        15.19         5.06        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42        17.56        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A494 
       14.66         1.58        12.33        20.71        21.40        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99         4.57        39.98        42.38        14.60        88.64 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 
       39.25        29.92        39.09        81.80        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       42.90        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        6.05         4.41        13.41        13.45         4.24        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       19.43         8.42        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 
       30.31         9.24         1.25        50.33        11.18        66.64 
TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       85.15        49.84       108.66         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
      129.53        39.95        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 
        9.57       104.19         8.02        53.33        39.35       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 
        5.88        31.13        34.39        38.04        20.55        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       32.65        23.05        21.47        14.60        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 
       30.84        27.58         0.62        28.34        26.50         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        12.23        27.68         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-97-7546 
        1.08        41.82        18.67        12.39        27.29        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        61.48        25.48         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       18.67         5.39        18.12        15.39        16.41        21.60 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        21.57        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 
       32.48        19.00        14.30        14.53        18.58        15.65 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       38.63        86.14        37.35         5.49        41.59        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG 
       24.36        14.10        11.15        19.13        73.91        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.92              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           238.29            232.18 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            26.01             21.40 
[1] "0.9 - 238.3 (26.0)" "0.0 - 232.2 (21.4)"
[1] "hr=" "1"  
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         3       16       27        0         7        12
  4P GAIN WILD-TYPE       2      117      112        1        43        60
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4P GAIN MUTATED            9          1        8
  4P GAIN WILD-TYPE         63         10       17
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                16               117
  STAGE IB                27               112
  STAGE II                 0                 1
  STAGE IIA                7                43
  STAGE IIB               12                60
  STAGE IIIA               9                63
  STAGE IIIB               1                10
  STAGE IV                 8                17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED    20  54   6   2
  4P GAIN WILD-TYPE 151 224  40  17
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              20               151
  T2              54               224
  T3               6                40
  T4               2                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  4P GAIN MUTATED    56  14    11
  4P GAIN WILD-TYPE 277  82    65
D7V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0                 56               277
  N1                 14                82
  N2+N3              11                65
[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"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    56   8
  4P GAIN WILD-TYPE 293  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     56    8
  4P GAIN WILD-TYPE  293   17
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              56               293
  1               8                17
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    45  38
  4P GAIN WILD-TYPE 231 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     45   38
  4P GAIN WILD-TYPE  231  202
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              45               231
  MALE                38               202
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    70   6
  4P GAIN WILD-TYPE 340  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     70    6
  4P GAIN WILD-TYPE  340   54
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               70               340
  YES               6                54
[1] 2 2
[1] FALSE
D7V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4P GAIN MUTATED                            2
  4P GAIN WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4P GAIN MUTATED                                  11
  4P GAIN WILD-TYPE                                96
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                   61
  4P GAIN WILD-TYPE                                                260
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4P GAIN MUTATED                                            0
  4P GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  4P GAIN MUTATED                                               3
  4P GAIN WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  4P GAIN MUTATED                                1
  4P GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  4P GAIN MUTATED                                    1
  4P GAIN WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  4P GAIN MUTATED                              0                             3
  4P GAIN WILD-TYPE                            2                            20
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  4P GAIN MUTATED                                 0
  4P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  4P GAIN MUTATED                                               1
  4P GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  4P GAIN MUTATED                              0
  4P GAIN WILD-TYPE                           10
D7V10, multiclass
                                                    clus
vv                                                   4P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              61
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   4P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               260
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
D7V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    55   3   0   4
  4P GAIN WILD-TYPE 289  10   4  22
D7V13, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              55               289
  R1               3                10
  R2               0                 4
  RX               4                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     3
  4P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           7    64
  4P GAIN WILD-TYPE                        45   326
D7V14, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                      7                45
  WHITE                                         64               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2  54
  4P GAIN WILD-TYPE   5 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2   54
  4P GAIN WILD-TYPE    5  330
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              54               330
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    29  17
  4Q GAIN WILD-TYPE 294 164
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               46               458 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               17               164 
$`4Q GAIN MUTATED`
TCGA-38-4629 TCGA-44-2662 TCGA-44-7661 TCGA-55-8091 TCGA-80-5611 TCGA-91-6836 
       28.41        42.08        18.31        19.73        85.32        13.71 
TCGA-95-7948 TCGA-38-4628 TCGA-44-2656 TCGA-44-2659 TCGA-44-4112 TCGA-44-5645 
       15.65        49.05        46.98        44.94        26.56        28.01 
TCGA-44-6775 TCGA-50-6591 TCGA-50-6594 TCGA-55-6712 TCGA-55-8089 TCGA-55-8096 
       23.18         3.91        12.16         5.62        23.08        23.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-A493 TCGA-55-A57B TCGA-62-8402 TCGA-62-A471 
       17.62        14.66         0.92        17.95        49.25        40.96 
TCGA-64-1676 TCGA-64-1680 TCGA-69-7980 TCGA-69-8253 TCGA-75-5125 TCGA-75-5147 
       56.81        37.02        13.51        14.01        66.64        43.82 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7154 TCGA-78-7163 TCGA-78-7542 TCGA-86-7953 
      100.57       163.10        19.50       238.29        10.55        32.78 
TCGA-86-8278 TCGA-86-A456 TCGA-91-6848 TCGA-93-A4JP TCGA-95-8494 TCGA-97-8552 
       31.04        29.46         7.36        19.00         2.76        20.58 
TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        49.35        86.04        58.85 

$`4Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       26.01        15.02        15.02        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       26.30        43.53        38.10        23.93        27.78        86.01 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       17.16        11.64       156.66        37.32        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       41.69        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       10.55        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        2.86        15.68        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       10.09        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        0.46         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 
       37.71        44.61         4.37        44.42        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       25.02        37.15        38.24        38.89        34.06        33.73 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       33.30        28.37        23.77        19.56        23.15        21.63 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       40.41       123.58       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
       48.46        60.72        57.53        53.16        42.35        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       11.05         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 
       67.89        30.58        14.30        80.52        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       23.15        25.41        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 
       18.44        19.82        29.23        29.72        15.19         5.06 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.79        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       19.96        26.01        17.10         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       21.40         3.25        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 
       54.35        67.96        72.30        13.61        39.25        29.92 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       39.09        81.80        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       28.41        51.25        28.47        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K 
        4.41        13.41        13.45         4.24        26.73        19.43 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        8.42        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5146 TCGA-75-6206 
        9.24         1.25        50.33        11.18        77.85        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       49.84        36.66       108.66        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
       20.58       129.53        21.90        39.95       119.51        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       39.35       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        22.82        32.65        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       12.23        27.68         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7039 
       19.82        22.45        17.46        23.61         1.08        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       18.67        12.39        27.29        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       21.60        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       34.85        36.76         1.45        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       35.47        32.48        19.00        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
       18.58        15.65        38.63        86.14        58.45        37.35 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       11.15        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        47.08         0.49         0.43        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.92              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           238.29            232.18 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            25.10             21.47 
[1] "0.9 - 238.3 (25.1)" "0.0 - 232.2 (21.5)"
[1] "hr=" "1.2"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         2        7       19        0         3         9
  4Q GAIN WILD-TYPE       3      126      120        1        47        63
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4Q GAIN MUTATED            6          0        3
  4Q GAIN WILD-TYPE         66         11       22
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 7               126
  STAGE IB                19               120
  STAGE II                 0                 1
  STAGE IIA                3                47
  STAGE IIB                9                63
  STAGE IIIA               6                66
  STAGE IIIB               0                11
  STAGE IV                 3                22
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED    12  31   5   0
  4Q GAIN WILD-TYPE 159 247  41  19
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              12               159
  T2              31               247
  T3               5                41
  T4               0                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  4Q GAIN MUTATED    30  10     7
  4Q GAIN WILD-TYPE 303  86    69
D8V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0                 30               303
  N1                 10                86
  N2+N3               7                69
[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"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    34   3
  4Q GAIN WILD-TYPE 315  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     34    3
  4Q GAIN WILD-TYPE  315   22
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              34               315
  1               3                22
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    25  24
  4Q GAIN WILD-TYPE 251 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     25   24
  4Q GAIN WILD-TYPE  251  216
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              25               251
  MALE                24               216
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    45   1
  4Q GAIN WILD-TYPE 365  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     45    1
  4Q GAIN WILD-TYPE  365   59
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               45               365
  YES               1                59
[1] 2 2
[1] FALSE
D8V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4Q GAIN MUTATED                            0
  4Q GAIN WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4Q GAIN MUTATED                                   5
  4Q GAIN WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                   39
  4Q GAIN WILD-TYPE                                                282
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4Q GAIN MUTATED                                            0
  4Q GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  4Q GAIN MUTATED                                               2
  4Q GAIN WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  4Q GAIN MUTATED                                0
  4Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  4Q GAIN MUTATED                                    0
  4Q GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  4Q GAIN MUTATED                              0                             2
  4Q GAIN WILD-TYPE                            2                            21
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  4Q GAIN MUTATED                                 0
  4Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  4Q GAIN MUTATED                                               1
  4Q GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  4Q GAIN MUTATED                              0
  4Q GAIN WILD-TYPE                           10
D8V10, multiclass
                                                    clus
vv                                                   4Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              39
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   4Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               282
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
D8V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    33   1   0   3
  4Q GAIN WILD-TYPE 311  12   4  23
D8V13, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              33               311
  R1               1                12
  R2               0                 4
  RX               3                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     2
  4Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           4    36
  4Q GAIN WILD-TYPE                        48   354
D8V14, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                      4                48
  WHITE                                         36               354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  35
  4Q GAIN WILD-TYPE   6 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   35
  4Q GAIN WILD-TYPE    6  349
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              35               349
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   176  95
  5P GAIN WILD-TYPE 147  86
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              271               233 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               95                86 
$`5P GAIN MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
        8.02        20.05        28.41        11.64        14.73        26.30 
TCGA-44-2662 TCGA-44-6147 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       42.08        27.78        29.00         9.37        11.08        46.72 
TCGA-49-6761 TCGA-49-AAR0 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64       156.66        21.47        41.69        23.05        48.62 
TCGA-55-6979 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8091 
        7.79        16.01        23.18        14.53        21.44        19.73 
TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF 
       16.93        32.12        18.15        22.65        20.58        20.19 
TCGA-67-6217 TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 
       13.87        52.60         8.48        50.24        85.32        13.71 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7947 TCGA-95-7948 TCGA-97-8172 
        1.45         6.12        17.29        15.68        15.65        17.92 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA 
       20.68        24.30        10.09        21.83         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4422 
        2.43        10.09         0.00        47.05         2.99        12.00 
TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       30.02        26.01        25.02         4.96        29.00        22.03 
TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        0.46         8.68       120.79        37.71        49.05        44.61 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2668 TCGA-44-3398 
       46.98        44.42        44.94        42.77        25.02        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6774 
       34.06        33.73        26.56        28.37        28.01        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       23.18        32.45        61.28        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A TCGA-44-A4SS 
       36.07        18.87        23.64        12.66        15.32        13.64 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
       28.11        28.57        12.66        14.07        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-4B-A93V 
       55.89        53.29        55.33        28.90         8.55         9.86 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
       71.47       101.72        15.72        47.41        49.28         9.27 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       78.67        48.46        53.16         3.91        25.55        11.05 
TCGA-50-7109 TCGA-50-8457 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 
       10.13        36.99        34.29        30.54        13.94        38.73 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6970 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 
       30.58        14.30        15.25        53.65        69.34        45.34 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 
       92.81        40.54        70.26        27.09        32.71         3.91 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 
       18.64        34.19        17.65        17.79        23.64        29.19 
TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       22.16        17.56        15.72         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       17.72        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       20.71        21.40         3.25         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46S 
        4.57        39.98        88.64        49.25        47.80        54.35 
TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1679 TCGA-64-1680 
       67.96        13.61        39.25        40.96        81.80        37.02 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-67-3770 TCGA-67-3773 TCGA-67-6215 
       87.98        42.90        51.25        20.05        14.04         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        4.64         6.64        22.68        13.61         5.42         7.56 
TCGA-69-8253 TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       14.01         8.42        15.35         4.31        30.31         9.24 
TCGA-73-7499 TCGA-75-5146 TCGA-75-5147 TCGA-75-6214 TCGA-78-7143 TCGA-78-7147 
       50.33        77.85        43.82        36.66       163.10        19.27 
TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7163 
      129.53       119.51        19.50        38.50        64.90       238.29 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-78-8655 
       26.53        31.20         8.02        26.01       232.18        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 
      110.50        93.11        27.09        12.36         5.88        34.39 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 
       32.78        37.74         4.08        24.33        22.82        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-86-8673 
       23.05        21.47        14.60        11.61         0.62        28.34 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6830 TCGA-91-6840 TCGA-91-8499 TCGA-91-A4BD 
        3.81        10.62         1.97        12.23         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       22.45        17.46         1.08        19.00        41.82        18.67 
TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 
       27.29         2.76        42.25        64.60        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 TCGA-97-8552 
       18.54         0.59         5.39        15.39        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       21.44        19.76        34.85        21.57        18.08        35.47 
TCGA-L4-A4E5 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY 
       19.00         1.91        18.58         2.76        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH 
       37.35        86.04        58.85         5.49        11.05        24.36 
TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       19.13        71.05        74.33        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

$`5P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4630 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 
       15.02        35.28        43.53        38.10        23.93        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-49-6742 TCGA-49-6745 TCGA-49-AARN TCGA-50-5932 
       18.31        29.23        16.04        17.16        37.32        40.60 
TCGA-55-6978 TCGA-55-7284 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8205 
        5.79         7.99         6.15        19.66        17.98        19.69 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 TCGA-64-1677 TCGA-73-4662 TCGA-73-7498 
       13.68        16.93        19.59        20.65        82.68        39.09 
TCGA-78-8660 TCGA-91-7771 TCGA-95-7043 TCGA-95-7562 TCGA-95-A4VK TCGA-95-A4VN 
       10.55        16.18        16.54         2.86        21.40        18.18 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A443 TCGA-MN-A4N1 
       20.19        20.52        17.75        23.80         6.35        27.19 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 
       50.07         3.98        45.01        37.02        24.03        19.00 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 TCGA-05-4432 TCGA-05-4433 TCGA-05-5429 
       14.96        29.98        21.99        25.02        24.00         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-A44F TCGA-44-2666 
        2.04         7.40         5.98        97.74         4.37         3.19 
TCGA-44-3396 TCGA-44-3917 TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       37.15        38.89        33.30        23.77        19.56        23.15 
TCGA-44-6779 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU 
       16.44         8.55        15.98         9.44        11.54        13.45 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6767 TCGA-49-AAQV 
       76.21        35.54        32.84         8.81        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       73.12        62.24        40.41       123.58       221.33       164.12 
TCGA-50-5044 TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 
       20.52        60.16         8.22        14.27         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       60.72        57.53        42.35        12.16         6.21         0.72 
TCGA-50-8459 TCGA-50-8460 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 
       36.79        27.25        35.21        67.89        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6975 TCGA-55-6982 TCGA-55-6984 
       42.51        40.73        46.03         3.88        32.71        24.99 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 
      107.21        28.67        20.02        22.03        23.15        25.41 
TCGA-55-7907 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       11.28        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8097 TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 
       23.08         5.06        15.65        15.42        14.47        19.96 
TCGA-55-8513 TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 TCGA-62-A46P TCGA-62-A46R 
       26.01        17.95        42.38        14.60        19.53        56.71 
TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 
       72.30        29.92        56.81        39.09        38.37         2.04 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 
       28.41        28.47        20.05        18.84        12.66        14.73 
TCGA-69-7761 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
        6.12         6.05         4.41        13.41        13.51        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4677 
        4.24        26.73        19.43        23.38        26.30         1.25 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       11.18        66.64        85.15        49.84       108.66       100.57 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 
       27.16         5.69        20.58        21.90        39.95        32.09 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 
        5.88        22.92         9.57       104.19        88.14        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 
       39.35        10.55        39.75        31.13        38.04        20.55 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
       19.89        35.24         4.57         0.79        32.65        31.04 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       13.91        30.84        27.58        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 
       13.64        26.47        41.36        10.19         2.60        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-93-A4JN TCGA-95-7944 
        7.36         1.15        16.60        14.27        23.61        12.39 
TCGA-95-A4VP TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 
       19.89        63.52        15.91        18.67        18.12        16.41 
TCGA-97-8179 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       14.30        20.84        18.67        24.56        36.76         1.45 
TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 
       21.63        32.48        14.30        14.53        15.65        38.63 
TCGA-MP-A4SV TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 
       86.14        41.59        29.46        14.10        11.15        73.91 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
        0.13         1.64        47.08         0.49         0.43 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.00              0.13 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           238.29            221.33 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            22.16             20.58 
[1] "0.0 - 238.3 (22.2)" "0.1 - 221.3 (20.6)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         2       71       79        0        32        32
  5P GAIN WILD-TYPE       3       62       60        1        18        40
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5P GAIN MUTATED           38          8       13
  5P GAIN WILD-TYPE         34          3       12
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                71                62
  STAGE IB                79                60
  STAGE II                 0                 1
  STAGE IIA               32                18
  STAGE IIB               32                40
  STAGE IIIA              38                34
  STAGE IIIB               8                 3
  STAGE IV                13                12
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P GAIN MUTATED    95 154  19   9
  5P GAIN WILD-TYPE  76 124  27  10
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              95                76
  T2             154               124
  T3              19                27
  T4               9                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  5P GAIN MUTATED   175  52    44
  5P GAIN WILD-TYPE 158  44    32
D9V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                175               158
  N1                 52                44
  N2+N3              44                32
[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"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   184  13
  5P GAIN WILD-TYPE 165  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    184   13
  5P GAIN WILD-TYPE  165   12
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             184               165
  1              13                12
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   157 122
  5P GAIN WILD-TYPE 119 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    157  122
  5P GAIN WILD-TYPE  119  118
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE             157               119
  MALE               122               118
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   225  34
  5P GAIN WILD-TYPE 185  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    225   34
  5P GAIN WILD-TYPE  185   26
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              225               185
  YES              34                26
[1] 2 2
[1] FALSE
D9V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5P GAIN MUTATED                            8
  5P GAIN WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5P GAIN MUTATED                                  53
  5P GAIN WILD-TYPE                                54
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                  187
  5P GAIN WILD-TYPE                                                134
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5P GAIN MUTATED                                            2
  5P GAIN WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  5P GAIN MUTATED                                              10
  5P GAIN WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  5P GAIN MUTATED                                2
  5P GAIN WILD-TYPE                              0
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  5P GAIN MUTATED                                    2
  5P GAIN WILD-TYPE                                  1
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  5P GAIN MUTATED                              0                            11
  5P GAIN WILD-TYPE                            2                            12
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  5P GAIN MUTATED                                 0
  5P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  5P GAIN MUTATED                                               2
  5P GAIN WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5P GAIN MUTATED                              2
  5P GAIN WILD-TYPE                            8
D9V10, multiclass
                                                    clus
vv                                                   5P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             187
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                   11
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   5P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               134
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     12
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
D9V12, continuous
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED   189   6   2  14
  5P GAIN WILD-TYPE 155   7   2  12
D9V13, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             189               155
  R1               6                 7
  R2               2                 2
  RX              14                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  1     4
  5P GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          25   217
  5P GAIN WILD-TYPE                        27   173
D9V14, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 3
  BLACK OR AFRICAN AMERICAN                     25                27
  WHITE                                        217               173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     4 212
  5P GAIN WILD-TYPE   3 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4  212
  5P GAIN WILD-TYPE    3  172
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             212               172
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    83  45
  5Q GAIN WILD-TYPE 240 136
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              128               376 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               45               136 
$`5Q GAIN MUTATED`
TCGA-05-4402 TCGA-38-6178 TCGA-38-7271 TCGA-44-2662 TCGA-44-8119 TCGA-44-A47F 
        8.02        14.73        26.30        42.08         9.37        11.08 
TCGA-49-4501 TCGA-49-6761 TCGA-49-AAR0 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 
       46.72        11.64       156.66        21.47        41.69        48.62 
TCGA-55-7573 TCGA-55-7724 TCGA-55-8091 TCGA-55-8204 TCGA-55-8207 TCGA-67-6217 
       16.01        23.18        19.73        16.93        32.12        13.87 
TCGA-78-7633 TCGA-91-6836 TCGA-93-A4JQ TCGA-95-7947 TCGA-97-8172 TCGA-97-A4M7 
       50.24        13.71        17.29        15.68        17.92        20.68 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4398 TCGA-05-4426 TCGA-05-5423 
        5.29        31.23        10.09        47.05        26.01         4.96 
TCGA-35-3615 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-3398 
        0.46        46.98        44.42        44.94        42.77        38.24 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5645 TCGA-44-6774 TCGA-44-6777 TCGA-44-7659 
       34.06        26.56        28.01        21.63        32.45        22.72 
TCGA-44-7672 TCGA-44-A47A TCGA-49-4490 TCGA-49-4512 TCGA-49-6743 TCGA-49-AAR9 
       23.64        15.32        12.66        29.75        53.29         8.55 
TCGA-50-5051 TCGA-50-6591 TCGA-50-6592 TCGA-50-8457 TCGA-53-7626 TCGA-53-7813 
       15.72         3.91        25.55        36.99        30.54        13.94 
TCGA-55-6543 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-7574 TCGA-55-7910 
       14.30        53.65        69.34        92.81        32.71        34.19 
TCGA-55-7911 TCGA-55-8206 TCGA-55-8208 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 
       17.65        29.19        22.16        20.28        17.10        17.62 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A493 TCGA-55-A4DG TCGA-62-A46S TCGA-62-A46U 
       12.33        21.40         0.92        19.99        54.35        67.96 
TCGA-62-A46Y TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-67-6215 TCGA-67-6216 
       13.61        37.02         2.04        51.25         5.72         4.64 
TCGA-69-7760 TCGA-69-7763 TCGA-69-8253 TCGA-73-4670 TCGA-73-4675 TCGA-75-5147 
        6.64        22.68        14.01         4.31        30.31        43.82 
TCGA-75-6214 TCGA-78-7143 TCGA-78-7147 TCGA-78-7153 TCGA-78-7154 TCGA-78-7163 
       36.66       163.10        19.27       119.51        19.50       238.29 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-80-5608 TCGA-83-5908 
       26.53        31.20         8.02        26.01        93.11        27.09 
TCGA-86-7711 TCGA-86-8055 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-A4D0 
       34.39         4.08        23.05        21.47        14.60         3.81 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JP TCGA-95-8039 TCGA-95-8494 
       19.82        22.45        17.46        19.00        27.29         2.76 
TCGA-97-7546 TCGA-97-7547 TCGA-97-8174 TCGA-97-8176 TCGA-97-8552 TCGA-97-A4M0 
       42.25        64.60         5.39        15.39        20.58        21.44 
TCGA-97-A4M1 TCGA-J2-A4AE TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
       19.76        35.47        49.35        37.35        86.04         5.49 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A55R TCGA-NJ-A7XG 
       11.05        24.36        19.13        74.33        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

$`5Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-44-2655 
       15.02        15.02        28.41        35.28        11.64        43.53 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-49-6742 TCGA-49-6745 TCGA-49-AARN TCGA-50-5932 TCGA-55-1592 
       29.23        16.04        17.16        37.32        40.60        23.05 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        5.79         7.79         7.99        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8203 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       19.66        17.98        19.69        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 
       22.65        20.58        19.59        20.19        20.65        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-8660 TCGA-80-5611 TCGA-91-7771 
       82.68        39.09         8.48        10.55        85.32        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK 
        1.45         6.12        16.54         2.86        15.65        21.40 
TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 
       18.18        20.19        20.52        17.75        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-05-4249 
        6.35        10.09        21.83        27.19         2.43        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 
        3.98        45.01        37.02         0.00        24.03        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        25.02        24.00        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2666 TCGA-44-2668 
       37.71        49.05        44.61         4.37         3.19        25.02 
TCGA-44-3396 TCGA-44-3917 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
       37.15        38.89        33.73        33.30        28.37        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       19.56        23.15        23.18        61.28        16.44        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        36.07        18.87        12.66         8.55        15.98 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       28.57        35.54        14.07        32.84         8.81        29.46 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       55.89        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       28.90        40.41       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47       101.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 
       48.46        60.72        57.53        53.16        42.35        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21         0.72        10.13        36.79        27.25 
TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
       34.29        35.21        38.73        67.89        30.58        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 
        5.62        42.51        40.73        15.25        46.03         3.88 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       45.34        32.71        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       28.67        20.02        27.09        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       25.41        18.64        11.28        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       15.65        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 
       13.74        17.72        19.96        26.01        14.66         1.58 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       20.71         3.25        15.81        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       56.71        72.30        39.25        40.96        29.92        56.81 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       39.09        81.80        38.37        87.98        42.90        28.41 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       28.47        20.05        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
       14.73         6.12        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        4.41        13.41        13.51        13.45         4.24        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
       19.43         8.42        23.38        26.30        15.35         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 
        1.25        50.33        11.18        66.64        77.85        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
       49.84       108.66       100.57        27.16         5.69        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
      129.53        21.90        39.95        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 
       64.90        22.92         9.57       104.19        88.14        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        31.13        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        35.24        37.74         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8585 TCGA-86-8668 
       22.82        32.65        31.04        31.20        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7039 
       16.60        14.27         1.18        23.61         1.08        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       18.67        12.39        19.89        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 
       18.54         0.59        15.91        18.67        18.12        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       14.30        21.60        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG 
       36.76         1.45        21.57        21.63        18.08        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       19.00        14.30        14.53         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4T9 
       38.63         2.76        86.14        58.45        58.85        41.59 
TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI 
       29.46        14.10        11.15        73.91        71.05         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
        1.64        47.08         0.49         0.43 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.46              0.00 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           238.29            232.18 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           21.895            21.585 
[1] "0.5 - 238.3 (21.9)" "0.0 - 232.2 (21.6)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         1       36       36        0        14        13
  5Q GAIN WILD-TYPE       4       97      103        1        36        59
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5Q GAIN MUTATED           21          3        8
  5Q GAIN WILD-TYPE         51          8       17
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                36                97
  STAGE IB                36               103
  STAGE II                 0                 1
  STAGE IIA               14                36
  STAGE IIB               13                59
  STAGE IIIA              21                51
  STAGE IIIB               3                 8
  STAGE IV                 8                17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED    46  72   9   4
  5Q GAIN WILD-TYPE 125 206  37  15
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              46               125
  T2              72               206
  T3               9                37
  T4               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  5Q GAIN MUTATED    84  22    21
  5Q GAIN WILD-TYPE 249  74    55
D10V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                 84               249
  N1                 22                74
  N2+N3              21                55
[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"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    88   8
  5Q GAIN WILD-TYPE 261  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     88    8
  5Q GAIN WILD-TYPE  261   17
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              88               261
  1               8                17
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    79  53
  5Q GAIN WILD-TYPE 197 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     79   53
  5Q GAIN WILD-TYPE  197  187
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              79               197
  MALE                53               187
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   109  15
  5Q GAIN WILD-TYPE 301  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    109   15
  5Q GAIN WILD-TYPE  301   45
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO              109               301
  YES              15                45
[1] 2 2
[1] FALSE
D10V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5Q GAIN MUTATED                            6
  5Q GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5Q GAIN MUTATED                                  22
  5Q GAIN WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                   87
  5Q GAIN WILD-TYPE                                                234
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5Q GAIN MUTATED                                            2
  5Q GAIN WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  5Q GAIN MUTATED                                               5
  5Q GAIN WILD-TYPE                                            14
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  5Q GAIN MUTATED                                2
  5Q GAIN WILD-TYPE                              0
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  5Q GAIN MUTATED                                    0
  5Q GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  5Q GAIN MUTATED                              0                             6
  5Q GAIN WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  5Q GAIN MUTATED                                 0
  5Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  5Q GAIN MUTATED                                               0
  5Q GAIN WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5Q GAIN MUTATED                              2
  5Q GAIN WILD-TYPE                            8
D10V10, multiclass
                                                    clus
vv                                                   5Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              87
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    6
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   5Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               234
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     14
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
D10V12, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    87   3   2   7
  5Q GAIN WILD-TYPE 257  10   2  19
D10V13, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              87               257
  R1               3                10
  R2               2                 2
  RX               7                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     2
  5Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                          10   106
  5Q GAIN WILD-TYPE                        42   284
D10V14, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                     10                42
  WHITE                                        106               284
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1 100
  5Q GAIN WILD-TYPE   6 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1  100
  5Q GAIN WILD-TYPE    6  284
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO             100               284
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    98  45
  6P GAIN WILD-TYPE 225 136
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              143               361 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               45               136 
$`6P GAIN MUTATED`
TCGA-38-6178 TCGA-44-6147 TCGA-44-7670 TCGA-49-6742 TCGA-49-6761 TCGA-49-AAR0 
       14.73        27.78        29.00        16.04        11.64       156.66 
TCGA-55-1592 TCGA-55-1595 TCGA-55-7573 TCGA-55-8203 TCGA-55-8205 TCGA-55-8511 
       23.05        48.62        16.01        17.98        19.69        18.15 
TCGA-55-A48X TCGA-64-1677 TCGA-73-4662 TCGA-73-7498 TCGA-78-7633 TCGA-91-6836 
       22.65        20.65        82.68        39.09        50.24        13.71 
TCGA-95-7562 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A444 TCGA-MP-A4TD TCGA-05-4249 
        2.86        20.68        23.80        10.09        10.09        50.07 
TCGA-05-4420 TCGA-05-4430 TCGA-05-5425 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 
       29.98        25.02        29.00         0.46         8.68        97.74 
TCGA-38-4628 TCGA-44-2659 TCGA-44-3918 TCGA-44-6774 TCGA-44-7662 TCGA-44-7667 
       49.05        44.94        34.06        21.63         7.17        36.07 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4510 TCGA-49-6767 TCGA-50-5931 
       13.45        28.11        12.66        29.46        22.26        14.27 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       78.67        48.46        57.53        53.16        42.35         3.91 
TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 
        0.72        10.13        34.29        13.94        35.21        67.89 
TCGA-55-6642 TCGA-55-6970 TCGA-55-7903 TCGA-55-7995 TCGA-55-8085 TCGA-55-8097 
       80.52        15.25        18.64        29.23        29.72        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8507 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 
       29.19        22.16        13.74        19.96        17.10        17.62 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 TCGA-62-8394 TCGA-62-8398 
       14.66        12.33        20.71         3.25         4.57        14.60 
TCGA-62-8399 TCGA-62-A46P TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 
       88.64        19.53        72.30        39.25        40.96        37.02 
TCGA-64-5774 TCGA-64-5779 TCGA-67-3771 TCGA-67-3773 TCGA-67-4679 TCGA-69-7763 
       87.98        28.41        20.05        14.04        14.73        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-8255 TCGA-73-4668 TCGA-73-4670 
       13.61         5.42        13.41         4.24        15.35         4.31 
TCGA-73-4677 TCGA-73-7499 TCGA-75-6206 TCGA-75-6214 TCGA-78-7147 TCGA-78-7149 
        1.25        50.33        85.15        36.66        19.27       129.53 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 
       38.50        64.90         9.57       104.19        88.14        26.53 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 TCGA-86-7954 
       26.01        10.55        77.59       110.50         5.88        19.89 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8674 TCGA-91-6835 
        0.79        22.82        31.20        21.47        26.50         2.60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7567 
       27.68         7.36         1.18        23.61        19.00        18.67 
TCGA-95-7944 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7553 TCGA-97-7938 TCGA-97-8171 
       12.39        19.89        42.25        61.48         0.59        18.67 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8033 
       15.39        16.41        14.30        19.76        34.85        21.57 
TCGA-J2-A4AE TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T6 
       35.47        18.58        38.63         2.76        86.14        58.85 
TCGA-MP-A4TE TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-O1-A52J 
       29.46         1.64         0.49        20.28        59.11 

$`6P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 
       26.30        43.53        38.10        42.08        23.93        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 
       18.31        29.23         9.37        11.08        46.72        17.16 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-6978 TCGA-55-6979 
       37.32        40.60        21.47        41.69         5.79         7.79 
TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
        7.99        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8204 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 
       19.73        16.93        32.12        13.68        16.93        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-4658 TCGA-78-7166 TCGA-78-8660 
       19.59        20.19        13.87        52.60         8.48        10.55 
TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       85.32        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 
       20.52        17.75        24.30         6.35        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        5.29        31.23         2.43         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 
       12.00        30.02        21.99        26.01        25.02        24.00 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
        4.96        22.03         9.04         2.04         7.40         5.98 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
      120.79        37.71        44.61         4.37        46.98        44.42 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       19.56        23.15        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       22.72        19.46        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       15.98        15.32         9.44        11.54        13.64        76.21 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 
       28.57        35.54        14.07        32.84         8.81        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       55.89        53.29        55.33        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        40.41       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        9.86        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5936 TCGA-50-5939 
       47.41        49.28         8.22         9.27         8.45        15.12 
TCGA-50-5942 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-8457 
       60.72        25.55        11.05        12.16         6.21        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 
       36.79        27.25        30.54        38.73        30.58        14.30 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        5.62        42.51        40.73        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
       22.03         3.91        23.15        25.41        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       17.65        18.44        19.82        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       17.79        23.64        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8513 TCGA-55-8616 TCGA-55-A48Z 
        0.36        20.28        17.72        26.01         1.58        21.40 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        19.99        17.95        39.98        42.38 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y 
       49.25        47.80        56.71        54.35        67.96        13.61 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
       29.92        56.81        39.09        81.80        38.37         2.04 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 
       42.90        51.25        28.47        20.05        18.84        12.66 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 TCGA-69-7974 
        5.72         4.64         6.64         6.12         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K 
        4.41        13.51        14.01        13.45        26.73        19.43 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS 
        8.42        23.38        26.30        30.31         9.24        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       66.64        77.85        43.82        49.84       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
      163.10        27.16         5.69        20.58        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7163 
      119.51        19.50        32.09         5.88        22.92       238.29 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 
       31.20         8.02        53.33        39.35       232.18        39.75 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       93.11        27.09        12.36        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        32.78        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       24.33        32.65        31.04        23.05        14.60        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 
       13.91        30.84        27.58         0.62        28.34        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
        1.97        10.19        12.23         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7039 TCGA-95-8039 
       19.82        22.45        17.46         1.08        41.82        27.29 
TCGA-95-8494 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
        2.76        64.60        63.52        25.48        18.54        15.91 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 
        5.39        18.12        21.60        20.58        21.44        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD 
       18.67        24.56        36.76         1.45        21.63        18.08 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 
       32.48        19.00        14.30        14.53         1.91        15.65 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
       58.45        49.35        37.35        86.04         5.49        41.59 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       11.05        24.36        14.10        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       71.05        74.33         0.13        47.08         0.43        19.82 
TCGA-S2-AA1A 
       16.87 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.46              0.00 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           156.66            238.29 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            21.47             21.83 
[1] "0.5 - 156.7 (21.5)" "0.0 - 238.3 (21.8)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         1       43       35        0        15        13
  6P GAIN WILD-TYPE       4       90      104        1        35        59
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6P GAIN MUTATED           21          4       11
  6P GAIN WILD-TYPE         51          7       14
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                43                90
  STAGE IB                35               104
  STAGE II                 0                 1
  STAGE IIA               15                35
  STAGE IIB               13                59
  STAGE IIIA              21                51
  STAGE IIIB               4                 7
  STAGE IV                11                14
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED    53  76   9   6
  6P GAIN WILD-TYPE 118 202  37  13
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              53               118
  T2              76               202
  T3               9                37
  T4               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  6P GAIN MUTATED    95  23    23
  6P GAIN WILD-TYPE 238  73    53
D11V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                 95               238
  N1                 23                73
  N2+N3              23                53
[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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   100  11
  6P GAIN WILD-TYPE 249  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    100   11
  6P GAIN WILD-TYPE  249   14
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0             100               249
  1              11                14
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    76  70
  6P GAIN WILD-TYPE 200 170
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     76   70
  6P GAIN WILD-TYPE  200  170
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              76               200
  MALE                70               170
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   114  19
  6P GAIN WILD-TYPE 296  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    114   19
  6P GAIN WILD-TYPE  296   41
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO              114               296
  YES              19                41
[1] 2 2
[1] FALSE
D11V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6P GAIN MUTATED                           10
  6P GAIN WILD-TYPE                          8
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6P GAIN MUTATED                                  28
  6P GAIN WILD-TYPE                                79
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                   90
  6P GAIN WILD-TYPE                                                231
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6P GAIN MUTATED                                            0
  6P GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  6P GAIN MUTATED                                               6
  6P GAIN WILD-TYPE                                            13
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  6P GAIN MUTATED                                1
  6P GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  6P GAIN MUTATED                                    1
  6P GAIN WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  6P GAIN MUTATED                              0                             8
  6P GAIN WILD-TYPE                            2                            15
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  6P GAIN MUTATED                                 0
  6P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  6P GAIN MUTATED                                               1
  6P GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  6P GAIN MUTATED                              1
  6P GAIN WILD-TYPE                            9
D11V10, multiclass
                                                    clus
vv                                                   6P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              90
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    6
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    8
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   6P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 79
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               231
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     13
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     15
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
D11V12, continuous
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    98   3   0   7
  6P GAIN WILD-TYPE 246  10   4  19
D11V13, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              98               246
  R1               3                10
  R2               0                 4
  RX               7                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  1     4
  6P GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           9   121
  6P GAIN WILD-TYPE                        43   269
D11V14, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 3
  BLACK OR AFRICAN AMERICAN                      9                43
  WHITE                                        121               269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     4 111
  6P GAIN WILD-TYPE   3 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4  111
  6P GAIN WILD-TYPE    3  273
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             111               273
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    40  19
  6Q GAIN WILD-TYPE 283 162
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               59               445 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               19               162 
$`6Q GAIN MUTATED`
TCGA-44-7670 TCGA-49-6742 TCGA-50-6597 TCGA-55-8511 TCGA-91-6836 TCGA-95-7562 
       29.00        16.04        41.69        18.15        13.71         2.86 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4420 TCGA-05-4432 TCGA-35-5375 TCGA-38-4625 
       10.09        50.07        29.98        25.02         8.68        97.74 
TCGA-38-4628 TCGA-49-4490 TCGA-49-6767 TCGA-50-6591 TCGA-50-6673 TCGA-50-7109 
       49.05        12.66        22.26         3.91         0.72        10.13 
TCGA-53-A4EZ TCGA-55-1596 TCGA-55-7910 TCGA-55-7995 TCGA-55-8097 TCGA-55-8206 
       35.21        67.89        34.19        29.23        15.65        29.19 
TCGA-55-8507 TCGA-55-8514 TCGA-55-8620 TCGA-62-8394 TCGA-62-A46P TCGA-62-A471 
       13.74        17.10        12.33         4.57        19.53        40.96 
TCGA-67-3773 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-73-4677 
       14.04        22.68        13.61         5.42        13.41         1.25 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-8662 TCGA-86-6851 TCGA-86-7954 
       88.14        26.53        26.01       110.50         5.88        19.89 
TCGA-86-8074 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-95-7944 TCGA-97-7546 
        0.79        27.68         7.36         1.18        12.39        42.25 
TCGA-97-8177 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AE TCGA-L9-A7SV 
       16.41        19.76        34.85        21.57        35.47        18.58 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-O1-A52J 
       38.63        86.14         0.49        20.28        59.11 

$`6Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       27.78        86.01        18.31        29.23         9.37        11.08 
TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       46.72        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       21.47        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 
       19.73        17.98        16.93        19.69        32.12        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       10.55        85.32        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
       16.54        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
        6.35        10.09        21.83        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
        2.43         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
       47.05        19.00         2.99        14.96        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       21.99        26.01        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
       22.03         9.04         2.04         0.46         7.40         5.98 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
      120.79        37.71        44.61         4.37        46.98        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.94        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.89        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.11        28.57        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       73.12        62.24        28.90         8.55        40.41       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      221.33       164.12         9.86        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       14.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       57.53        53.16        42.35        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        6.21        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        38.73        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       22.03         3.91        23.15        25.41        18.64        11.28 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        18.44        19.82        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        5.06        17.79        23.64        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       15.72        14.47         0.36        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z 
       26.01        17.62        14.66         1.58        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 
        3.25         0.92        15.81        19.99        17.95        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R 
       42.38        14.60        88.64        49.25        47.80        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 
       54.35        67.96        72.30        13.61        39.25        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       56.81        39.09        81.80        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
        6.64         6.12         7.56         6.05         4.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 
       14.01        13.45         4.24        26.73        19.43         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
       50.33        11.18        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 
       22.92         9.57       104.19       238.29        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       53.33        39.35        10.55       232.18        39.75        77.59 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       93.11        27.09        12.36        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        32.78        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       24.33        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
        0.62        28.34        26.50        29.46         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
        2.60        12.23         1.15        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       18.67        27.29         2.76        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        5.39        18.12        15.39        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       21.44        20.84        18.67        24.56        36.76         1.45 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
       21.63        18.08        32.48        19.00        14.30        14.53 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
        1.91        15.65         2.76        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       24.36        14.10        11.15        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       74.33         0.13         1.64        47.08         0.43        19.82 
TCGA-S2-AA1A 
       16.87 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.49              0.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           110.50            238.29 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            19.76             21.90 
[1] "0.5 - 110.5 (19.8)" "0.0 - 238.3 (21.9)"
[1] "hr=" "1"  
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         1       14       17        0         9         5
  6Q GAIN WILD-TYPE       4      119      122        1        41        67
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6Q GAIN MUTATED            7          1        4
  6Q GAIN WILD-TYPE         65         10       21
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                14               119
  STAGE IB                17               122
  STAGE II                 0                 1
  STAGE IIA                9                41
  STAGE IIB                5                67
  STAGE IIIA               7                65
  STAGE IIIB               1                10
  STAGE IV                 4                21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED    19  34   3   3
  6Q GAIN WILD-TYPE 152 244  43  16
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              19               152
  T2              34               244
  T3               3                43
  T4               3                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  6Q GAIN MUTATED    39  13     7
  6Q GAIN WILD-TYPE 294  83    69
D12V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0                 39               294
  N1                 13                83
  N2+N3               7                69
[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"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    41   4
  6Q GAIN WILD-TYPE 308  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     41    4
  6Q GAIN WILD-TYPE  308   21
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              41               308
  1               4                21
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    33  27
  6Q GAIN WILD-TYPE 243 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     33   27
  6Q GAIN WILD-TYPE  243  213
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              33               243
  MALE                27               213
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    48   8
  6Q GAIN WILD-TYPE 362  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     48    8
  6Q GAIN WILD-TYPE  362   52
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               48               362
  YES               8                52
[1] 2 2
[1] FALSE
D12V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6Q GAIN MUTATED                            3
  6Q GAIN WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6Q GAIN MUTATED                                  12
  6Q GAIN WILD-TYPE                                95
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                   42
  6Q GAIN WILD-TYPE                                                279
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6Q GAIN MUTATED                                            0
  6Q GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  6Q GAIN MUTATED                                               1
  6Q GAIN WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  6Q GAIN MUTATED                                0
  6Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  6Q GAIN MUTATED                                    0
  6Q GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  6Q GAIN MUTATED                              0                             1
  6Q GAIN WILD-TYPE                            2                            22
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  6Q GAIN MUTATED                                 0
  6Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  6Q GAIN MUTATED                                               0
  6Q GAIN WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  6Q GAIN MUTATED                              1
  6Q GAIN WILD-TYPE                            9
D12V10, multiclass
                                                    clus
vv                                                   6Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               12
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              42
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   6Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
D12V12, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    39   0   0   3
  6Q GAIN WILD-TYPE 305  13   4  23
D12V13, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              39               305
  R1               0                13
  R2               0                 4
  RX               3                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     1
  6Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           7    46
  6Q GAIN WILD-TYPE                        45   344
D12V14, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      7                45
  WHITE                                         46               344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  46
  6Q GAIN WILD-TYPE   5 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   46
  6Q GAIN WILD-TYPE    5  338
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              46               338
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   156 103
  7P GAIN WILD-TYPE 167  78
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              259               245 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              103                78 
$`7P GAIN MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-38-4629 TCGA-38-4631 
       19.96         8.02        20.05         9.01        28.41        11.64 
TCGA-38-6178 TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 TCGA-44-7661 TCGA-44-A47F 
       14.73        38.10        42.08        27.78        18.31        11.08 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-50-6597 TCGA-55-6978 TCGA-55-6979 
       17.16        11.64       156.66        41.69         5.79         7.79 
TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 TCGA-55-8091 TCGA-55-8205 TCGA-55-8511 
        7.99        23.18        21.44        19.73        19.69        18.15 
TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-80-5611 
       20.58        19.59        13.87        52.60        82.68        85.32 
TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN TCGA-97-A4M7 
        1.45        17.29         2.86        15.68        18.18        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
       31.23         2.43        10.09         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-5423 
        0.00        47.05         2.99        14.96        29.98         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
       29.00        22.03         7.40         5.98         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       37.71        49.05        44.61        46.98        44.42        44.94 
TCGA-44-3396 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 
       37.15        38.89        33.73        26.56        28.37        28.01 
TCGA-44-6144 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       23.77        23.18        32.45        61.28        16.44        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-A479 TCGA-44-A4SS 
        7.17        36.07        18.87        12.66        15.98        13.64 
TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       13.45        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR4 TCGA-49-AARE 
       29.46        29.75        22.26        22.26        28.90        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
      123.58       221.33         9.86        71.47       101.72        60.16 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 
       47.41         8.22        78.67         8.45        48.46        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       53.16        42.35         3.91        11.05        12.16         6.21 
TCGA-50-6673 TCGA-53-7624 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
        0.72        34.29        67.89        30.58        14.30         5.62 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 
       40.54        70.26        20.02        22.03         3.91        11.28 
TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8092 TCGA-55-8096 
       34.19        18.44        19.82        29.72         5.06        23.64 
TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8514 
       29.19        17.56        15.72        14.47        17.72        17.10 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
       14.66         1.58        12.33        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99        17.95         4.57        42.38        14.60 
TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 
       88.64        19.53        56.71        13.61        29.92        56.81 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 
       81.80        37.02        38.37        28.41        51.25        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-69-7760 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
       20.05        18.84         6.64        13.61         5.42         6.05 
TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 
       13.41         4.24        19.43         8.42        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-6214 
       30.31         9.24        50.33        11.18        66.64        36.66 
TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 
      108.66       163.10        27.16        19.27        21.90        19.50 
TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 TCGA-78-7540 
       38.50        22.92         9.57       238.29        31.20        39.35 
TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       10.55        77.59       110.50        27.09        12.36        31.13 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 
       38.04        32.78        35.24         4.08        24.33         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       22.82        31.20        23.05        21.47        14.60        13.91 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6831 TCGA-91-6835 
        0.62        28.34        29.46        13.64        10.19         2.60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP 
       27.68         7.36        16.60        17.46         1.08        19.00 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       18.67        12.39         2.76        61.48        25.48        18.54 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       18.67        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
       20.58        34.85        21.57        18.08        35.47        19.00 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SY 
       14.53         1.91        18.58        38.63         2.76        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J 
       37.35        58.85        41.59        19.13        71.05        59.11 
TCGA-S2-AA1A 
       16.87 

$`7P GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 
       14.01         9.96        26.01        15.02        15.02        35.28 
TCGA-38-7271 TCGA-44-2655 TCGA-44-6146 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 
       26.30        43.53        23.93        86.01        29.00        29.23 
TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
        9.37        46.72        16.04        37.32        40.60        21.47 
TCGA-55-1592 TCGA-55-1595 TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 
       23.05        48.62        16.01        14.53         6.15        19.66 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.98        16.93        32.12        13.68        16.93        22.65 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       20.19        20.65        39.09         8.48        50.24        10.55 
TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK 
       13.71        16.18         6.12        16.54        15.65        21.40 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-L9-A743 TCGA-05-4249 
       17.92        20.19        20.52        17.75        21.83        50.07 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       24.03        19.00        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       25.02        25.02        24.00         9.04         2.04         0.46 
TCGA-38-4626 TCGA-38-A44F TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 
      120.79         4.37        42.77         3.19        25.02        38.24 
TCGA-44-3918 TCGA-44-5643 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-7659 
       34.06        33.30        19.56        23.15        21.63        22.72 
TCGA-44-7672 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 
       23.64         8.55        15.32         9.44        11.54        76.21 
TCGA-49-4487 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR2 
       28.11         8.81        55.89        53.29        55.33        73.12 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARR TCGA-50-5044 TCGA-50-5051 TCGA-50-5068 
       62.24         8.55       164.12        20.52        15.72        49.28 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5939 TCGA-50-5942 TCGA-50-6592 TCGA-50-7109 
        9.27        14.27        15.12        60.72        25.55        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99        36.79        27.25        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6983 
       38.73        80.52        42.51        40.73        15.25        92.81 
TCGA-55-6984 TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 
       24.99       107.21        28.67        27.09        32.71        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 
       25.41        18.64        17.65        29.23        15.19        23.08 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8506 TCGA-55-8507 
       17.79        15.65        22.16        15.42         0.36        13.74 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-A48Y TCGA-62-8395 
       20.28        19.96        26.01        17.62        20.71        39.98 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 
       49.25        47.80        54.35        67.96        72.30        39.25 
TCGA-62-A471 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 
       40.96        39.09        87.98         2.04        42.90        28.47 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
       14.04        12.66        14.73         5.72         4.64         6.12 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
       22.68         7.56         4.41        13.51        14.01        13.45 
TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4677 TCGA-75-5146 TCGA-75-5147 
       26.73        23.38        26.30         1.25        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       85.15        49.84       100.57         5.69        20.58       129.53 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
       39.95       119.51        32.09         5.88        64.90       104.19 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-8640 
       88.14        26.53         8.02        53.33        26.01       232.18 
TCGA-78-8648 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
       39.75        93.11         5.88        34.39        20.55        19.89 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 TCGA-86-8669 
       37.74         4.57        32.65        31.04        11.61        30.84 
TCGA-86-8671 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 
       27.58        26.50         3.81        24.23        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 
       41.36         1.97        12.23         1.15        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-95-7039 TCGA-95-8039 TCGA-95-A4VP 
       19.82        22.45        23.61        41.82        27.29        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 
       42.25        64.60        63.52         0.59        15.91         5.39 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       21.44        19.76        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A8F4 TCGA-MP-A4SV 
        1.45        21.63        32.48        14.30        15.65        86.14 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.45        86.04         5.49        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       14.10        11.15        73.91        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       47.08         0.49         0.43        19.82        20.28 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.00              0.13 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           238.29            232.18 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            20.05             22.72 
[1] "0.0 - 238.3 (20.1)" "0.1 - 232.2 (22.7)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         4       62       71        1        26        34
  7P GAIN WILD-TYPE       1       71       68        0        24        38
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7P GAIN MUTATED           45          6       15
  7P GAIN WILD-TYPE         27          5       10
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                62                71
  STAGE IB                71                68
  STAGE II                 1                 0
  STAGE IIA               26                24
  STAGE IIB               34                38
  STAGE IIIA              45                27
  STAGE IIIB               6                 5
  STAGE IV                15                10
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P GAIN MUTATED    83 146  28   8
  7P GAIN WILD-TYPE  88 132  18  11
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              83                88
  T2             146               132
  T3              28                18
  T4               8                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  7P GAIN MUTATED   158  48    53
  7P GAIN WILD-TYPE 175  48    23
D13V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                158               175
  N1                 48                48
  N2+N3              53                23
[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"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   173  15
  7P GAIN WILD-TYPE 176  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    173   15
  7P GAIN WILD-TYPE  176   10
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             173               176
  1              15                10
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   145 122
  7P GAIN WILD-TYPE 131 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    145  122
  7P GAIN WILD-TYPE  131  118
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             145               131
  MALE               122               118
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   212  33
  7P GAIN WILD-TYPE 198  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    212   33
  7P GAIN WILD-TYPE  198   27
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              212               198
  YES              33                27
[1] 2 2
[1] FALSE
D13V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7P GAIN MUTATED                            6
  7P GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7P GAIN MUTATED                                  50
  7P GAIN WILD-TYPE                                57
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                  180
  7P GAIN WILD-TYPE                                                141
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7P GAIN MUTATED                                            4
  7P GAIN WILD-TYPE                                          1
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  7P GAIN MUTATED                                              10
  7P GAIN WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  7P GAIN MUTATED                                0
  7P GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  7P GAIN MUTATED                                    2
  7P GAIN WILD-TYPE                                  1
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  7P GAIN MUTATED                              0                            10
  7P GAIN WILD-TYPE                            2                            13
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  7P GAIN MUTATED                                 0
  7P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  7P GAIN MUTATED                                               4
  7P GAIN WILD-TYPE                                             1
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7P GAIN MUTATED                              1
  7P GAIN WILD-TYPE                            9
D13V10, multiclass
                                                    clus
vv                                                   7P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             180
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                   10
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    4
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   7P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 57
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               141
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     13
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      1
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
D13V12, continuous
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   179   7   3  15
  7P GAIN WILD-TYPE 165   6   1  11
D13V13, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             179               165
  R1               7                 6
  R2               3                 1
  RX              15                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     5
  7P GAIN WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          33   196
  7P GAIN WILD-TYPE                        19   194
D13V14, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          5                 2
  BLACK OR AFRICAN AMERICAN                     33                19
  WHITE                                        196               194
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     3 202
  7P GAIN WILD-TYPE   4 182
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3  202
  7P GAIN WILD-TYPE    4  182
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             202               182
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   128  87
  7Q GAIN WILD-TYPE 195  94
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              215               289 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               87                94 
$`7Q GAIN MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 
        8.02        20.05         9.01        14.73        42.08        27.78 
TCGA-44-7661 TCGA-44-A47F TCGA-49-6745 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       18.31        11.08        17.16        21.47        41.69        23.05 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 TCGA-55-8091 
        5.79         7.79         7.99        23.18        21.44        19.73 
TCGA-55-8205 TCGA-55-8511 TCGA-55-A492 TCGA-73-4658 TCGA-73-4662 TCGA-91-A4BC 
       19.69        18.15        19.59        52.60        82.68         1.45 
TCGA-95-7562 TCGA-95-7947 TCGA-J2-8192 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
        2.86        15.68        24.30        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
       31.23         2.43        10.09         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-5423 TCGA-05-5425 
        0.00        47.05         2.99        29.98         4.96        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
       22.03         7.40         5.98         8.68        97.74        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-3396 
       49.05        44.61        46.98        44.42        44.94        37.15 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 
       38.89        34.06        33.73        26.56        28.01        23.77 
TCGA-44-6145 TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 
       19.56        32.45        61.28        19.46         7.17        18.87 
TCGA-44-8117 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       12.66        13.64        13.45        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAQV 
       14.07        32.84        29.46        29.75        22.26        22.26 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 
       28.90        40.41       123.58       221.33         9.86        71.47 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5941 TCGA-50-5944 
      101.72        47.41         8.22         9.27        48.46        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-53-7624 TCGA-53-A4EZ 
       53.16        42.35         3.91        11.05        34.29        35.21 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       67.89        14.30         5.62        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7576 
       69.34        45.34        40.54        70.26        20.02        22.03 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 TCGA-55-8092 TCGA-55-8096 
       11.28        34.19        18.44        19.82         5.06        23.64 
TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 
       29.19        17.56        15.72        14.47        13.74        17.72 
TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
       17.10         1.58        12.33        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       15.81        17.95         4.57        42.38        14.60        88.64 
TCGA-62-A46R TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 
       56.71        13.61        29.92        56.81        81.80        37.02 
TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3772 TCGA-69-7760 TCGA-69-7763 
       38.37        28.41        51.25        18.84         6.64        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-A59K 
       13.61         5.42         6.05         4.41        13.41        19.43 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
        8.42        23.38        26.30         4.31        30.31         9.24 
TCGA-73-7499 TCGA-75-5125 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7160 
       50.33        66.64       163.10        27.16        19.27        22.92 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7540 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 
      238.29        26.53        39.35        77.59        27.09        12.36 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 
       31.13        38.04        32.78        35.24         4.08        24.33 
TCGA-86-8075 TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 
       22.82        23.05        14.60        13.91         0.62        28.34 
TCGA-86-A4P7 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-93-7348 
       13.64         2.60        27.68         7.36        16.60        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-97-7553 
       23.61         1.08        18.67        12.39         2.76        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
       25.48        18.54        18.67        18.12        15.39        14.30 
TCGA-97-8552 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A50W 
       20.58        34.85        21.57        18.08        19.00        14.53 
TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
       18.58        38.63        86.14        49.35        37.35        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J TCGA-S2-AA1A 
       41.59        19.13        71.05        59.11        16.87 

$`7Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 
       19.96        14.01         9.96        26.01        15.02        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       28.41        35.28        11.64        26.30        43.53        38.10 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 
       23.93        86.01        29.00        29.23         9.37        46.72 
TCGA-49-6742 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-55-1595 
       16.04        11.64       156.66        37.32        40.60        48.62 
TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 
       16.01        14.53         6.15        19.66        17.98        16.93 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF 
       32.12        13.68        16.93        22.65        20.58        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       20.65        13.87        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       85.32        13.71        16.18         6.12        17.29        16.54 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.65        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 TCGA-05-4249 
       17.75        20.68        23.80         6.35        21.83        50.07 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       24.03        19.00        14.96        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5429 TCGA-05-5715 
       26.01        25.02        25.02        24.00         9.04         2.04 
TCGA-35-3615 TCGA-38-4626 TCGA-38-A44F TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        0.46       120.79         4.37        42.77         3.19        25.02 
TCGA-44-3398 TCGA-44-5643 TCGA-44-5644 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       38.24        33.30        28.37        23.15        21.63        23.18 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 
       16.44        22.72        36.07        23.64         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4487 TCGA-49-4507 
       15.32         9.44        11.54        76.21        28.11         8.81 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 
       55.89        53.29        55.33        73.12        62.24         8.55 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5931 
      164.12        20.52        15.72        60.16        49.28        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6592 TCGA-50-6594 
       78.67         8.45        15.12        60.72        25.55        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 
       30.54        13.94        38.73        30.58        80.52        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
       40.73        15.25        32.71        92.81        24.99       107.21 
TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       28.67        27.09        32.71         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.64        17.65        29.23        29.72        15.19        23.08 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8506 TCGA-55-8508 
       17.79        15.65        22.16        15.42         0.36        20.28 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A4DG 
       19.96        26.01        17.62        14.66        20.71        19.99 
TCGA-62-8395 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U 
       39.98        49.25        47.80        19.53        54.35        67.96 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 
       72.30        39.25        40.96        39.09        87.98         2.04 
TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
       42.90        28.47        20.05        20.05        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7973 TCGA-69-7980 
       14.73         5.72         4.64         6.12         7.56        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4668 TCGA-73-4677 
       14.01        13.45         4.24        26.73        15.35         1.25 
TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       11.18        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      108.66       100.57         5.69        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
       64.90         9.57       104.19        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 
       53.33        26.01        10.55       232.18        39.75       110.50 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
       93.11         5.88        34.39        20.55        19.89        37.74 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 
        4.57         0.79        32.65        31.04        31.20        21.47 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       11.61        30.84        27.58        26.50        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       24.23        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6840 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       12.23         1.15        14.27         1.18        19.82        22.45 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       19.00        41.82        27.29        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 
       63.52         0.59        15.91         5.39        16.41        21.60 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       21.44        19.76        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP 
        1.45        21.63        35.47        32.48        14.30         1.91 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE 
       15.65         2.76        58.45        86.04         5.49        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG 
       11.05        24.36        14.10        11.15        73.91        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG 
       20.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.00              0.13 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           238.29            232.18 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            22.03             21.60 
[1] "0.0 - 238.3 (22.0)" "0.1 - 232.2 (21.6)"
[1] "hr=" "1.3"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         3       54       54        1        22        26
  7Q GAIN WILD-TYPE       2       79       85        0        28        46
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7Q GAIN MUTATED           39          5       14
  7Q GAIN WILD-TYPE         33          6       11
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                54                79
  STAGE IB                54                85
  STAGE II                 1                 0
  STAGE IIA               22                28
  STAGE IIB               26                46
  STAGE IIIA              39                33
  STAGE IIIB               5                 6
  STAGE IV                14                11
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q GAIN MUTATED    69 124  19   7
  7Q GAIN WILD-TYPE 102 154  27  12
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              69               102
  T2             124               154
  T3              19                27
  T4               7                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  7Q GAIN MUTATED   129  40    44
  7Q GAIN WILD-TYPE 204  56    32
D14V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                129               204
  N1                 40                56
  N2+N3              44                32
[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"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   141  14
  7Q GAIN WILD-TYPE 208  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    141   14
  7Q GAIN WILD-TYPE  208   11
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             141               208
  1              14                11
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   118 102
  7Q GAIN WILD-TYPE 158 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    118  102
  7Q GAIN WILD-TYPE  158  138
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             118               158
  MALE               102               138
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   174  31
  7Q GAIN WILD-TYPE 236  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    174   31
  7Q GAIN WILD-TYPE  236   29
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              174               236
  YES              31                29
[1] 2 2
[1] FALSE
D14V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7Q GAIN MUTATED                            7
  7Q GAIN WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7Q GAIN MUTATED                                  45
  7Q GAIN WILD-TYPE                                62
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                  145
  7Q GAIN WILD-TYPE                                                176
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7Q GAIN MUTATED                                            4
  7Q GAIN WILD-TYPE                                          1
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  7Q GAIN MUTATED                                              10
  7Q GAIN WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  7Q GAIN MUTATED                                0
  7Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  7Q GAIN MUTATED                                    1
  7Q GAIN WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  7Q GAIN MUTATED                              0                             7
  7Q GAIN WILD-TYPE                            2                            16
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  7Q GAIN MUTATED                                 0
  7Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  7Q GAIN MUTATED                                               1
  7Q GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7Q GAIN MUTATED                              0
  7Q GAIN WILD-TYPE                           10
D14V10, multiclass
                                                    clus
vv                                                   7Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             145
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    7
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   7Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               176
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     16
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
D14V12, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   144   5   3  13
  7Q GAIN WILD-TYPE 200   8   1  13
D14V13, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             144               200
  R1               5                 8
  R2               3                 1
  RX              13                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     3
  7Q GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          27   167
  7Q GAIN WILD-TYPE                        25   223
D14V14, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                     27                25
  WHITE                                        167               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 173
  7Q GAIN WILD-TYPE   5 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  173
  7Q GAIN WILD-TYPE    5  211
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             173               211
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    76  46
  8P GAIN WILD-TYPE 247 135
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              122               382 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               46               135 
$`8P GAIN MUTATED`
TCGA-05-4405 TCGA-05-4418 TCGA-38-4629 TCGA-38-6178 TCGA-44-7671 TCGA-44-8119 
       20.05         9.01        28.41        14.73        29.23         9.37 
TCGA-44-A47F TCGA-49-6742 TCGA-55-1592 TCGA-55-6978 TCGA-55-7724 TCGA-55-8203 
       11.08        16.04        23.05         5.79        23.18        17.98 
TCGA-55-8204 TCGA-64-1677 TCGA-73-4658 TCGA-91-7771 TCGA-95-7948 TCGA-97-8172 
       16.93        20.65        52.60        16.18        15.65        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TA TCGA-05-4250 
       20.19        20.52        10.09        21.83        31.23         3.98 
TCGA-05-4398 TCGA-05-4417 TCGA-05-4424 TCGA-05-4432 TCGA-05-5428 TCGA-35-5375 
       47.05        14.96        30.02        25.02        22.03         8.68 
TCGA-38-4625 TCGA-44-2656 TCGA-44-6775 TCGA-44-6778 TCGA-44-7667 TCGA-44-7669 
       97.74        46.98        23.18        61.28        36.07        18.87 
TCGA-44-7672 TCGA-44-8120 TCGA-44-A47B TCGA-49-4512 TCGA-49-AARE TCGA-4B-A93V 
       23.64         8.55         9.44        29.75        40.41         9.86 
TCGA-50-5051 TCGA-50-5072 TCGA-50-5933 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 
       15.72         8.22        78.67        57.53        53.16        25.55 
TCGA-50-7109 TCGA-50-8457 TCGA-55-1596 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       10.13        36.99        67.89        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-7574 TCGA-55-7907 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 
       53.65        32.71        11.28        23.64        29.19        17.56 
TCGA-55-8507 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
       13.74        17.62        14.66         1.58        12.33        21.40 
TCGA-55-A490 TCGA-55-A494 TCGA-62-8398 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
        3.25        15.81        14.60        19.53        56.71        54.35 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5779 TCGA-69-7763 TCGA-69-7764 
       39.25        40.96        37.02        28.41        22.68        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4670 
        7.56         6.05        19.43         8.42        23.38         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 TCGA-75-6206 TCGA-75-7027 
       30.31         9.24         1.25        66.64        85.15       100.57 
TCGA-78-7143 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 
      163.10        20.58       129.53       119.51         5.88        64.90 
TCGA-78-7535 TCGA-86-7701 TCGA-86-8280 TCGA-86-8585 TCGA-86-8669 TCGA-86-8674 
       31.20        31.13        23.05        11.61        30.84        26.50 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6840 TCGA-93-7347 TCGA-93-A4JO TCGA-93-A4JP 
       10.62        10.19        12.23        22.45         1.08        19.00 
TCGA-95-7567 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7553 TCGA-97-8176 TCGA-97-8552 
       18.67        19.89        64.60        61.48        15.39        20.58 
TCGA-99-8025 TCGA-99-8033 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4TE TCGA-MP-A4TF 
       34.85        21.57        49.35        37.35        29.46        11.05 
TCGA-MP-A4TH TCGA-NJ-A4YG 
       24.36        74.33 

$`8P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         8.02        26.01        15.02 
TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       15.02        35.28        11.64        26.30        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       42.08        23.93        27.78        86.01        18.31        29.00 
TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       46.72        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       21.47        41.69        48.62         7.79         7.99        16.01 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8205 
       14.53        21.44         6.15        19.66        19.73        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       19.59        20.19        13.87        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 
       50.24        10.55        85.32        13.71         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN 
       17.29        16.54         2.86        15.68        21.40        18.18 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-MN-A4N1 
       17.75        20.68        24.30        23.80         6.35        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 
        5.29         2.43        10.09        50.07        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 
        0.00        24.03        19.00         2.99        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       21.99        26.01        25.02        24.00         4.96        29.00 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 
        9.04         2.04         0.46         7.40         5.98       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 
       37.71        49.05        44.61         4.37        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6779 
       23.77        19.56        23.15        21.63        32.45        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A 
       22.72        19.46         7.17        12.66        15.98        15.32 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        14.07        32.84         8.81        29.46 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       55.89        53.29        55.33        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90         8.55       123.58       221.33       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47       101.72        60.16        47.41        49.28 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        14.27         8.45        15.12        48.46        60.72 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       42.35         3.91        11.05        12.16         6.21         0.72 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       38.73        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
       40.54       107.21        70.26        28.67        20.02        27.09 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
       22.03         3.91        23.15        25.41        18.64        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 
       23.08         5.06        17.79        15.65        22.16        15.42 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       15.72        14.47         0.36        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-A48Y TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B 
       26.01        17.10        20.71         0.92        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        42.38        88.64        49.25        47.80 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
       67.96        72.30        13.61        29.92        56.81        39.09 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
       81.80        38.37        87.98         2.04        42.90        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       28.47        20.05        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 
       14.73         5.72         4.64         6.64         6.12         5.42 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-8453 TCGA-73-4666 TCGA-73-4668 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5146 
       26.73        26.30        15.35        50.33        11.18        77.85 
TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 
       43.82        49.84        36.66       108.66        27.16         5.69 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       19.27        21.90        39.95        19.50        38.50        32.09 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
       22.82        32.65        31.04        31.20        21.47        14.60 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 
       13.91        27.58         0.62        28.34        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
       24.23        13.64        26.47        41.36         1.97         2.60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 
       19.82        17.46        23.61        41.82        12.39        27.29 
TCGA-95-8494 TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
        2.76        42.25        63.52        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       15.91        18.67         5.39        18.12        16.41        14.30 
TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       21.60        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.63        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       19.00        14.30        14.53         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T6 
       38.63         2.76        86.14        58.45        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
        5.49        41.59        14.10        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05         0.13         1.64        47.08         0.49         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.08              0.00 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           163.10            238.29 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           21.700            21.615 
[1] "1.1 - 163.1 (21.7)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         1       26       41        0        12        15
  8P GAIN WILD-TYPE       4      107       98        1        38        57
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8P GAIN MUTATED           18          5        6
  8P GAIN WILD-TYPE         54          6       19
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                26               107
  STAGE IB                41                98
  STAGE II                 0                 1
  STAGE IIA               12                38
  STAGE IIB               15                57
  STAGE IIIA              18                54
  STAGE IIIB               5                 6
  STAGE IV                 6                19
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED    30  77  12   4
  8P GAIN WILD-TYPE 141 201  34  15
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              30               141
  T2              77               201
  T3              12                34
  T4               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  8P GAIN MUTATED    82  20    20
  8P GAIN WILD-TYPE 251  76    56
D15V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                 82               251
  N1                 20                76
  N2+N3              20                56
[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"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    87   6
  8P GAIN WILD-TYPE 262  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     87    6
  8P GAIN WILD-TYPE  262   19
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              87               262
  1               6                19
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    56  69
  8P GAIN WILD-TYPE 220 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     56   69
  8P GAIN WILD-TYPE  220  171
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              56               220
  MALE                69               171
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   103  17
  8P GAIN WILD-TYPE 307  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    103   17
  8P GAIN WILD-TYPE  307   43
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              103               307
  YES              17                43
[1] 2 2
[1] FALSE
D15V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8P GAIN MUTATED                            6
  8P GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8P GAIN MUTATED                                  32
  8P GAIN WILD-TYPE                                75
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                   74
  8P GAIN WILD-TYPE                                                247
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8P GAIN MUTATED                                            0
  8P GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  8P GAIN MUTATED                                               4
  8P GAIN WILD-TYPE                                            15
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  8P GAIN MUTATED                                0
  8P GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  8P GAIN MUTATED                                    0
  8P GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  8P GAIN MUTATED                              0                             7
  8P GAIN WILD-TYPE                            2                            16
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  8P GAIN MUTATED                                 0
  8P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  8P GAIN MUTATED                                               1
  8P GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  8P GAIN MUTATED                              1
  8P GAIN WILD-TYPE                            9
D15V10, multiclass
                                                    clus
vv                                                   8P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              74
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    4
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    7
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   8P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               247
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     15
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     16
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
D15V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    79   6   1   6
  8P GAIN WILD-TYPE 265   7   3  20
D15V13, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              79               265
  R1               6                 7
  R2               1                 3
  RX               6                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     3
  8P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          10    98
  8P GAIN WILD-TYPE                        42   292
D15V14, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                     10                42
  WHITE                                         98               292
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1  95
  8P GAIN WILD-TYPE   6 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   95
  8P GAIN WILD-TYPE    6  289
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              95               289
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   143  97
  8Q GAIN WILD-TYPE 180  84
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              240               264 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               97                84 
$`8Q GAIN MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-5420 TCGA-38-4629 TCGA-38-4631 
        8.02        20.05         9.01        15.02        28.41        11.64 
TCGA-38-6178 TCGA-44-6147 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       14.73        27.78        29.00        29.23         9.37        11.08 
TCGA-49-6761 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7724 
       11.64        23.05        48.62         5.79         7.79        23.18 
TCGA-55-7914 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-A491 
        6.15        17.98        16.93        19.69        18.15        20.58 
TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-78-8660 TCGA-91-7771 TCGA-93-8067 
       20.65        52.60        82.68        10.55        16.18         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VN TCGA-97-8172 
       17.29        16.54         2.86        15.65        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       20.19        20.52        23.80         6.35        10.09        21.83 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4417 TCGA-05-4424 TCGA-05-4432 
       37.02         0.00        47.05        14.96        30.02        25.02 
TCGA-05-5423 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
        4.96        22.03         7.40         8.68        97.74        49.05 
TCGA-38-4632 TCGA-44-2656 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-5644 
       44.61        46.98        25.02        38.89        34.06        28.37 
TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.77        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A47B 
        7.17        36.07        18.87        23.64         8.55         9.44 
TCGA-44-A4SU TCGA-49-4488 TCGA-49-4510 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAQV 
       13.45        28.57        29.46        29.75        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARE TCGA-49-AARO TCGA-4B-A93V TCGA-50-5051 
       73.12        62.24        40.41       123.58         9.86        15.72 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 
       47.41         8.22        14.27        78.67        48.46        57.53 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6673 TCGA-50-7109 
       53.16         3.91        25.55        11.05         0.72        10.13 
TCGA-50-8457 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
       36.99        13.94        35.21        67.89        30.58        80.52 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6981 
        5.62        40.73        15.25        46.03        53.65        45.34 
TCGA-55-6982 TCGA-55-6985 TCGA-55-7283 TCGA-55-7574 TCGA-55-7907 TCGA-55-7913 
       32.71        40.54        20.02        32.71        11.28        18.44 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.82        29.72         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 
       29.19        17.56        15.72        13.74        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
        0.92        15.81        39.98        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       19.53        56.71        54.35        39.25        40.96        29.92 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 
       39.09        37.02         2.04        28.41        20.05        20.05 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
        6.64        22.68        13.61         7.56         6.05        13.41 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 
        4.24        19.43         8.42        23.38         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 
        9.24         1.25        50.33        66.64        43.82        85.15 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       36.66       100.57       163.10         5.69        20.58       129.53 
TCGA-78-7152 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7220 TCGA-78-7535 
       39.95         5.88        64.90         9.57        26.53        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8662 TCGA-80-5608 TCGA-86-7701 
        8.02        26.01        10.55       110.50        93.11        31.13 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
       19.89        37.74        23.05        14.60        11.61        30.84 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 
        0.62        26.50        29.46         3.81        13.64        10.62 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 TCGA-93-7347 TCGA-93-A4JO 
       10.19        12.23        27.68         1.18        22.45         1.08 
TCGA-93-A4JP TCGA-95-7567 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7553 TCGA-97-7938 
       19.00        18.67        19.89        64.60        61.48         0.59 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       15.39        14.30        20.58        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N5 
       21.57        18.08        14.53         1.91        15.65         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.14        58.45        49.35        37.35        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A7XG 
       24.36        14.10        11.15        71.05        74.33        20.28 

$`8Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4427 TCGA-05-4434 TCGA-38-4630 
       19.96        14.01         9.96        26.01        15.02        35.28 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 
       26.30        43.53        38.10        42.08        23.93        86.01 
TCGA-44-7661 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 TCGA-49-AARN 
       18.31        46.72        16.04        17.16       156.66        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 
       40.60        21.47        41.69         7.99        16.01        14.53 
TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 
       21.44        19.66        19.73        32.12        13.68        16.93 
TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 
       22.65        19.59        20.19        13.87        39.09         8.48 
TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-95-7947 TCGA-95-A4VK 
       50.24        85.32        13.71         1.45        15.68        21.40 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-05-4397 
       17.75        20.68        24.30        27.19         5.29        24.03 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       19.00         2.99        29.98        12.00        21.99        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       25.02        24.00        29.00         9.04         2.04         0.46 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 
        5.98       120.79        37.71         4.37        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       42.77         3.19        37.15        38.24        33.73        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-7659 TCGA-44-7660 
       33.30        28.01        19.56        23.15        22.72        19.46 
TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       12.66        15.98        15.32        11.54        13.64        76.21 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.11        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARQ 
       55.89        53.29        55.33        28.90         8.55       221.33 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5068 
      164.12        20.52        71.47       101.72        60.16        49.28 
TCGA-50-5930 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6594 
        9.27         8.45        15.12        60.72        42.35        12.16 
TCGA-50-6595 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
        6.21        36.79        27.25        34.29        30.54        38.73 
TCGA-55-6543 TCGA-55-6968 TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 
       14.30        42.51         3.88        69.34        92.81        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 
      107.21        70.26        28.67        27.09        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 
       23.15        25.41        18.64        34.19        17.65        29.23 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 
       15.19        23.08        22.16        15.42        14.47         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-A4DG TCGA-55-A57B 
       20.28        17.72        19.96        26.01        19.99        17.95 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
        4.57        42.38        88.64        67.96        72.30        13.61 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 
       56.81        81.80        38.37        87.98        42.90        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       28.47        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7761 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        4.64         6.12         5.42         4.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-73-4666 TCGA-73-4668 TCGA-73-A9RS TCGA-75-5146 
       13.45        26.73        26.30        15.35        11.18        77.85 
TCGA-75-6212 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7153 
       49.84       108.66        27.16        19.27        21.90       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
       19.50        38.50        32.09        22.92       104.19       238.29 
TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       88.14        53.33        39.35       232.18        39.75        77.59 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36         5.88        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       32.78        35.24         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8668 
       22.82        32.65        31.04        31.20        21.47        13.91 
TCGA-86-8671 TCGA-86-8673 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       27.58        28.34        24.23        26.47        41.36         1.97 
TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
        2.60         7.36         1.15        16.60        14.27        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       17.46        23.61        41.82        12.39        27.29         2.76 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
       42.25        63.52        25.48        18.54        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 
        5.39        18.12        16.41        21.60        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG 
       20.84        18.67        24.56        21.63        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T6 
       19.00        14.30        18.58        38.63        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YP 
        5.49        41.59        19.13        73.91         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       47.08         0.49         0.43        19.82        59.11        16.87 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.00              0.13 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           163.10            238.29 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            20.55             22.77 
[1] "0.0 - 163.1 (20.5)" "0.1 - 238.3 (22.8)"
[1] "hr=" "1.4"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2       57       70        1        23        34
  8Q GAIN WILD-TYPE       3       76       69        0        27        38
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8Q GAIN MUTATED           36          7       12
  8Q GAIN WILD-TYPE         36          4       13
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                57                76
  STAGE IB                70                69
  STAGE II                 1                 0
  STAGE IIA               23                27
  STAGE IIB               34                38
  STAGE IIIA              36                36
  STAGE IIIB               7                 4
  STAGE IV                12                13
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q GAIN MUTATED    72 138  25   8
  8Q GAIN WILD-TYPE  99 140  21  11
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              72                99
  T2             138               140
  T3              25                21
  T4               8                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  8Q GAIN MUTATED   159  41    39
  8Q GAIN WILD-TYPE 174  55    37
D16V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                159               174
  N1                 41                55
  N2+N3              39                37
[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"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   163  12
  8Q GAIN WILD-TYPE 186  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    163   12
  8Q GAIN WILD-TYPE  186   13
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             163               186
  1              12                13
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   128 117
  8Q GAIN WILD-TYPE 148 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    128  117
  8Q GAIN WILD-TYPE  148  123
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             128               148
  MALE               117               123
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   196  32
  8Q GAIN WILD-TYPE 214  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    196   32
  8Q GAIN WILD-TYPE  214   28
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              196               214
  YES              32                28
[1] 2 2
[1] FALSE
D16V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8Q GAIN MUTATED                           12
  8Q GAIN WILD-TYPE                          6
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8Q GAIN MUTATED                                  52
  8Q GAIN WILD-TYPE                                55
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                  157
  8Q GAIN WILD-TYPE                                                164
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8Q GAIN MUTATED                                            0
  8Q GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  8Q GAIN MUTATED                                               8
  8Q GAIN WILD-TYPE                                            11
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  8Q GAIN MUTATED                                1
  8Q GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  8Q GAIN MUTATED                                    0
  8Q GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  8Q GAIN MUTATED                              0                            11
  8Q GAIN WILD-TYPE                            2                            12
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  8Q GAIN MUTATED                                 1
  8Q GAIN WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  8Q GAIN MUTATED                                               3
  8Q GAIN WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  8Q GAIN MUTATED                              0
  8Q GAIN WILD-TYPE                           10
D16V10, multiclass
                                                    clus
vv                                                   8Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             157
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    8
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                   11
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   8Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               164
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     11
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     12
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
D16V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   162   9   3  14
  8Q GAIN WILD-TYPE 182   4   1  12
D16V13, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             162               182
  R1               9                 4
  R2               3                 1
  RX              14                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     6
  8Q GAIN WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          27   182
  8Q GAIN WILD-TYPE                        25   208
D16V14, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                 1
  BLACK OR AFRICAN AMERICAN                     27                25
  WHITE                                        182               208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     4 177
  8Q GAIN WILD-TYPE   3 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4  177
  8Q GAIN WILD-TYPE    3  207
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             177               207
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    29  14
  9P GAIN WILD-TYPE 294 167
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               43               461 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               14               167 
$`9P GAIN MUTATED`
TCGA-05-4427 TCGA-44-6147 TCGA-44-8119 TCGA-44-A47F TCGA-50-6597 TCGA-55-A4DF 
       26.01        27.78         9.37        11.08        41.69        20.19 
TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN TCGA-L9-A444 TCGA-MP-A4TC TCGA-05-4390 
        2.86        15.68        18.18        10.09         2.43        37.02 
TCGA-44-6774 TCGA-49-AARQ TCGA-50-5051 TCGA-55-6972 TCGA-55-7903 TCGA-55-7995 
       21.63       221.33        15.72        53.65        18.64        29.23 
TCGA-55-8301 TCGA-55-8514 TCGA-55-8620 TCGA-55-A48Z TCGA-62-A46R TCGA-64-5775 
       17.56        17.10        12.33        21.40        56.71         2.04 
TCGA-69-7973 TCGA-69-7979 TCGA-69-8253 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 
        7.56        13.41        14.01        19.43        23.38        26.30 
TCGA-73-7499 TCGA-78-7163 TCGA-78-8662 TCGA-80-5608 TCGA-86-7953 TCGA-86-8669 
       50.33       238.29       110.50        93.11        32.78        30.84 
TCGA-91-6828 TCGA-95-7039 TCGA-97-7553 TCGA-97-7554 TCGA-L9-A5IP TCGA-MP-A4TJ 
       10.62        41.82        61.48        25.48         1.91        11.15 
TCGA-S2-AA1A 
       16.87 

$`9P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 
       26.30        43.53        38.10        42.08        23.93        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       18.31        29.00        29.23        46.72        16.04        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 
       11.64       156.66        37.32        40.60        21.47        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       22.65        20.58        19.59        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       15.65        21.40        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 
       20.68        24.30        23.80         6.35        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
        5.29        31.23        10.09        50.07         3.98        45.01 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        2.04         0.46         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       38.24        38.89        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 
       28.37        28.01        23.77        19.56        23.15        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
       40.41       123.58       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
      101.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       14.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       67.89        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25        46.03         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       23.15        25.41        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       19.82        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
       23.64        15.65        29.19        22.16        15.42        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A490 
       26.01        17.62        14.66         1.58        20.71         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        19.99        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       29.92        56.81        39.09        81.80        37.02        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       87.98        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       20.05        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        6.05         4.41        13.51        13.45         4.24        26.73 
TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
        8.42        15.35         4.31        30.31         9.24         1.25 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       11.18        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        9.57       104.19        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       77.59        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       38.04        20.55        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60        11.61        13.91 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       27.58         0.62        28.34        26.50        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       24.23        13.64        26.47        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7938 
       19.89        42.25        64.60        63.52        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.53        18.58        15.65        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.49         0.43        19.82        20.28        59.11 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.91              0.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           238.29            232.18 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            20.19             21.83 
[1] "1.9 - 238.3 (20.2)" "0.0 - 232.2 (21.8)"
[1] "hr=" "1.2"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         1       13       12        0         3         5
  9P GAIN WILD-TYPE       4      120      127        1        47        67
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9P GAIN MUTATED            7          1        3
  9P GAIN WILD-TYPE         65         10       22
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                13               120
  STAGE IB                12               127
  STAGE II                 0                 1
  STAGE IIA                3                47
  STAGE IIB                5                67
  STAGE IIIA               7                65
  STAGE IIIB               1                10
  STAGE IV                 3                22
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED    19  20   5   1
  9P GAIN WILD-TYPE 152 258  41  18
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              19               152
  T2              20               258
  T3               5                41
  T4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  9P GAIN MUTATED    30   6     8
  9P GAIN WILD-TYPE 303  90    68
D17V5, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0                 30               303
  N1                  6                90
  N2+N3               8                68
[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"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    31   3
  9P GAIN WILD-TYPE 318  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     31    3
  9P GAIN WILD-TYPE  318   22
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              31               318
  1               3                22
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    29  16
  9P GAIN WILD-TYPE 247 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     29   16
  9P GAIN WILD-TYPE  247  224
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              29               247
  MALE                16               224
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    39   5
  9P GAIN WILD-TYPE 371  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     39    5
  9P GAIN WILD-TYPE  371   55
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               39               371
  YES               5                55
[1] 2 2
[1] FALSE
D17V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9P GAIN MUTATED                            1
  9P GAIN WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9P GAIN MUTATED                                  10
  9P GAIN WILD-TYPE                                97
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                   27
  9P GAIN WILD-TYPE                                                294
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9P GAIN MUTATED                                            1
  9P GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  9P GAIN MUTATED                                               1
  9P GAIN WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  9P GAIN MUTATED                                0
  9P GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  9P GAIN MUTATED                                    0
  9P GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  9P GAIN MUTATED                              0                             3
  9P GAIN WILD-TYPE                            2                            20
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  9P GAIN MUTATED                                 1
  9P GAIN WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  9P GAIN MUTATED                                               1
  9P GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9P GAIN MUTATED                              0
  9P GAIN WILD-TYPE                           10
D17V10, multiclass
                                                    clus
vv                                                   9P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              27
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   9P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               294
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
D17V12, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    30   1   1   3
  9P GAIN WILD-TYPE 314  12   3  23
D17V13, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              30               314
  R1               1                12
  R2               1                 3
  RX               3                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           7    31
  9P GAIN WILD-TYPE                        45   359
D17V14, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      7                45
  WHITE                                         31               359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  37
  9P GAIN WILD-TYPE   7 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   37
  9P GAIN WILD-TYPE    7  347
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              37               347
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    20  13
  9Q GAIN WILD-TYPE 303 168
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               33               471 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               13               168 
$`9Q GAIN MUTATED`
TCGA-05-4427 TCGA-44-8119 TCGA-44-A47F TCGA-50-6597 TCGA-55-8091 TCGA-91-6836 
       26.01         9.37        11.08        41.69        19.73        13.71 
TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN TCGA-MP-A4TC TCGA-05-4390 TCGA-44-6778 
        2.86        15.68        18.18         2.43        37.02        61.28 
TCGA-4B-A93V TCGA-50-5051 TCGA-50-6590 TCGA-55-6972 TCGA-55-7995 TCGA-55-8301 
        9.86        15.72        42.35        53.65        29.23        17.56 
TCGA-55-8620 TCGA-55-A48Z TCGA-69-8253 TCGA-73-4666 TCGA-73-7499 TCGA-78-7160 
       12.33        21.40        14.01        26.30        50.33        22.92 
TCGA-78-7163 TCGA-78-7542 TCGA-78-8662 TCGA-86-7953 TCGA-86-8669 TCGA-97-7553 
      238.29        10.55       110.50        32.78        30.84        61.48 
TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-S2-AA1A 
        1.91         2.76        16.87 

$`9Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 
       26.30        43.53        38.10        42.08        23.93        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-49-4501 TCGA-49-6742 
       86.01        18.31        29.00        29.23        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       17.16        11.64       156.66        37.32        40.60        21.47 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 
       23.18        14.53        21.44         6.15        19.66        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       85.32        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       15.65        21.40        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       20.68        24.30        23.80         6.35        10.09        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
       27.19         5.29        31.23        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       45.01         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
        9.04         2.04         0.46         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        44.42        44.94        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        32.45        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.33        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 
        8.55        40.41       123.58       221.33       164.12        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       71.47       101.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       60.72        57.53        53.16         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       67.89        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25        46.03         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       23.15        25.41        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       18.44        19.82        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       20.71         3.25         0.92        15.81        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
       13.61        39.25        40.96        29.92        56.81        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       81.80        37.02        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       28.41        51.25        28.47        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        4.41        13.41        13.51        13.45         4.24        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       19.43         8.42        23.38        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        11.18        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       64.90         9.57       104.19        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 
        8.02        53.33        26.01        39.35       232.18        39.75 
TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        38.04        20.55        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60        11.61 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       34.85        36.76         1.45        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV 
       35.47        32.48        19.00        14.30        14.53        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       15.65        38.63        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       24.36        14.10        11.15        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       74.33         0.13         1.64        47.08         0.49         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       19.82        20.28        59.11 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.91              0.00 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           238.29            232.18 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            19.73             21.63 
[1] "1.9 - 238.3 (19.7)" "0.0 - 232.2 (21.6)"
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         0        9       12        0         3         3
  9Q GAIN WILD-TYPE       5      124      127        1        47        69
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9Q GAIN MUTATED            2          1        4
  9Q GAIN WILD-TYPE         70         10       21
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 9               124
  STAGE IB                12               127
  STAGE II                 0                 1
  STAGE IIA                3                47
  STAGE IIB                3                69
  STAGE IIIA               2                70
  STAGE IIIB               1                10
  STAGE IV                 4                21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED    14  17   2   1
  9Q GAIN WILD-TYPE 157 261  44  18
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              14               157
  T2              17               261
  T3               2                44
  T4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  9Q GAIN MUTATED    23   6     5
  9Q GAIN WILD-TYPE 310  90    71
D18V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                 23               310
  N1                  6                90
  N2+N3               5                71
[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"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    23   4
  9Q GAIN WILD-TYPE 326  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     23    4
  9Q GAIN WILD-TYPE  326   21
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              23               326
  1               4                21
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    19  15
  9Q GAIN WILD-TYPE 257 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19   15
  9Q GAIN WILD-TYPE  257  225
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              19               257
  MALE                15               225
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    28   5
  9Q GAIN WILD-TYPE 382  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     28    5
  9Q GAIN WILD-TYPE  382   55
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               28               382
  YES               5                55
[1] 2 2
[1] FALSE
D18V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9Q GAIN MUTATED                            0
  9Q GAIN WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9Q GAIN MUTATED                                   8
  9Q GAIN WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                   22
  9Q GAIN WILD-TYPE                                                299
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9Q GAIN MUTATED                                            1
  9Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  9Q GAIN MUTATED                                               1
  9Q GAIN WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  9Q GAIN MUTATED                                0
  9Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  9Q GAIN MUTATED                                    0
  9Q GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  9Q GAIN MUTATED                              0                             1
  9Q GAIN WILD-TYPE                            2                            22
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  9Q GAIN MUTATED                                 0
  9Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  9Q GAIN MUTATED                                               1
  9Q GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9Q GAIN MUTATED                              0
  9Q GAIN WILD-TYPE                           10
D18V10, multiclass
                                                    clus
vv                                                   9Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              22
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   9Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               299
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
D18V12, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    24   1   0   2
  9Q GAIN WILD-TYPE 320  12   4  24
D18V13, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              24               320
  R1               1                12
  R2               0                 4
  RX               2                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     0
  9Q GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           6    24
  9Q GAIN WILD-TYPE                        46   366
D18V14, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      6                46
  WHITE                                         24               366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  26
  9Q GAIN WILD-TYPE   7 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   26
  9Q GAIN WILD-TYPE    7  358
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              26               358
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    69  42
  10P GAIN WILD-TYPE 254 139
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               111                393 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                42                139 
$`10P GAIN MUTATED`
TCGA-05-4405 TCGA-05-5420 TCGA-44-7671 TCGA-55-6978 TCGA-55-8511 TCGA-55-A491 
       20.05        15.02        29.23         5.79        18.15        20.58 
TCGA-73-4658 TCGA-78-7633 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-95-A4VN 
       52.60        50.24        13.71        16.18         6.12        18.18 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TD 
       23.80         6.35        10.09        27.19         5.29        10.09 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       45.01        37.02         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 TCGA-05-5425 TCGA-35-4122 TCGA-38-4632 
       30.02        25.02        25.02        29.00         7.40        44.61 
TCGA-44-3396 TCGA-44-6144 TCGA-44-6145 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 
       37.15        23.77        19.56        36.07        23.64        12.66 
TCGA-44-8120 TCGA-49-4487 TCGA-49-AAR2 TCGA-49-AARE TCGA-4B-A93V TCGA-50-5049 
        8.55        28.11        73.12        40.41         9.86       101.72 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5933 TCGA-50-5946 TCGA-50-6592 TCGA-50-7109 
       15.72        49.28        78.67        53.16        25.55        10.13 
TCGA-53-7624 TCGA-53-7813 TCGA-55-6642 TCGA-55-6970 TCGA-55-6972 TCGA-55-7283 
       34.29        13.94        80.52        15.25        53.65        20.02 
TCGA-55-7907 TCGA-55-7910 TCGA-55-8092 TCGA-55-8302 TCGA-55-8615 TCGA-55-8620 
       11.28        34.19         5.06        15.72        14.66        12.33 
TCGA-62-8398 TCGA-62-A46S TCGA-62-A470 TCGA-64-1678 TCGA-69-7763 TCGA-69-7979 
       14.60        54.35        39.25        39.09        22.68        13.41 
TCGA-71-6725 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5125 
        8.42         4.31        30.31         1.25        11.18        66.64 
TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 
       85.15        36.66       100.57       129.53        19.50        38.50 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7539 TCGA-78-7542 TCGA-78-8662 
       64.90        22.92         9.57        26.01        10.55       110.50 
TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7955 TCGA-86-8358 
       93.11        31.13        34.39        38.04        35.24        21.47 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6829 TCGA-95-7567 
        0.62        28.34        29.46         3.81        41.36        18.67 
TCGA-95-7944 TCGA-95-A4VP TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 
       12.39        19.89        61.48        25.48        18.54        14.30 
TCGA-99-8025 TCGA-99-8032 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T7 
       34.85         1.45        18.58        38.63         2.76         5.49 
TCGA-MP-A4TE TCGA-NJ-A4YF TCGA-NJ-A4YQ 
       29.46        71.05        47.08 

$`10P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       43.53        38.10        42.08        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.00         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       17.16        11.64       156.66        37.32        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       41.69        23.05        48.62         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        19.69        32.12        13.68        16.93 
TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 
       22.65        19.59        20.19        20.65        13.87        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-8660 TCGA-80-5611 TCGA-91-A4BC TCGA-93-A4JQ 
       39.09         8.48        10.55        85.32         1.45        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 
       16.54         2.86        15.68        15.65        21.40        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A743 
       20.19        20.52        17.75        20.68        24.30        21.83 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 TCGA-05-4395 TCGA-05-4397 
       31.23         2.43        50.07         3.98         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 
       47.05        19.00        21.99        26.01        24.00         4.96 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 
       22.03         9.04         2.04         0.46         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F TCGA-44-2656 
       97.74       120.79        37.71        49.05         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 
       44.42        44.94        42.77         3.19        25.02        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.89        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       28.01        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-A479 
       16.44        22.72        19.46         7.17        18.87        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ 
       22.26        62.24        28.90         8.55       123.58       221.33 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
      164.12        20.52        71.47        60.16        47.41         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        14.27         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       57.53        42.35         3.91        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ 
        0.72        36.99        36.79        27.25        30.54        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       38.73        67.89        30.58        14.30         5.62        42.51 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       40.73        46.03         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       18.64        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19        23.08        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42        17.56        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
        1.58        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
       19.99        17.95         4.57        39.98        42.38        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V 
       49.25        47.80        19.53        56.71        67.96        72.30 
TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 
       13.61        40.96        29.92        56.81        81.80        37.02 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       28.47        20.05        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
       14.73         5.72         4.64         6.64         6.12        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05         4.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 
       13.45         4.24        26.73        19.43        23.38        26.30 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 
       15.35         9.24        50.33        77.85        43.82        49.84 
TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      108.66       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 
       21.90        39.95       119.51        32.09         5.88       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 
       39.35       232.18        39.75        77.59        27.09        12.36 
TCGA-86-6851 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
        5.88        20.55        32.78        19.89        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.20        23.05        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       27.58        26.50        24.23        13.64        26.47        10.62 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 
       17.46        23.61         1.08        19.00        41.82        27.29 
TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 TCGA-97-7941 
        2.76        42.25        64.60        63.52         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       18.67         5.39        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76        21.57        21.63        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MP-A4SV 
       19.00        14.30        14.53         1.91        15.65        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 
       58.45        49.35        37.35        86.04        58.85        41.59 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       11.05        24.36        14.10        11.15        19.13        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       74.33         0.13         1.64         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.62               0.00 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            129.53             238.29 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             23.77              21.44 
[1] "0.6 - 129.5 (23.8)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         0       26       34        0        11        13
  10P GAIN WILD-TYPE       5      107      105        1        39        59
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10P GAIN MUTATED           15          4        7
  10P GAIN WILD-TYPE         57          7       18
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 26                107
  STAGE IB                 34                105
  STAGE II                  0                  1
  STAGE IIA                11                 39
  STAGE IIB                13                 59
  STAGE IIIA               15                 57
  STAGE IIIB                4                  7
  STAGE IV                  7                 18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED    26  68  13   5
  10P GAIN WILD-TYPE 145 210  33  14
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               26                145
  T2               68                210
  T3               13                 33
  T4                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  10P GAIN MUTATED    81  13    17
  10P GAIN WILD-TYPE 252  83    59
D19V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                  81                252
  N1                  13                 83
  N2+N3               17                 59
[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"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    79   7
  10P GAIN WILD-TYPE 270  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     79    7
  10P GAIN WILD-TYPE  270   18
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               79                270
  1                7                 18
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    46  66
  10P GAIN WILD-TYPE 230 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     46   66
  10P GAIN WILD-TYPE  230  174
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               46                230
  MALE                 66                174
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    90  13
  10P GAIN WILD-TYPE 320  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     90   13
  10P GAIN WILD-TYPE  320   47
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                90                320
  YES               13                 47
[1] 2 2
[1] FALSE
D19V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10P GAIN MUTATED                            5
  10P GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10P GAIN MUTATED                                  26
  10P GAIN WILD-TYPE                                81
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                   68
  10P GAIN WILD-TYPE                                                253
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10P GAIN MUTATED                                            0
  10P GAIN WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  10P GAIN MUTATED                                               5
  10P GAIN WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  10P GAIN MUTATED                                0
  10P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  10P GAIN MUTATED                                    1
  10P GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  10P GAIN MUTATED                              0                             6
  10P GAIN WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  10P GAIN MUTATED                                 0
  10P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  10P GAIN MUTATED                                               1
  10P GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  10P GAIN MUTATED                              0
  10P GAIN WILD-TYPE                           10
D19V10, multiclass
                                                    clus
vv                                                   10P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               68
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   10P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                253
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                       10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
D19V12, continuous
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    74   3   0   9
  10P GAIN WILD-TYPE 270  10   4  17
D19V13, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               74                270
  R1                3                 10
  R2                0                  4
  RX                9                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     3
  10P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                          12    76
  10P GAIN WILD-TYPE                        40   314
D19V14, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                      12                 40
  WHITE                                          76                314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  74
  10P GAIN WILD-TYPE   5 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   74
  10P GAIN WILD-TYPE    5  310
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               74                310
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    49  30
  10Q GAIN WILD-TYPE 274 151
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                79                425 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                30                151 
$`10Q GAIN MUTATED`
TCGA-05-5420 TCGA-44-7671 TCGA-55-6978 TCGA-55-8205 TCGA-55-A491 TCGA-73-4658 
       15.02        29.23         5.79        19.69        20.58        52.60 
TCGA-91-7771 TCGA-J2-8194 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4390 
       16.18        23.80         5.29        10.09        45.01        37.02 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4430 TCGA-05-4432 TCGA-05-5425 
        2.99        14.96        12.00        25.02        25.02        29.00 
TCGA-35-4122 TCGA-38-4632 TCGA-44-6144 TCGA-44-6145 TCGA-44-7667 TCGA-49-4487 
        7.40        44.61        23.77        19.56        36.07        28.11 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 TCGA-50-5933 TCGA-50-5946 TCGA-50-6593 
      101.72        15.72        49.28        78.67        53.16        11.05 
TCGA-53-7624 TCGA-55-6642 TCGA-55-6970 TCGA-55-6972 TCGA-55-7283 TCGA-55-7907 
       34.29        80.52        15.25        53.65        20.02        11.28 
TCGA-55-7913 TCGA-55-8302 TCGA-55-8615 TCGA-62-8398 TCGA-62-A46S TCGA-62-A470 
       18.44        15.72        14.66        14.60        54.35        39.25 
TCGA-69-7763 TCGA-71-6725 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-75-6206 
       22.68         8.42         4.31        30.31         1.25        85.15 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 
       36.66       100.57       129.53        19.50        64.90        22.92 
TCGA-78-7161 TCGA-78-8662 TCGA-86-7701 TCGA-86-7713 TCGA-86-8279 TCGA-86-8358 
        9.57       110.50        31.13        38.04        31.20        21.47 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-95-7567 TCGA-95-8494 
        0.62        28.34        29.46         3.81        18.67         2.76 
TCGA-95-A4VP TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 TCGA-99-8025 
       19.89        61.48        25.48        18.54        14.30        34.85 
TCGA-99-8032 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T7 TCGA-MP-A4TE 
        1.45        18.58        38.63         2.76         5.49        29.46 
TCGA-MP-A5C7 
       73.91 

$`10Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       26.01        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 
       26.30        43.53        38.10        42.08        23.93        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       86.01        18.31        29.00         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       16.04        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6979 TCGA-55-7284 
       21.47        41.69        23.05        48.62         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       19.73        17.98        16.93        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       16.93        22.65        19.59        20.19        20.65        13.87 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       13.71         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 
       20.52        17.75        20.68        24.30         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 
       21.83        27.19        31.23         2.43        50.07         3.98 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4420 TCGA-05-4424 
        0.00        24.03        47.05        19.00        29.98        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       21.99        26.01        24.00         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         0.46         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       37.71        49.05         4.37        46.98        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       22.72        19.46         7.17        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.45        76.21        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.33        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
       20.52        71.47        60.16        47.41         8.22         9.27 
TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       14.27         8.45        15.12        48.46        60.72        57.53 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       42.35         3.91        25.55        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        36.99        36.79        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
       35.21        38.73        67.89        30.58        14.30         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       42.51        40.73        46.03         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       28.67        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
       25.41        18.64        34.19        17.65        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
       15.65        29.19        22.16        15.42        17.56        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.10        17.62         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
        3.25         0.92        15.81        19.99        17.95         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 
       56.71        67.96        72.30        13.61        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       56.81        39.09        81.80        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       20.05        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        4.64         6.64         6.12        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
        4.24        26.73        19.43        23.38        26.30        15.35 
TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24        50.33        11.18        66.64        77.85        43.82 
TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       49.84       108.66       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
       20.58        21.90        39.95       119.51        38.50        32.09 
TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        5.88       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        93.11        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.04        23.05        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       27.58        26.50        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7944 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 
       12.39        27.29        42.25        64.60        63.52         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       24.56        36.76        21.57        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 
       32.48        19.00        14.30        14.53         1.91        15.65 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       41.59        11.05        24.36        14.10        11.15        19.13 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82        20.28        59.11        16.87 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.62               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            129.53             238.29 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             22.92              21.57 
[1] "0.6 - 129.5 (22.9)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         0       17       19        0         9         9
  10Q GAIN WILD-TYPE       5      116      120        1        41        63
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10Q GAIN MUTATED           15          3        6
  10Q GAIN WILD-TYPE         57          8       19
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 17                116
  STAGE IB                 19                120
  STAGE II                  0                  1
  STAGE IIA                 9                 41
  STAGE IIB                 9                 63
  STAGE IIIA               15                 57
  STAGE IIIB                3                  8
  STAGE IV                  6                 19
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED    17  48  10   4
  10Q GAIN WILD-TYPE 154 230  36  15
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               17                154
  T2               48                230
  T3               10                 36
  T4                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  10Q GAIN MUTATED    51  10    17
  10Q GAIN WILD-TYPE 282  86    59
D20V5, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                  51                282
  N1                  10                 86
  N2+N3               17                 59
[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"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    56   6
  10Q GAIN WILD-TYPE 293  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     56    6
  10Q GAIN WILD-TYPE  293   19
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               56                293
  1                6                 19
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    30  49
  10Q GAIN WILD-TYPE 246 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     30   49
  10Q GAIN WILD-TYPE  246  191
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               30                246
  MALE                 49                191
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    65   9
  10Q GAIN WILD-TYPE 345  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     65    9
  10Q GAIN WILD-TYPE  345   51
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                65                345
  YES                9                 51
[1] 2 2
[1] FALSE
D20V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10Q GAIN MUTATED                            3
  10Q GAIN WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10Q GAIN MUTATED                                  19
  10Q GAIN WILD-TYPE                                88
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                   47
  10Q GAIN WILD-TYPE                                                274
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10Q GAIN MUTATED                                            0
  10Q GAIN WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  10Q GAIN MUTATED                                               3
  10Q GAIN WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  10Q GAIN MUTATED                                0
  10Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  10Q GAIN MUTATED                                    1
  10Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  10Q GAIN MUTATED                              0                             6
  10Q GAIN WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  10Q GAIN MUTATED                                 0
  10Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  10Q GAIN MUTATED                                               0
  10Q GAIN WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  10Q GAIN MUTATED                              0
  10Q GAIN WILD-TYPE                           10
D20V10, multiclass
                                                    clus
vv                                                   10Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               47
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   10Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  88
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                274
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                       10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
D20V12, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    54   2   0   5
  10Q GAIN WILD-TYPE 290  11   4  21
D20V13, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               54                290
  R1                2                 11
  R2                0                  4
  RX                5                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           5    57
  10Q GAIN WILD-TYPE                        47   333
D20V14, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  5
  BLACK OR AFRICAN AMERICAN                       5                 47
  WHITE                                          57                333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V15, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  52
  10Q GAIN WILD-TYPE   6 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   52
  10Q GAIN WILD-TYPE    6  332
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               52                332
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    53  40
  11P GAIN WILD-TYPE 270 141
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                93                411 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                40                141 
$`11P GAIN MUTATED`
TCGA-05-4402 TCGA-05-5420 TCGA-38-4629 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 
        8.02        15.02        28.41        18.31        29.00         9.37 
TCGA-50-6597 TCGA-55-1592 TCGA-55-6979 TCGA-55-8203 TCGA-55-8205 TCGA-55-A4DF 
       41.69        23.05         7.79        17.98        19.69        20.19 
TCGA-64-1677 TCGA-73-4662 TCGA-95-7043 TCGA-95-7562 TCGA-L9-A443 TCGA-MP-A4TA 
       20.65        82.68        16.54         2.86         6.35        31.23 
TCGA-MP-A4TC TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 TCGA-05-4432 
        2.43         2.99        14.96        29.98        21.99        25.02 
TCGA-05-5423 TCGA-05-5429 TCGA-38-4628 TCGA-44-2659 TCGA-44-6775 TCGA-44-6778 
        4.96         9.04        49.05        44.94        23.18        61.28 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7669 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       16.44        19.46        18.87        15.98        15.32         9.44 
TCGA-49-4488 TCGA-49-4512 TCGA-49-6743 TCGA-49-AAR3 TCGA-50-5933 TCGA-53-7813 
       28.57        29.75        53.29        62.24        78.67        13.94 
TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 TCGA-55-6981 
       38.73        14.30         5.62        46.03         3.88        45.34 
TCGA-55-7995 TCGA-55-8092 TCGA-55-8096 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 
       29.23         5.06        23.64        17.10        14.66        12.33 
TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8399 TCGA-62-8402 TCGA-62-A470 
       15.81        17.95         4.57        88.64        49.25        39.25 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-6215 
       38.37         2.04        28.41        20.05        20.05         5.72 
TCGA-69-7973 TCGA-69-7974 TCGA-71-6725 TCGA-75-6214 TCGA-78-7163 TCGA-78-7542 
        7.56         6.05         8.42        36.66       238.29        10.55 
TCGA-78-8655 TCGA-80-5608 TCGA-86-6851 TCGA-86-7955 TCGA-86-8278 TCGA-86-8280 
       77.59        93.11         5.88        35.24        31.04        23.05 
TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6840 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JO 
       13.64        41.36        12.23         7.36        17.46         1.08 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8177 TCGA-99-8033 TCGA-MN-A4N4 TCGA-MP-A4T6 
       25.48        18.54        16.41        21.57        38.63        58.85 
TCGA-MP-A4TJ TCGA-O1-A52J TCGA-S2-AA1A 
       11.15        59.11        16.87 

$`11P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       15.02        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 
       38.10        42.08        23.93        27.78        86.01        29.23 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       11.08        46.72        16.04        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 
       37.32        40.60        21.47        48.62         5.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       19.73        16.93        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 
       22.65        20.58        19.59        13.87        52.60        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
        8.48        50.24        10.55        85.32        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
        1.45         6.12        17.29        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80        10.09        21.83        27.19         5.29 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 
       24.03        47.05        19.00        12.00        30.02        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 
       25.02        24.00        29.00        22.03         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 
       44.61         4.37        46.98        44.42        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       25.02        37.15        38.24        38.89        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 
       23.15        21.63        32.45        22.72         7.17        36.07 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       23.64        12.66         8.55        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       76.21        28.11        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV 
        8.81        29.46        55.89        55.33        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ 
       73.12        28.90         8.55        40.41       123.58       221.33 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 
       30.54        35.21        67.89        30.58        80.52        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 
       40.73        15.25        53.65        69.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
       24.99        40.54       107.21        70.26        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 
       29.72        15.19        23.08        17.79        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       13.74        20.28        17.72        19.96        26.01        17.62 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG 
        1.58        20.71        21.40         3.25         0.92        19.99 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       39.98        42.38        14.60        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 
       54.35        67.96        72.30        13.61        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 
       56.81        39.09        81.80        37.02        87.98        42.90 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       51.25        28.47        18.84        14.04        12.66        14.73 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       26.73        19.43        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 
       30.31         9.24         1.25        50.33        11.18        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       77.85        43.82        85.15        49.84       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
        5.88        64.90        22.92         9.57       104.19        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
      232.18        39.75       110.50        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
       34.39        38.04        20.55        32.78        19.89        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.20        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       27.58         0.62        28.34        26.50        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       24.23        26.47        10.62         1.97        10.19         2.60 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
       27.68         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       22.45        23.61        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       61.48         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.53         1.91        18.58        15.65         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
       58.45        49.35        37.35        86.04         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.43        19.82        20.28 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.08               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            238.29             232.18 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             19.46              22.16 
[1] "1.1 - 238.3 (19.5)" "0.0 - 232.2 (22.2)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         0       24       24        0         7        12
  11P GAIN WILD-TYPE       5      109      115        1        43        60
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11P GAIN MUTATED           19          4        4
  11P GAIN WILD-TYPE         53          7       21
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 24                109
  STAGE IB                 24                115
  STAGE II                  0                  1
  STAGE IIA                 7                 43
  STAGE IIB                12                 60
  STAGE IIIA               19                 53
  STAGE IIIB                4                  7
  STAGE IV                  4                 21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED    32  51   5   5
  11P GAIN WILD-TYPE 139 227  41  14
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               32                139
  T2               51                227
  T3                5                 41
  T4                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  11P GAIN MUTATED    56  15    21
  11P GAIN WILD-TYPE 277  81    55
D21V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                  56                277
  N1                  15                 81
  N2+N3               21                 55
[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"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    60   4
  11P GAIN WILD-TYPE 289  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     60    4
  11P GAIN WILD-TYPE  289   21
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               60                289
  1                4                 21
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    58  36
  11P GAIN WILD-TYPE 218 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     58   36
  11P GAIN WILD-TYPE  218  204
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               58                218
  MALE                 36                204
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    79   7
  11P GAIN WILD-TYPE 331  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     79    7
  11P GAIN WILD-TYPE  331   53
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                79                331
  YES                7                 53
[1] 2 2
[1] FALSE
D21V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11P GAIN MUTATED                            2
  11P GAIN WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11P GAIN MUTATED                                  18
  11P GAIN WILD-TYPE                                89
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                   63
  11P GAIN WILD-TYPE                                                258
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11P GAIN MUTATED                                            2
  11P GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  11P GAIN MUTATED                                               3
  11P GAIN WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  11P GAIN MUTATED                                1
  11P GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  11P GAIN MUTATED                                    1
  11P GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  11P GAIN MUTATED                              0                             3
  11P GAIN WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  11P GAIN MUTATED                                 1
  11P GAIN WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  11P GAIN MUTATED                                               0
  11P GAIN WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  11P GAIN MUTATED                              0
  11P GAIN WILD-TYPE                           10
D21V10, multiclass
                                                    clus
vv                                                   11P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               63
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   11P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                258
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                       10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
D21V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    63   3   1   5
  11P GAIN WILD-TYPE 281  10   3  21
D21V13, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               63                281
  R1                3                 10
  R2                1                  3
  RX                5                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     1
  11P GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           9    70
  11P GAIN WILD-TYPE                        43   320
D21V14, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                       9                 43
  WHITE                                          70                320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  69
  11P GAIN WILD-TYPE   5 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   69
  11P GAIN WILD-TYPE    5  315
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               69                315
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    69  46
  11Q GAIN WILD-TYPE 254 135
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               115                389 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                46                135 
$`11Q GAIN MUTATED`
TCGA-05-4402 TCGA-38-4629 TCGA-44-2662 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 
        8.02        28.41        42.08        18.31        29.00         9.37 
TCGA-50-6597 TCGA-55-1592 TCGA-55-6979 TCGA-55-8203 TCGA-55-8205 TCGA-55-A4DF 
       41.69        23.05         7.79        17.98        19.69        20.19 
TCGA-64-1677 TCGA-73-4658 TCGA-91-A4BC TCGA-95-7043 TCGA-95-7562 TCGA-L9-A443 
       20.65        52.60         1.45        16.54         2.86         6.35 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4415 TCGA-05-4420 TCGA-05-4425 TCGA-05-4432 
       31.23         2.43         2.99        29.98        21.99        25.02 
TCGA-05-5423 TCGA-05-5429 TCGA-38-4628 TCGA-44-2656 TCGA-44-2659 TCGA-44-5645 
        4.96         9.04        49.05        46.98        44.94        28.01 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 
       21.63        23.18        61.28        16.44        19.46         7.17 
TCGA-44-7669 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4512 
       18.87        12.66        15.98        15.32         9.44        29.75 
TCGA-49-6743 TCGA-49-AAR3 TCGA-49-AARO TCGA-50-5933 TCGA-50-6593 TCGA-53-7624 
       53.29        62.24       123.58        78.67        11.05        34.29 
TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 
       13.94        38.73        67.89        14.30         5.62        46.03 
TCGA-55-6975 TCGA-55-6981 TCGA-55-7910 TCGA-55-7994 TCGA-55-8092 TCGA-55-8096 
        3.88        45.34        34.19        19.82         5.06        23.64 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 
        0.36        13.74        17.72        17.10         1.58        12.33 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8399 TCGA-62-8402 
       15.81        19.99        17.95         4.57        88.64        49.25 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-6215 
       38.37         2.04        28.41        20.05        20.05         5.72 
TCGA-69-7973 TCGA-69-7974 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 
        7.56         6.05        19.43         8.42        26.30        15.35 
TCGA-73-4676 TCGA-75-5125 TCGA-78-7154 TCGA-78-7155 TCGA-78-7163 TCGA-78-7535 
        9.24        66.64        19.50        38.50       238.29        31.20 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7955 TCGA-86-8278 
       77.59       110.50        93.11         5.88        35.24        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6840 
       31.20        23.05        14.60        13.64        41.36        12.23 
TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JO TCGA-97-7553 TCGA-97-7937 TCGA-97-8177 
        7.36        17.46         1.08        61.48        18.54        16.41 
TCGA-97-A4M1 TCGA-99-8033 TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MP-A4T6 TCGA-O1-A52J 
       19.76        21.57         1.91        38.63        58.85        59.11 
TCGA-S2-AA1A 
       16.87 

$`11Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        35.28        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 
       43.53        38.10        23.93        27.78        86.01        29.23 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       11.08        46.72        16.04        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 
       37.32        40.60        21.47        48.62         5.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       19.73        16.93        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 
       22.65        20.58        19.59        13.87        82.68        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
        8.48        50.24        10.55        85.32        13.71        16.18 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
        6.12        17.29        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TD 
       23.80        10.09        21.83        27.19         5.29        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 
       47.05        19.00        14.96        12.00        30.02        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 
       25.02        24.00        29.00        22.03         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.61         4.37        44.42        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6777 
       33.30        28.37        23.77        19.56        23.15        32.45 
TCGA-44-7659 TCGA-44-7667 TCGA-44-7672 TCGA-44-8120 TCGA-44-A47G TCGA-44-A4SS 
       22.72        36.07        23.64         8.55        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 
       14.07        32.84         8.81        29.46        55.89        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        22.26        73.12        28.90         8.55        40.41 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      221.33       164.12         9.86        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       14.27         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       53.16        42.35         3.91        25.55        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        0.72        10.13        36.99        36.79        27.25        30.54 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       35.21        30.58        80.52        42.51        40.73        15.25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       53.65        69.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       22.03         3.91        23.15        25.41        18.64        11.28 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        18.44        29.23        29.72        15.19        23.08 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.79        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       15.72        14.47        20.28        19.96        26.01        17.62 
TCGA-55-8615 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-62-8395 
       14.66        20.71        21.40         3.25         0.92        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       42.38        14.60        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 
       56.81        39.09        81.80        37.02        87.98        42.90 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       51.25        28.47        18.84        14.04        12.66        14.73 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-8453 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 
       26.73        23.38         4.31        30.31         1.25        50.33 
TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       11.18        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
       20.58       129.53        21.90        39.95       119.51        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
        5.88        64.90        22.92         9.57       104.19        88.14 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
      232.18        39.75        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       38.04        20.55        32.78        19.89        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8358 
        4.57        24.33         0.79        22.82        32.65        21.47 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       11.61        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 
       26.50        29.46         3.81        24.23        26.47        10.62 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 
        1.97        10.19         2.60        27.68         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP 
       14.27         1.18        19.82        22.45        23.61        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 
       42.25        64.60        63.52        25.48         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 
       18.67         5.39        18.12        15.39        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       20.58        21.44        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.63        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 
       19.00        14.30        14.53        18.58        15.65         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        86.04         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       47.08         0.49         0.43        19.82        20.28 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.36               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            238.29             232.18 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             19.76              22.26 
[1] "0.4 - 238.3 (19.8)" "0.0 - 232.2 (22.3)"
[1] "hr=" "1.2"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         0       26       33        0        11        18
  11Q GAIN WILD-TYPE       5      107      106        1        39        54
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11Q GAIN MUTATED           19          4        7
  11Q GAIN WILD-TYPE         53          7       18
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 26                107
  STAGE IB                 33                106
  STAGE II                  0                  1
  STAGE IIA                11                 39
  STAGE IIB                18                 54
  STAGE IIIA               19                 53
  STAGE IIIB                4                  7
  STAGE IV                  7                 18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED    37  65  10   5
  11Q GAIN WILD-TYPE 134 213  36  14
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               37                134
  T2               65                213
  T3               10                 36
  T4                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  11Q GAIN MUTATED    73  20    22
  11Q GAIN WILD-TYPE 260  76    54
D22V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                  73                260
  N1                  20                 76
  N2+N3               22                 54
[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"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    73   7
  11Q GAIN WILD-TYPE 276  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     73    7
  11Q GAIN WILD-TYPE  276   18
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               73                276
  1                7                 18
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    70  48
  11Q GAIN WILD-TYPE 206 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     70   48
  11Q GAIN WILD-TYPE  206  192
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               70                206
  MALE                 48                192
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    92  13
  11Q GAIN WILD-TYPE 318  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     92   13
  11Q GAIN WILD-TYPE  318   47
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                92                318
  YES               13                 47
[1] 2 2
[1] FALSE
D22V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11Q GAIN MUTATED                            1
  11Q GAIN WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11Q GAIN MUTATED                                  21
  11Q GAIN WILD-TYPE                                86
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                   84
  11Q GAIN WILD-TYPE                                                237
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11Q GAIN MUTATED                                            2
  11Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  11Q GAIN MUTATED                                               4
  11Q GAIN WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  11Q GAIN MUTATED                                1
  11Q GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  11Q GAIN MUTATED                                    2
  11Q GAIN WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  11Q GAIN MUTATED                              0                             3
  11Q GAIN WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  11Q GAIN MUTATED                                 0
  11Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  11Q GAIN MUTATED                                               0
  11Q GAIN WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  11Q GAIN MUTATED                              0
  11Q GAIN WILD-TYPE                           10
D22V10, multiclass
                                                    clus
vv                                                   11Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               84
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   11Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                237
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                       10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
D22V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    76   4   1   6
  11Q GAIN WILD-TYPE 268   9   3  20
D22V13, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               76                268
  R1                4                  9
  R2                1                  3
  RX                6                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  1     2
  11Q GAIN WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                          14    87
  11Q GAIN WILD-TYPE                        38   303
D22V14, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  5
  BLACK OR AFRICAN AMERICAN                      14                 38
  WHITE                                          87                303
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V15, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3  90
  11Q GAIN WILD-TYPE   4 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   90
  11Q GAIN WILD-TYPE    4  294
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               90                294
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    81  54
  12P GAIN WILD-TYPE 242 127
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               135                369 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                54                127 
$`12P GAIN MUTATED`
TCGA-05-4402 TCGA-05-4418 TCGA-05-5420 TCGA-44-7670 TCGA-44-8119 TCGA-49-6742 
        8.02         9.01        15.02        29.00         9.37        16.04 
TCGA-49-AAR0 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7726 
      156.66        41.69        48.62         5.79         7.99        21.44 
TCGA-55-A4DF TCGA-91-6836 TCGA-93-8067 TCGA-97-A4M7 TCGA-L9-A443 TCGA-MN-A4N1 
       20.19        13.71         6.12        20.68         6.35        27.19 
TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 TCGA-05-4417 
       10.09        45.01        37.02         0.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4432 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 TCGA-38-4632 
       29.98        25.02        22.03         7.40         8.68        44.61 
TCGA-44-2668 TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-7660 TCGA-44-7667 
       25.02        34.06        33.30        28.37        19.46        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-A47A TCGA-49-4510 TCGA-49-6767 TCGA-49-AAR9 
       18.87        23.64        15.32        29.46        22.26         8.55 
TCGA-49-AARO TCGA-50-5045 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 
      123.58        71.47         8.22        14.27        48.46        57.53 
TCGA-50-6592 TCGA-50-6673 TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 TCGA-55-6971 
       25.55         0.72        38.73        67.89         5.62        46.03 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6985 TCGA-55-6987 TCGA-55-7576 TCGA-55-7728 
       69.34        45.34        40.54        70.26        22.03        23.15 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 
       11.28        34.19        17.65        29.23        23.08        17.79 
TCGA-55-8096 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       23.64        22.16        15.72        14.47        13.74        20.28 
TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8398 TCGA-62-8402 
       14.66         3.25         0.92        15.81        14.60        49.25 
TCGA-62-A46O TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 
       47.80        13.61        39.25        40.96        39.09        38.37 
TCGA-64-5775 TCGA-67-3774 TCGA-69-7973 TCGA-69-7980 TCGA-69-A59K TCGA-73-4666 
        2.04        12.66         7.56        13.51        19.43        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-75-5125 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 
        4.31        30.31        66.64       100.57        27.16         5.69 
TCGA-78-7148 TCGA-78-7154 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 TCGA-78-8655 
       20.58        19.50        64.90        88.14        26.53        77.59 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8278 
       12.36         5.88        38.04        32.78        19.89        31.04 
TCGA-86-8280 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
       23.05        11.61        30.84         3.81        10.62        41.36 
TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 
       12.23         7.36         1.18        18.67        12.39         2.76 
TCGA-95-A4VP TCGA-97-8176 TCGA-97-8552 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A5IP 
       19.89        15.39        20.58         1.45        21.57         1.91 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE 
       38.63        86.14        49.35        58.85         5.49        29.46 
TCGA-MP-A4TI TCGA-NJ-A55R TCGA-S2-AA1A 
       14.10        19.82        16.87 

$`12P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96        20.05        26.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       28.41        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN 
       29.23        11.08        46.72        17.16        11.64        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-6979 TCGA-55-7573 TCGA-55-7724 
       40.60        21.47        23.05         7.79        16.01        23.18 
TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       14.53         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       20.58        19.59        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-7771 
       39.09         8.48        50.24        10.55        85.32        16.18 
TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        1.45        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA 
       24.30        23.80        10.09        21.83         5.29        31.23 
TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
        2.43        50.07         3.98        24.03        47.05        19.00 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 
       12.00        30.02        21.99        26.01        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
        4.96        29.00         9.04         2.04         0.46         5.98 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F TCGA-44-2656 
       97.74       120.79        37.71        49.05         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       44.42        44.94        42.77         3.19        37.15        38.24 
TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       38.89        33.73        26.56        28.01        23.77        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7662 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       22.72         7.17        12.66         8.55        15.98         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 
       12.66        35.54        14.07        32.84         8.81        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       55.89        53.29        55.33        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       28.90        40.41       221.33       164.12         9.86        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
      101.72        15.72        60.16        47.41        49.28         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
       78.67         8.45        15.12        60.72        53.16        42.35 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 
        3.91        11.05        12.16         6.21        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       30.58        14.30        80.52        42.51        40.73        15.25 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
       53.65         3.88        32.71        92.81        24.99       107.21 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7815 
       28.67        20.02        27.09        32.71         3.91        25.41 
TCGA-55-7903 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 
       18.64        18.44        19.82        29.72        15.19         5.06 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 
       15.65        29.19        15.42        17.56         0.36        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 
       19.96        26.01        17.10        17.62         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       20.71        21.40        19.99        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       42.38        88.64        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
       72.30        29.92        56.81        81.80        37.02        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       42.90        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         5.42         6.05         4.41 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 
       13.41        14.01        13.45         4.24        26.73         8.42 
TCGA-73-4659 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS 
       23.38        15.35         9.24         1.25        50.33        11.18 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-78-7143 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
      163.10        19.27       129.53        21.90        39.95       119.51 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
      238.29        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
       10.55       232.18        39.75       110.50        93.11        27.09 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       31.13        34.39        20.55        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
        4.57        24.33         0.79        22.82        32.65        31.20 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       21.47        14.60        13.91        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 
       26.50        29.46        24.23        13.64        26.47         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       10.19         2.60        27.68         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       41.82        27.29        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 
       18.12        16.41        14.30        21.60        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R 
       20.84        18.67        24.56        34.85        36.76        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
       18.08        35.47        32.48        19.00        14.30        14.53 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
       18.58        15.65         2.76        58.45        37.35        86.04 
TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       41.59        11.05        24.36        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
        0.43        20.28        59.11 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.00               0.13 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            156.66             238.29 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             20.58              21.90 
[1] "0.0 - 156.7 (20.6)" "0.1 - 238.3 (21.9)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         3       32       30        0        19        15
  12P GAIN WILD-TYPE       2      101      109        1        31        57
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12P GAIN MUTATED           25          2       10
  12P GAIN WILD-TYPE         47          9       15
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 32                101
  STAGE IB                 30                109
  STAGE II                  0                  1
  STAGE IIA                19                 31
  STAGE IIB                15                 57
  STAGE IIIA               25                 47
  STAGE IIIB                2                  9
  STAGE IV                 10                 15
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED    43  77  13   4
  12P GAIN WILD-TYPE 128 201  33  15
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               43                128
  T2               77                201
  T3               13                 33
  T4                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  12P GAIN MUTATED    84  26    25
  12P GAIN WILD-TYPE 249  70    51
D23V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                  84                249
  N1                  26                 70
  N2+N3               25                 51
[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"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    91  10
  12P GAIN WILD-TYPE 258  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     91   10
  12P GAIN WILD-TYPE  258   15
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               91                258
  1               10                 15
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    67  71
  12P GAIN WILD-TYPE 209 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     67   71
  12P GAIN WILD-TYPE  209  169
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               67                209
  MALE                 71                169
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   112  15
  12P GAIN WILD-TYPE 298  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    112   15
  12P GAIN WILD-TYPE  298   45
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO               112                298
  YES               15                 45
[1] 2 2
[1] FALSE
D23V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12P GAIN MUTATED                            4
  12P GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12P GAIN MUTATED                                  23
  12P GAIN WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                   96
  12P GAIN WILD-TYPE                                                225
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12P GAIN MUTATED                                            1
  12P GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12P GAIN MUTATED                                               6
  12P GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  12P GAIN MUTATED                                1
  12P GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  12P GAIN MUTATED                                    0
  12P GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  12P GAIN MUTATED                              0                             3
  12P GAIN WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  12P GAIN MUTATED                                 0
  12P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  12P GAIN MUTATED                                               1
  12P GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12P GAIN MUTATED                              3
  12P GAIN WILD-TYPE                            7
D23V10, multiclass
                                                    clus
vv                                                   12P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               96
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   12P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                225
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
D23V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    99   3   2   6
  12P GAIN WILD-TYPE 245  10   2  20
D23V13, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               99                245
  R1                3                 10
  R2                2                  2
  RX                6                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     3
  12P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          15   101
  12P GAIN WILD-TYPE                        37   289
D23V14, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                      15                 37
  WHITE                                         101                289
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1 100
  12P GAIN WILD-TYPE   6 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1  100
  12P GAIN WILD-TYPE    6  284
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              100                284
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    80  49
  12Q GAIN WILD-TYPE 243 132
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               129                375 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                49                132 
$`12Q GAIN MUTATED`
TCGA-05-4402 TCGA-05-4418 TCGA-05-5420 TCGA-44-7670 TCGA-44-8119 TCGA-49-6742 
        8.02         9.01        15.02        29.00         9.37        16.04 
TCGA-49-AAR0 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7726 TCGA-55-A491 
      156.66        48.62         5.79         7.99        21.44        20.58 
TCGA-55-A4DF TCGA-91-6836 TCGA-93-8067 TCGA-97-A4M7 TCGA-L9-A443 TCGA-MP-A4TD 
       20.19        13.71         6.12        20.68         6.35        10.09 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       45.01        37.02         0.00         2.99        14.96        29.98 
TCGA-05-4432 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 TCGA-38-4632 TCGA-44-2656 
       25.02        29.00         7.40         8.68        44.61        46.98 
TCGA-44-2668 TCGA-44-3918 TCGA-44-5644 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 
       25.02        34.06        28.37        61.28        19.46        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4510 
       18.87        23.64        15.98        15.32         9.44        29.46 
TCGA-49-6767 TCGA-49-AAR9 TCGA-50-5045 TCGA-50-5051 TCGA-50-5072 TCGA-50-5931 
       22.26         8.55        71.47        15.72         8.22        14.27 
TCGA-50-5941 TCGA-50-5944 TCGA-50-6592 TCGA-50-6673 TCGA-53-7813 TCGA-55-1594 
       48.46        57.53        25.55         0.72        13.94        38.73 
TCGA-55-1596 TCGA-55-6712 TCGA-55-6971 TCGA-55-6981 TCGA-55-6987 TCGA-55-7728 
       67.89         5.62        46.03        45.34        70.26        23.15 
TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-8089 TCGA-55-8208 TCGA-55-8302 
       25.41        34.19        17.65        23.08        22.16        15.72 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 
       14.47        13.74        20.28        14.66         3.25         0.92 
TCGA-55-A494 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V TCGA-62-A470 
       15.81        14.60        49.25        47.80        72.30        39.25 
TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 TCGA-64-5779 TCGA-67-3774 TCGA-69-7973 
       40.96        39.09        38.37        28.41        12.66         7.56 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
       13.51         4.24        19.43        26.30         4.31        30.31 
TCGA-75-5125 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7167 
       66.64       100.57        27.16         5.69        20.58        88.14 
TCGA-78-7220 TCGA-78-8655 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 
       26.53        77.59        12.36         5.88        31.13        38.04 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 
       32.78        19.89        31.04        23.05        21.47        11.61 
TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6840 TCGA-95-7567 TCGA-95-7944 
       30.84         3.81        10.62        12.23        18.67        12.39 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-8176 TCGA-97-8552 TCGA-99-8032 TCGA-99-8033 
        2.76        19.89        15.39        20.58         1.45        21.57 
TCGA-L9-A5IP TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE 
        1.91        86.14        49.35        58.85         5.49        29.46 
TCGA-MP-A4TI TCGA-NJ-A4YI TCGA-NJ-A55R 
       14.10         0.13        19.82 

$`12Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96        20.05        26.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       28.41        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN 
       29.23        11.08        46.72        17.16        11.64        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6979 TCGA-55-7573 
       40.60        21.47        41.69        23.05         7.79        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       23.18        14.53         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       22.65        19.59        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-7771 
       39.09         8.48        50.24        10.55        85.32        16.18 
TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        1.45        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80        10.09        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 TCGA-05-4397 TCGA-05-4398 
       31.23         2.43        50.07         3.98        24.03        47.05 
TCGA-05-4403 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       19.00        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       24.00         4.96        22.03         9.04         2.04         0.46 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F 
        5.98        97.74       120.79        37.71        49.05         4.37 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       44.42        44.94        42.77         3.19        37.15        38.24 
TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
       38.89        33.73        26.56        33.30        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       19.56        23.15        21.63        23.18        32.45        16.44 
TCGA-44-7659 TCGA-44-7662 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47G TCGA-44-A4SS 
       22.72         7.17        12.66         8.55        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       14.07        32.84         8.81        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE 
       55.33        22.26        73.12        62.24        28.90        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5049 
      123.58       221.33       164.12         9.86        20.52       101.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 
       60.16        47.41        49.28         9.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 
       15.12        60.72        53.16        42.35         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       34.29        30.54        35.21        30.58        14.30        80.52 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       42.51        40.73        15.25        53.65         3.88        69.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 
       32.71        92.81        24.99        40.54       107.21        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 
       20.02        27.09        32.71        22.03         3.91        18.64 
TCGA-55-7907 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       11.28        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 
        5.06        17.79        23.64        15.65        29.19        15.42 
TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       17.56         0.36        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A4DG 
       17.62         1.58        12.33        20.71        21.40        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46P 
       17.95         4.57        39.98        42.38        88.64        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 
       56.71        54.35        67.96        13.61        29.92        56.81 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
       81.80        37.02        87.98         2.04        42.90        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       28.47        20.05        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        5.42         6.05         4.41        13.41        14.01        13.45 
TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 
       26.73         8.42        23.38        15.35         9.24         1.25 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        11.18        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
       36.66       108.66       163.10        19.27       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 
       64.90        22.92         9.57       104.19       238.29        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-7711 TCGA-86-7714 
       39.75       110.50        93.11        27.09        34.39        20.55 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 
       22.82        32.65        31.20        14.60        13.91        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 
       26.47        41.36         1.97        10.19         2.60        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       27.29        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       16.41        14.30        21.60        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AD 
       18.67        24.56        34.85        36.76        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV 
       35.47        32.48        19.00        14.30        14.53        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
       15.65        38.63         2.76        58.45        37.35        86.04 
TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       41.59        11.05        24.36        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        74.33         1.64        47.08         0.49         0.43 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.00               0.36 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            156.66             238.29 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             20.58              22.03 
[1] "0.0 - 156.7 (20.6)" "0.4 - 238.3 (22.0)"
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         3       28       32        0        16        16
  12Q GAIN WILD-TYPE       2      105      107        1        34        56
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12Q GAIN MUTATED           23          3       10
  12Q GAIN WILD-TYPE         49          8       15
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 28                105
  STAGE IB                 32                107
  STAGE II                  0                  1
  STAGE IIA                16                 34
  STAGE IIB                16                 56
  STAGE IIIA               23                 49
  STAGE IIIB                3                  8
  STAGE IV                 10                 15
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED    38  78  12   4
  12Q GAIN WILD-TYPE 133 200  34  15
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               38                133
  T2               78                200
  T3               12                 34
  T4                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  12Q GAIN MUTATED    83  24    24
  12Q GAIN WILD-TYPE 250  72    52
D24V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                  83                250
  N1                  24                 72
  N2+N3               24                 52
[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"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    89  10
  12Q GAIN WILD-TYPE 260  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     89   10
  12Q GAIN WILD-TYPE  260   15
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               89                260
  1               10                 15
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    65  68
  12Q GAIN WILD-TYPE 211 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     65   68
  12Q GAIN WILD-TYPE  211  172
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               65                211
  MALE                 68                172
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   110  13
  12Q GAIN WILD-TYPE 300  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    110   13
  12Q GAIN WILD-TYPE  300   47
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO               110                300
  YES               13                 47
[1] 2 2
[1] FALSE
D24V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12Q GAIN MUTATED                            5
  12Q GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12Q GAIN MUTATED                                  22
  12Q GAIN WILD-TYPE                                85
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                   92
  12Q GAIN WILD-TYPE                                                229
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12Q GAIN MUTATED                                            0
  12Q GAIN WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12Q GAIN MUTATED                                               5
  12Q GAIN WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  12Q GAIN MUTATED                                1
  12Q GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  12Q GAIN MUTATED                                    0
  12Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  12Q GAIN MUTATED                              0                             3
  12Q GAIN WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  12Q GAIN MUTATED                                 0
  12Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  12Q GAIN MUTATED                                               2
  12Q GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12Q GAIN MUTATED                              3
  12Q GAIN WILD-TYPE                            7
D24V10, multiclass
                                                    clus
vv                                                   12Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               92
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   12Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                229
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
D24V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    93   3   2   6
  12Q GAIN WILD-TYPE 251  10   2  20
D24V13, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               93                251
  R1                3                 10
  R2                2                  2
  RX                6                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     3
  12Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          12    97
  12Q GAIN WILD-TYPE                        40   293
D24V14, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                      12                 40
  WHITE                                          97                293
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  94
  12Q GAIN WILD-TYPE   5 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   94
  12Q GAIN WILD-TYPE    5  290
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               94                290
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    23  20
  13Q GAIN WILD-TYPE 300 161
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                43                461 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                20                161 
$`13Q GAIN MUTATED`
TCGA-05-4382 TCGA-38-4631 TCGA-44-2655 TCGA-44-7671 TCGA-49-6742 TCGA-55-7726 
       19.96        11.64        43.53        29.23        16.04        21.44 
TCGA-55-8205 TCGA-55-A492 TCGA-05-4249 TCGA-05-5428 TCGA-44-2659 TCGA-44-7660 
       19.69        19.59        50.07        22.03        44.94        19.46 
TCGA-50-6673 TCGA-53-7624 TCGA-53-7626 TCGA-55-6968 TCGA-55-7281 TCGA-55-7907 
        0.72        34.29        30.54        42.51        28.67        11.28 
TCGA-55-7910 TCGA-55-8089 TCGA-55-8620 TCGA-62-8402 TCGA-64-1678 TCGA-64-1680 
       34.19        23.08        12.33        49.25        39.09        37.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-69-8253 TCGA-73-4677 TCGA-75-6214 
       20.05        18.84         5.72        14.01         1.25        36.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7149 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 
      100.57       163.10       129.53        88.14        26.53        53.33 
TCGA-86-6562 TCGA-86-8074 TCGA-86-8672 TCGA-97-7547 TCGA-MP-A4SW TCGA-MP-A4T7 
       12.36         0.79         0.62        64.60        58.45         5.49 
TCGA-NJ-A4YG 
       74.33 

$`13Q GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        35.28        14.73        26.30 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 
       29.00         9.37        11.08        46.72        17.16        11.64 
TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
      156.66        37.32        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       14.53         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 
       20.19        20.65        13.87        52.60        82.68        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
        8.48        50.24        10.55        85.32        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
        1.45         6.12        17.29        16.54         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.65        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       17.75        20.68        24.30        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       21.83        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
        3.98        45.01        37.02         0.00        24.03        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
       29.00         9.04         2.04         0.46         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        4.37        46.98        44.42        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.33        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 
        3.91        25.55        11.05        12.16         6.21        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       36.99        36.79        27.25        13.94        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       67.89        30.58        14.30        80.52         5.62        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       25.41        18.64        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z 
       17.10        17.62        14.66         1.58        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
        3.25         0.92        15.81        19.99        17.95         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        14.60        88.64        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        56.81        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       14.04        12.66        14.73         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K 
       13.41        13.51        13.45         4.24        26.73        19.43 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        8.42        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24        50.33        11.18        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       85.15        49.84       108.66        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       20.58        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
      238.29        31.20         8.02        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       14.60        11.61        13.91        30.84        27.58        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       26.50        29.46         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       42.25        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        18.58        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 
       86.14        49.35        37.35        86.04        58.85        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       29.46        11.05        24.36        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82        20.28        59.11        16.87 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.62               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            163.10             238.29 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             26.53              21.47 
[1] "0.6 - 163.1 (26.5)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         1        6       12        0         9         3
  13Q GAIN WILD-TYPE       4      127      127        1        41        69
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  13Q GAIN MUTATED            3          1        6
  13Q GAIN WILD-TYPE         69         10       19
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  6                127
  STAGE IB                 12                127
  STAGE II                  0                  1
  STAGE IIA                 9                 41
  STAGE IIB                 3                 69
  STAGE IIIA                3                 69
  STAGE IIIB                1                 10
  STAGE IV                  6                 19
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED    14  27   1   1
  13Q GAIN WILD-TYPE 157 251  45  18
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               14                157
  T2               27                251
  T3                1                 45
  T4                1                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  13Q GAIN MUTATED    29  10     4
  13Q GAIN WILD-TYPE 304  86    72
D25V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                  29                304
  N1                  10                 86
  N2+N3                4                 72
[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"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    31   6
  13Q GAIN WILD-TYPE 318  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     31    6
  13Q GAIN WILD-TYPE  318   19
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               31                318
  1                6                 19
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    23  20
  13Q GAIN WILD-TYPE 253 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     23   20
  13Q GAIN WILD-TYPE  253  220
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               23                253
  MALE                 20                220
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    33   7
  13Q GAIN WILD-TYPE 377  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     33    7
  13Q GAIN WILD-TYPE  377   53
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                33                377
  YES                7                 53
[1] 2 2
[1] FALSE
D25V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  13Q GAIN MUTATED                            0
  13Q GAIN WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  13Q GAIN MUTATED                                   9
  13Q GAIN WILD-TYPE                                98
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                   30
  13Q GAIN WILD-TYPE                                                291
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  13Q GAIN MUTATED                                            0
  13Q GAIN WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  13Q GAIN MUTATED                                               1
  13Q GAIN WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  13Q GAIN MUTATED                                0
  13Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  13Q GAIN MUTATED                                    0
  13Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  13Q GAIN MUTATED                              0                             2
  13Q GAIN WILD-TYPE                            2                            21
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  13Q GAIN MUTATED                                 0
  13Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  13Q GAIN MUTATED                                               0
  13Q GAIN WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  13Q GAIN MUTATED                              1
  13Q GAIN WILD-TYPE                            9
D25V10, multiclass
                                                    clus
vv                                                   13Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               30
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   13Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                291
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      21
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
D25V12, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    36   0   0   0
  13Q GAIN WILD-TYPE 308  13   4  26
D25V13, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               36                308
  R1                0                 13
  R2                0                  4
  RX                0                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           4    32
  13Q GAIN WILD-TYPE                        48   358
D25V14, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       4                 48
  WHITE                                          32                358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V15, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  27
  13Q GAIN WILD-TYPE   6 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   27
  13Q GAIN WILD-TYPE    6  357
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               27                357
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    82  45
  14Q GAIN WILD-TYPE 241 136
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               127                377 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                45                136 
$`14Q GAIN MUTATED`
TCGA-05-4402 TCGA-38-4629 TCGA-44-6147 TCGA-44-8119 TCGA-55-7724 TCGA-55-8091 
        8.02        28.41        27.78         9.37        23.18        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-64-1677 TCGA-73-4658 TCGA-80-5611 TCGA-91-6836 
       17.98        16.93        20.65        52.60        85.32        13.71 
TCGA-93-8067 TCGA-95-7562 TCGA-97-A4LX TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 
        6.12         2.86        20.19        24.30         6.35        10.09 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4424 TCGA-35-4123 
       45.01        37.02         2.99        14.96        30.02         5.98 
TCGA-35-5375 TCGA-38-4627 TCGA-44-2659 TCGA-44-2668 TCGA-44-3917 TCGA-44-6778 
        8.68        37.71        44.94        25.02        38.89        61.28 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-A479 TCGA-44-A47A 
       16.44        19.46         7.17        36.07        15.98        15.32 
TCGA-44-A47B TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4512 
        9.44        13.45        76.21        28.57        12.66        29.75 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V 
       22.26        22.26        28.90       123.58       221.33         9.86 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 TCGA-50-7109 
       48.46        53.16        42.35         3.91        12.16        10.13 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6970 TCGA-55-6971 
       35.21        30.58        14.30         5.62        15.25        46.03 
TCGA-55-6975 TCGA-55-6983 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 
        3.88        92.81        25.41        11.28        34.19        29.23 
TCGA-55-8085 TCGA-55-8096 TCGA-55-8206 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
       29.72        23.64        29.19        15.72         0.36        13.74 
TCGA-55-8510 TCGA-55-8614 TCGA-55-A490 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       17.72        17.62         3.25        19.99        17.95         4.57 
TCGA-64-5774 TCGA-64-5775 TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 TCGA-69-7973 
       87.98         2.04        20.05        20.05        22.68         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4677 
        6.05        13.41         8.42        23.38        26.30         1.25 
TCGA-73-7499 TCGA-75-6212 TCGA-75-7025 TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 
       50.33        49.84       108.66        27.16        20.58       129.53 
TCGA-78-7159 TCGA-78-7161 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7955 
       64.90         9.57        93.11        27.09        12.36        35.24 
TCGA-86-8074 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-91-6828 
        0.79        31.04        23.05        21.47        11.61        10.62 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        2.60        12.23        27.68        16.60        14.27         1.18 
TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7567 TCGA-95-A4VP TCGA-97-7546 TCGA-97-8179 
       23.61        19.00        18.67        19.89        42.25        14.30 
TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-NJ-A55R 
       49.35        58.85        41.59        29.46        11.05        19.82 
TCGA-O1-A52J 
       59.11 

$`14Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        35.28        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 
       43.53        38.10        42.08        23.93        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.00        29.23        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       11.64       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8205 TCGA-55-8207 
       14.53        21.44         6.15        19.66        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       18.15        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       20.19        13.87        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 
       10.55        16.18         1.45        17.29        16.54        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 
       15.65        21.40        18.18        17.92        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       20.68        23.80        21.83        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4395 TCGA-05-4397 
        2.43        10.09        50.07         3.98         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       47.05        19.00        29.98        12.00        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         0.46         7.40        97.74       120.79 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         4.37        46.98        44.42        42.77 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
        3.19        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7669 TCGA-44-7672 
       21.63        23.18        32.45        22.72        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47G TCGA-44-A4SS TCGA-49-4487 TCGA-49-4494 
       12.66         8.55        11.54        13.64        28.11        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 
       14.07        32.84         8.81        29.46        55.89        53.29 
TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARR 
       55.33        73.12        62.24         8.55        40.41       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       15.12        60.72        57.53        25.55        11.05         6.21 
TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        0.72        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 
       13.94        38.73        67.89        80.52        42.51        40.73 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 
       53.65        69.34        45.34        32.71        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 
       22.03         3.91        23.15        18.64        17.65        18.44 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
       19.82        15.19        23.08         5.06        17.79        15.65 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 
       22.16        15.42        17.56        14.47        20.28        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       26.01        17.10        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       21.40         0.92        15.81        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 
       56.81        39.09        81.80        37.02        38.37        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       28.41        51.25        28.47        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
       14.73         5.72         4.64         6.64         6.12        13.61 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        5.42         4.41        13.51        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       26.73        19.43        15.35         4.31        30.31         9.24 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 
       11.18        66.64        77.85        43.82        85.15        36.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 
      100.57       163.10         5.69        19.27        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
      119.51        19.50        38.50        32.09         5.88        22.92 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       77.59       110.50         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        32.78        19.89        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 
       24.33        22.82        32.65        31.20        14.60        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
        3.81        24.23        13.64        26.47        41.36         1.97 
TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       10.19         7.36         1.15        19.82        22.45        17.46 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7547 
        1.08        41.82        12.39        27.29         2.76        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       18.67         5.39        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       34.85        36.76         1.45        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       35.47        32.48        19.00        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       18.58        15.65        38.63         2.76        86.14        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       37.35        86.04         5.49        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-S2-AA1A 
       47.08         0.49         0.43        20.28        16.87 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.36               0.00 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            221.33             238.29 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             20.05              21.99 
[1] "0.4 - 221.3 (20.1)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         1       36       36        1        13        16
  14Q GAIN WILD-TYPE       4       97      103        0        37        56
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  14Q GAIN MUTATED           15          3        6
  14Q GAIN WILD-TYPE         57          8       19
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 36                 97
  STAGE IB                 36                103
  STAGE II                  1                  0
  STAGE IIA                13                 37
  STAGE IIB                16                 56
  STAGE IIIA               15                 57
  STAGE IIIB                3                  8
  STAGE IV                  6                 19
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED    43  71   9   5
  14Q GAIN WILD-TYPE 128 207  37  14
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               43                128
  T2               71                207
  T3                9                 37
  T4                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  14Q GAIN MUTATED    88  20    16
  14Q GAIN WILD-TYPE 245  76    60
D26V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                  88                245
  N1                  20                 76
  N2+N3               16                 60
[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"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    72   6
  14Q GAIN WILD-TYPE 277  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     72    6
  14Q GAIN WILD-TYPE  277   19
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               72                277
  1                6                 19
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    74  55
  14Q GAIN WILD-TYPE 202 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     74   55
  14Q GAIN WILD-TYPE  202  185
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               74                202
  MALE                 55                185
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED   109  13
  14Q GAIN WILD-TYPE 301  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    109   13
  14Q GAIN WILD-TYPE  301   47
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO               109                301
  YES               13                 47
[1] 2 2
[1] FALSE
D26V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  14Q GAIN MUTATED                            6
  14Q GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  14Q GAIN MUTATED                                  22
  14Q GAIN WILD-TYPE                                85
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                   89
  14Q GAIN WILD-TYPE                                                232
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  14Q GAIN MUTATED                                            1
  14Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  14Q GAIN MUTATED                                               2
  14Q GAIN WILD-TYPE                                            17
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  14Q GAIN MUTATED                                0
  14Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  14Q GAIN MUTATED                                    1
  14Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  14Q GAIN MUTATED                              0                             5
  14Q GAIN WILD-TYPE                            2                            18
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  14Q GAIN MUTATED                                 0
  14Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  14Q GAIN MUTATED                                               2
  14Q GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  14Q GAIN MUTATED                              1
  14Q GAIN WILD-TYPE                            9
D26V10, multiclass
                                                    clus
vv                                                   14Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               89
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     5
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   14Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                232
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      18
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
D26V12, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    80   6   1   9
  14Q GAIN WILD-TYPE 264   7   3  17
D26V13, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               80                264
  R1                6                  7
  R2                1                  3
  RX                9                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     3
  14Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                          12   101
  14Q GAIN WILD-TYPE                        40   289
D26V14, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                      12                 40
  WHITE                                         101                289
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V15, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  99
  14Q GAIN WILD-TYPE   6 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   99
  14Q GAIN WILD-TYPE    6  285
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               99                285
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    18  20
  15Q GAIN WILD-TYPE 305 161
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                38                466 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                20                161 
$`15Q GAIN MUTATED`
TCGA-05-4418 TCGA-05-5420 TCGA-44-2661 TCGA-49-6742 TCGA-55-7284 TCGA-55-8207 
        9.01        15.02        38.10        16.04         7.99        32.12 
TCGA-05-4403 TCGA-05-4415 TCGA-44-5645 TCGA-49-4506 TCGA-4B-A93V TCGA-50-5072 
       19.00         2.99        28.01        32.84         9.86         8.22 
TCGA-50-5936 TCGA-50-5944 TCGA-55-1594 TCGA-55-8505 TCGA-62-8398 TCGA-62-8402 
        8.45        57.53        38.73        14.47        14.60        49.25 
TCGA-64-1678 TCGA-69-7980 TCGA-71-6725 TCGA-73-4670 TCGA-73-A9RS TCGA-78-7148 
       39.09        13.51         8.42         4.31        11.18        20.58 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7220 TCGA-78-7540 TCGA-78-8662 TCGA-86-8055 
      129.53        19.50        26.53        39.35       110.50         4.08 
TCGA-95-7944 TCGA-97-7553 TCGA-97-8174 TCGA-97-8552 TCGA-L9-A5IP TCGA-MP-A4T7 
       12.39        61.48         5.39        20.58         1.91         5.49 
TCGA-NJ-A4YP TCGA-S2-AA1A 
        1.64        16.87 

$`15Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 
       19.96        14.01         9.96         8.02        20.05        26.01 
TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       43.53        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 
       29.00        29.23         9.37        11.08        46.72        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       11.64       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7573 TCGA-55-7724 
       23.05        48.62         5.79         7.79        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       16.93        19.69        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
        6.35        10.09        21.83        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
        0.00        24.03        47.05        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
        4.96        29.00        22.03         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       49.05        44.61         4.37        46.98        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
       34.06        33.73        26.56        33.30        28.37        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       12.66        35.54        14.07         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       55.89        53.29        55.33        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ 
       62.24        28.90         8.55        40.41       123.58       221.33 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
      164.12        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 
       47.41        49.28         9.27        14.27        78.67        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       48.46        60.72        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       67.89        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        3.91        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42        17.56        15.72         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        19.99        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       42.38        88.64        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        81.80        37.02        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       42.90        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        13.41        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 
       26.73        19.43        23.38        26.30        15.35        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       27.16         5.69        19.27        21.90        39.95       119.51 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      104.19       238.29        88.14        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 
       26.01        10.55       232.18        39.75        77.59        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
       20.55        32.78        19.89        35.24        37.74         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       27.58         0.62        28.34        26.50        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 
       23.61         1.08        19.00        41.82        18.67        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 
        2.76        19.89        42.25        64.60        63.52        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 
       18.54         0.59        15.91        18.67        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       16.41        14.30        21.60        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.53        18.58        15.65        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 
       58.45        49.35        37.35        86.04        58.85        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       29.46        11.05        24.36        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        74.33         0.13        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.43        19.82        20.28        59.11 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.64               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            129.53             238.29 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             15.53              22.03 
[1] "1.6 - 129.5 (15.5)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1.9"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         2        7        6        0         3         4
  15Q GAIN WILD-TYPE       3      126      133        1        47        68
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  15Q GAIN MUTATED           10          2        3
  15Q GAIN WILD-TYPE         62          9       22
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  7                126
  STAGE IB                  6                133
  STAGE II                  0                  1
  STAGE IIA                 3                 47
  STAGE IIB                 4                 68
  STAGE IIIA               10                 62
  STAGE IIIB                2                  9
  STAGE IV                  3                 22
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED    10  21   5   2
  15Q GAIN WILD-TYPE 161 257  41  17
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               10                161
  T2               21                257
  T3                5                 41
  T4                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  15Q GAIN MUTATED    21   4    12
  15Q GAIN WILD-TYPE 312  92    64
D27V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                  21                312
  N1                   4                 92
  N2+N3               12                 64
[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"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    29   3
  15Q GAIN WILD-TYPE 320  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     29    3
  15Q GAIN WILD-TYPE  320   22
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               29                320
  1                3                 22
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    18  20
  15Q GAIN WILD-TYPE 258 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     18   20
  15Q GAIN WILD-TYPE  258  220
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               18                258
  MALE                 20                220
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    28   5
  15Q GAIN WILD-TYPE 382  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     28    5
  15Q GAIN WILD-TYPE  382   55
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                28                382
  YES                5                 55
[1] 2 2
[1] FALSE
D27V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  15Q GAIN MUTATED                            2
  15Q GAIN WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  15Q GAIN MUTATED                                   9
  15Q GAIN WILD-TYPE                                98
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                   17
  15Q GAIN WILD-TYPE                                                304
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  15Q GAIN MUTATED                                            2
  15Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  15Q GAIN MUTATED                                               3
  15Q GAIN WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  15Q GAIN MUTATED                                0
  15Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  15Q GAIN MUTATED                                    0
  15Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  15Q GAIN MUTATED                              0                             3
  15Q GAIN WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  15Q GAIN MUTATED                                 0
  15Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  15Q GAIN MUTATED                                               0
  15Q GAIN WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  15Q GAIN MUTATED                              2
  15Q GAIN WILD-TYPE                            8
D27V10, multiclass
                                                    clus
vv                                                   15Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   15Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                304
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
D27V12, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    27   2   0   1
  15Q GAIN WILD-TYPE 317  11   4  25
D27V13, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               27                317
  R1                2                 11
  R2                0                  4
  RX                1                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           5    26
  15Q GAIN WILD-TYPE                        47   364
D27V14, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                       5                 47
  WHITE                                          26                364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  26
  15Q GAIN WILD-TYPE   7 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   26
  15Q GAIN WILD-TYPE    7  358
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               26                358
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    80  52
  16P GAIN WILD-TYPE 243 129
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               132                372 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                52                129 
$`16P GAIN MUTATED`
TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 TCGA-49-AAR0 
       28.41        11.64        14.73        42.08        27.78       156.66 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-7284 TCGA-55-7573 TCGA-55-7726 
       21.47        41.69        23.05         7.99        16.01        21.44 
TCGA-55-8091 TCGA-67-6217 TCGA-73-4658 TCGA-95-7947 TCGA-95-A4VK TCGA-97-A4M7 
       19.73        13.87        52.60        15.68        21.40        20.68 
TCGA-L9-A443 TCGA-05-4249 TCGA-05-4390 TCGA-05-4395 TCGA-05-5423 TCGA-38-4627 
        6.35        50.07        37.02         0.00         4.96        37.71 
TCGA-38-4628 TCGA-44-2659 TCGA-44-2665 TCGA-44-3919 TCGA-44-5645 TCGA-44-6775 
       49.05        44.94        42.77        33.73        28.01        23.18 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B 
       61.28        16.44         7.17        18.87        15.32         9.44 
TCGA-44-A4SU TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 
       13.45        12.66        14.07         8.81        29.75        55.33 
TCGA-49-AARE TCGA-49-AARO TCGA-4B-A93V TCGA-50-5933 TCGA-50-6673 TCGA-50-8457 
       40.41       123.58         9.86        78.67         0.72        36.99 
TCGA-50-8460 TCGA-55-6712 TCGA-55-6980 TCGA-55-7281 TCGA-55-7907 TCGA-55-7910 
       27.25         5.62        69.34        28.67        11.28        34.19 
TCGA-55-7995 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8512 
       29.23         5.06        23.64        15.65        29.19        19.96 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B 
       14.66        12.33         3.25         0.92        19.99        17.95 
TCGA-62-8394 TCGA-62-8398 TCGA-62-A46S TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 
        4.57        14.60        54.35        56.81        81.80        37.02 
TCGA-64-1681 TCGA-67-3772 TCGA-67-6215 TCGA-69-7760 TCGA-69-7764 TCGA-69-7978 
       38.37        18.84         5.72         6.64        13.61         4.41 
TCGA-69-7980 TCGA-71-6725 TCGA-73-4668 TCGA-73-4675 TCGA-75-5125 TCGA-75-6206 
       13.51         8.42        15.35        30.31        66.64        85.15 
TCGA-75-7025 TCGA-78-7152 TCGA-78-7154 TCGA-78-7156 TCGA-78-7163 TCGA-78-7542 
      108.66        39.95        19.50        32.09       238.29        10.55 
TCGA-78-8640 TCGA-86-7701 TCGA-86-7713 TCGA-86-7955 TCGA-86-8055 TCGA-86-8075 
      232.18        31.13        38.04        35.24         4.08        22.82 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.04        31.20        23.05        14.60        11.61        13.91 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6840 TCGA-91-8496 TCGA-91-8497 TCGA-93-7348 
       29.46         3.81        12.23        16.60        14.27        17.46 
TCGA-93-A4JN TCGA-93-A4JP TCGA-97-7546 TCGA-97-7547 TCGA-97-8177 TCGA-97-8179 
       23.61        19.00        42.25        64.60        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG 
       20.58        19.76        34.85        21.57        18.08        32.48 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-NJ-A4YG 
        1.91        15.65        38.63        58.45        58.85        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.13         1.64        19.82        20.28        59.11        16.87 

$`16P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 
       26.01        15.02        15.02        35.28        26.30        43.53 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 
       38.10        23.93        86.01        18.31        29.00        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
        9.37        11.08        46.72        16.04        17.16        11.64 
TCGA-49-AARN TCGA-50-5932 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7724 
       37.32        40.60        48.62         5.79         7.79        23.18 
TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
       14.53         6.15        19.66        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       19.59        20.19        20.65        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VN 
        6.12        17.29        16.54         2.86        15.65        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 
       17.92        20.19        20.52        17.75        24.30        23.80 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       10.09        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       10.09         3.98        45.01        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 
       26.01        25.02        25.02        24.00        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
        9.04         2.04         0.46         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       97.74       120.79        44.61         4.37        46.98        44.42 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
        3.19        25.02        37.15        38.24        38.89        34.06 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       26.56        33.30        28.37        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7672 
       21.63        32.45        22.72        19.46        36.07        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       12.66         8.55        15.98        11.54        13.64        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 
       28.11        28.57        35.54        32.84        29.46        55.89 
TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       53.29        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
        8.55       221.33       164.12        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       14.27         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-7109 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
        6.21        10.13        36.79        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        38.73        67.89        30.58        14.30        80.52 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       70.26        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       23.15        25.41        18.64        17.65        18.44        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8208 TCGA-55-8299 
       29.72        15.19        23.08        17.79        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-A48Y 
       17.72        26.01        17.10        17.62         1.58        20.71 
TCGA-55-A48Z TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 
       21.40        15.81        39.98        42.38        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       47.80        19.53        56.71        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 
       39.25        40.96        29.92        39.09        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       42.90        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
       14.04        12.66        14.73         4.64         6.12        22.68 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        5.42         7.56         6.05        13.41        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 
        4.24        26.73        19.43        23.38        26.30         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        11.18        77.85        43.82 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       49.84        36.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7155 
       19.27        20.58       129.53        21.90       119.51        38.50 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
        5.88        64.90        22.92         9.57       104.19        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
        5.88        34.39        20.55        32.78        19.89        37.74 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8358 TCGA-86-8669 
        4.57        24.33         0.79        32.65        21.47        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 
       27.58         0.62        28.34        26.50        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       27.68         7.36         1.15         1.18        19.82        22.45 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       19.89        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8547 
       15.91        18.67         5.39        18.12        15.39        21.60 
TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       21.44        20.84        18.67        24.56        36.76         1.45 
TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV 
       21.63        35.47        19.00        14.30        14.53        18.58 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
        2.76        86.14        49.35        37.35        86.04         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       19.13        73.91        71.05        47.08         0.49         0.43 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.00               0.36 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            238.29             221.33 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             20.63              22.01 
[1] "0.0 - 238.3 (20.6)" "0.4 - 221.3 (22.0)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         3       42       33        0        14        15
  16P GAIN WILD-TYPE       2       91      106        1        36        57
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16P GAIN MUTATED           17          3       10
  16P GAIN WILD-TYPE         55          8       15
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 42                 91
  STAGE IB                 33                106
  STAGE II                  0                  1
  STAGE IIA                14                 36
  STAGE IIB                15                 57
  STAGE IIIA               17                 55
  STAGE IIIB                3                  8
  STAGE IV                 10                 15
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED    52  65  13   5
  16P GAIN WILD-TYPE 119 213  33  14
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               52                119
  T2               65                213
  T3               13                 33
  T4                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  16P GAIN MUTATED    86  26    20
  16P GAIN WILD-TYPE 247  70    56
D28V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                  86                247
  N1                  26                 70
  N2+N3               20                 56
[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"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    87  10
  16P GAIN WILD-TYPE 262  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     87   10
  16P GAIN WILD-TYPE  262   15
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               87                262
  1               10                 15
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    74  63
  16P GAIN WILD-TYPE 202 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     74   63
  16P GAIN WILD-TYPE  202  177
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               74                202
  MALE                 63                177
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   113  16
  16P GAIN WILD-TYPE 297  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    113   16
  16P GAIN WILD-TYPE  297   44
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO               113                297
  YES               16                 44
[1] 2 2
[1] FALSE
D28V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16P GAIN MUTATED                            3
  16P GAIN WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16P GAIN MUTATED                                  20
  16P GAIN WILD-TYPE                                87
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                   94
  16P GAIN WILD-TYPE                                                227
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16P GAIN MUTATED                                            2
  16P GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  16P GAIN MUTATED                                               6
  16P GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  16P GAIN MUTATED                                0
  16P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  16P GAIN MUTATED                                    1
  16P GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  16P GAIN MUTATED                              0                            10
  16P GAIN WILD-TYPE                            2                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  16P GAIN MUTATED                                 0
  16P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  16P GAIN MUTATED                                               1
  16P GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  16P GAIN MUTATED                              0
  16P GAIN WILD-TYPE                           10
D28V10, multiclass
                                                    clus
vv                                                   16P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               94
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                    10
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   16P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                227
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                       10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
D28V12, continuous
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    93   4   1   9
  16P GAIN WILD-TYPE 251   9   3  17
D28V13, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               93                251
  R1                4                  9
  R2                1                  3
  RX                9                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  1     3
  16P GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          15   105
  16P GAIN WILD-TYPE                        37   285
D28V14, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                      15                 37
  WHITE                                         105                285
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1 108
  16P GAIN WILD-TYPE   6 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1  108
  16P GAIN WILD-TYPE    6  276
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              108                276
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    60  37
  16Q GAIN WILD-TYPE 263 144
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                97                407 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                144 
$`16Q GAIN MUTATED`
TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-6147 TCGA-49-AAR0 TCGA-50-5935 
       28.41        11.64        14.73        27.78       156.66        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-7284 TCGA-55-7726 TCGA-55-8091 TCGA-67-6217 
       41.69        23.05         7.99        21.44        19.73        13.87 
TCGA-97-A4M7 TCGA-05-4249 TCGA-05-4395 TCGA-05-5423 TCGA-38-4627 TCGA-44-2659 
       20.68        50.07         0.00         4.96        37.71        44.94 
TCGA-44-2665 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-A47A TCGA-49-4505 
       42.77        61.28        16.44         7.17        15.32        14.07 
TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-AARE TCGA-4B-A93V TCGA-50-5933 
        8.81        29.75        55.33        40.41         9.86        78.67 
TCGA-50-6673 TCGA-50-8460 TCGA-55-1594 TCGA-55-6712 TCGA-55-6980 TCGA-55-7910 
        0.72        27.25        38.73         5.62        69.34        34.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8097 TCGA-55-8206 TCGA-55-8512 TCGA-55-8615 
       23.08         5.06        15.65        29.19        19.96        14.66 
TCGA-55-A490 TCGA-55-A4DG TCGA-62-8398 TCGA-62-8402 TCGA-62-A46S TCGA-64-1676 
        3.25        19.99        14.60        49.25        54.35        56.81 
TCGA-64-1679 TCGA-64-1681 TCGA-67-6215 TCGA-69-7760 TCGA-69-7764 TCGA-69-7980 
       81.80        38.37         5.72         6.64        13.61        13.51 
TCGA-71-6725 TCGA-73-4668 TCGA-73-4675 TCGA-75-6206 TCGA-75-7025 TCGA-75-7027 
        8.42        15.35        30.31        85.15       108.66       100.57 
TCGA-78-7145 TCGA-78-7154 TCGA-78-7163 TCGA-78-7542 TCGA-78-8640 TCGA-86-7701 
       27.16        19.50       238.29        10.55       232.18        31.13 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 
       35.24         4.08        31.04        31.20        23.05        11.61 
TCGA-86-8668 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6831 TCGA-91-6840 TCGA-91-8497 
       13.91        29.46         3.81        10.19        12.23        14.27 
TCGA-93-A4JN TCGA-97-7547 TCGA-97-7553 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
       23.61        64.60        61.48        16.41        14.30        20.58 
TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-L9-A5IP TCGA-L9-A8F4 
       19.76        34.85        21.57        18.08         1.91        15.65 
TCGA-MN-A4N4 TCGA-MP-A4T6 TCGA-NJ-A4YG TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       38.63        58.85        74.33        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

$`16Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 
       26.01        15.02        15.02        35.28        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        42.08        23.93        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       11.64        37.32        40.60        48.62         5.79         7.79 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 
       16.01        23.18        14.53         6.15        19.66        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 
       22.65        20.58        19.59        20.19        20.65        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.19        20.52        17.75        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       10.09        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 
       10.09         3.98        45.01        37.02        24.03        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5425 
       21.99        26.01        25.02        25.02        24.00        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
       22.03         9.04         2.04         0.46         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F 
        8.68        97.74       120.79        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       46.98        44.42         3.19        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.89        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       32.45        22.72        19.46        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       12.66         8.55        15.98         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV 
       32.84        29.46        55.89        53.29        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ 
       73.12        62.24        28.90         8.55       123.58       221.33 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
      164.12        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 
       47.41        49.28         8.22         9.27        14.27         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 
        3.91        25.55        11.05        12.16         6.21        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99        36.79        34.29        30.54        13.94        35.21 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 
       67.89        30.58        14.30        80.52        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6981 TCGA-55-6982 
       15.25        46.03        53.65         3.88        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       25.41        18.64        11.28        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8094 TCGA-55-8096 TCGA-55-8208 
       29.23        29.72        15.19        17.79        23.64        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
       20.28        17.72        26.01        17.10        17.62         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B 
       12.33        20.71        21.40         0.92        15.81        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
        4.57        39.98        42.38        88.64        47.80        19.53 
TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       56.71        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       29.92        39.09        37.02        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       28.41        51.25        28.47        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
       14.04        12.66        14.73         4.64         6.12        22.68 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
        5.42         7.56         6.05         4.41        13.41        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 
       13.45         4.24        26.73        19.43        23.38        26.30 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 
        4.31         9.24         1.25        50.33        11.18        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 TCGA-78-7143 TCGA-78-7146 
       77.85        43.82        49.84        36.66       163.10         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      104.19        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       26.01        39.35        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36         5.88        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       32.78        19.89        37.74         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 
       22.82        32.65        21.47        14.60        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        28.34        26.50        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
       10.62        41.36         1.97         2.60        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
        1.15        16.60         1.18        19.82        22.45        17.46 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
        2.76        19.89        42.25        63.52        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       21.60        21.44        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
        1.45        21.63        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.53        18.58         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       37.35        86.04         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       24.36        14.10        11.15        19.13        73.91        71.05 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
        0.13         1.64        47.08         0.49         0.43 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.00               0.13 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            238.29             221.33 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             21.44              21.83 
[1] "0.0 - 238.3 (21.4)" "0.1 - 221.3 (21.8)"
[1] "hr=" "1"  
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         3       30       23        0        11        11
  16Q GAIN WILD-TYPE       2      103      116        1        39        61
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16Q GAIN MUTATED           15          2        6
  16Q GAIN WILD-TYPE         57          9       19
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 30                103
  STAGE IB                 23                116
  STAGE II                  0                  1
  STAGE IIA                11                 39
  STAGE IIB                11                 61
  STAGE IIIA               15                 57
  STAGE IIIB                2                  9
  STAGE IV                  6                 19
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED    38  47  11   4
  16Q GAIN WILD-TYPE 133 231  35  15
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               38                133
  T2               47                231
  T3               11                 35
  T4                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  16Q GAIN MUTATED    65  19    15
  16Q GAIN WILD-TYPE 268  77    61
D29V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                  65                268
  N1                  19                 77
  N2+N3               15                 61
[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"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    67   6
  16Q GAIN WILD-TYPE 282  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     67    6
  16Q GAIN WILD-TYPE  282   19
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               67                282
  1                6                 19
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    51  50
  16Q GAIN WILD-TYPE 225 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     51   50
  16Q GAIN WILD-TYPE  225  190
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               51                225
  MALE                 50                190
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    86  10
  16Q GAIN WILD-TYPE 324  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     86   10
  16Q GAIN WILD-TYPE  324   50
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                86                324
  YES               10                 50
[1] 2 2
[1] FALSE
D29V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16Q GAIN MUTATED                            2
  16Q GAIN WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16Q GAIN MUTATED                                  11
  16Q GAIN WILD-TYPE                                96
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                   72
  16Q GAIN WILD-TYPE                                                249
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16Q GAIN MUTATED                                            2
  16Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  16Q GAIN MUTATED                                               6
  16Q GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  16Q GAIN MUTATED                                0
  16Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  16Q GAIN MUTATED                                    1
  16Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  16Q GAIN MUTATED                              0                             6
  16Q GAIN WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  16Q GAIN MUTATED                                 0
  16Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  16Q GAIN MUTATED                                               1
  16Q GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  16Q GAIN MUTATED                              0
  16Q GAIN WILD-TYPE                           10
D29V10, multiclass
                                                    clus
vv                                                   16Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               72
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   16Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                249
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                       10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
D29V12, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    69   5   1   5
  16Q GAIN WILD-TYPE 275   8   3  21
D29V13, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               69                275
  R1                5                  8
  R2                1                  3
  RX                5                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  1     2
  16Q GAIN WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          10    77
  16Q GAIN WILD-TYPE                        42   313
D29V14, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  5
  BLACK OR AFRICAN AMERICAN                      10                 42
  WHITE                                          77                313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  79
  16Q GAIN WILD-TYPE   7 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   79
  16Q GAIN WILD-TYPE    7  305
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               79                305
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    51  32
  17P GAIN WILD-TYPE 272 149
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                83                421 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                149 
$`17P GAIN MUTATED`
TCGA-05-4382 TCGA-05-4418 TCGA-49-6742 TCGA-50-5935 TCGA-55-6979 TCGA-64-1677 
       19.96         9.01        16.04        21.47         7.79        20.65 
TCGA-80-5611 TCGA-91-6836 TCGA-95-7043 TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 
       85.32        13.71        16.54         6.35        21.83        27.19 
TCGA-MP-A4TD TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4432 TCGA-35-5375 
       10.09        47.05         2.99        14.96        25.02         8.68 
TCGA-38-4628 TCGA-44-3396 TCGA-44-6148 TCGA-44-6777 TCGA-44-A479 TCGA-50-5930 
       49.05        37.15        23.15        32.45        15.98         9.27 
TCGA-50-6592 TCGA-50-6593 TCGA-55-5899 TCGA-55-6642 TCGA-55-6971 TCGA-55-7815 
       25.55        11.05        30.58        80.52        46.03        25.41 
TCGA-55-7907 TCGA-55-7995 TCGA-55-8094 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 
       11.28        29.23        17.79        22.16        15.72        13.74 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       14.66        12.33        15.81        19.99        17.95         4.57 
TCGA-62-8398 TCGA-62-A46Y TCGA-62-A471 TCGA-64-1680 TCGA-67-3772 TCGA-69-7973 
       14.60        13.61        40.96        37.02        18.84         7.56 
TCGA-69-7980 TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
       13.51         8.42        26.30        15.35        30.31         9.24 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 TCGA-78-7167 TCGA-78-7220 TCGA-78-8662 
       19.27       129.53        19.50        88.14        26.53       110.50 
TCGA-86-6562 TCGA-86-7713 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8585 
       12.36        38.04        35.24         4.08         0.79        11.61 
TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6835 TCGA-93-A4JP TCGA-97-8177 
       30.84         3.81        10.62         2.60        19.00        16.41 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-8032 TCGA-MN-A4N5 
       14.30        20.58        19.76        18.67         1.45         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T9 TCGA-NJ-A4YG TCGA-NJ-A7XG 
       86.14        49.35        41.59        74.33        20.28 

$`17P GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 
       14.01         9.96         8.02        20.05        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       43.53        38.10        42.08        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-6597 
       17.16        11.64       156.66        37.32        40.60        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       23.05        48.62         5.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-4658 
       22.65        20.58        19.59        20.19        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-7771 
       82.68        39.09         8.48        50.24        10.55        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        1.45         6.12        17.29         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-MP-A4T8 TCGA-MP-A4TA 
       20.68        24.30        23.80        10.09         5.29        31.23 
TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        2.43        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       24.03        19.00        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       26.01        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
        9.04         2.04         0.46         7.40         5.98        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
      120.79        37.71        44.61         4.37        46.98        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-3917 
       44.94        42.77         3.19        25.02        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
       23.77        19.56        21.63        23.18        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       12.66         8.55        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       53.29        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        40.41       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        9.86        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       47.41        49.28         8.22        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
        3.91        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       38.73        67.89        14.30         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       15.25        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 
       18.64        34.19        17.65        18.44        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19        23.08         5.06        23.64        15.65        29.19 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
       15.42        17.56        14.47         0.36        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-A48Y 
       19.96        26.01        17.10        17.62         1.58        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
       21.40         3.25         0.92        39.98        42.38        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       72.30        39.25        29.92        56.81        39.09        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       28.47        20.05        20.05        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        5.42         6.05         4.41        13.41        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4670 TCGA-73-4677 
        4.24        26.73        19.43        23.38         4.31         1.25 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
       50.33        11.18        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        5.69        20.58        21.90        39.95       119.51        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
      238.29        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 
       10.55       232.18        39.75        77.59        93.11        27.09 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        34.39        20.55        32.78        19.89 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
       37.74         4.57        24.33        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 
       31.20        23.05        21.47        14.60        13.91        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 
       26.47        41.36         1.97        10.19        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 
       22.45        17.46        23.61         1.08        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4M0 
       18.67         5.39        18.12        15.39        21.60        21.44 
TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R 
       20.84        24.56        34.85        36.76        21.57        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
       18.08        35.47        32.48        19.00        14.30        14.53 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T2 
        1.91        18.58        15.65        38.63        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       86.04        58.85         5.49        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI 
       14.10        11.15        19.13        73.91        71.05         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 
TCGA-S2-AA1A 
       16.87 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.79               0.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            129.53             238.29 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             18.84              22.68 
[1] "0.8 - 129.5 (18.8)" "0.0 - 238.3 (22.7)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         2       17       21        0        10         7
  17P GAIN WILD-TYPE       3      116      118        1        40        65
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17P GAIN MUTATED           15          4        7
  17P GAIN WILD-TYPE         57          7       18
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 17                116
  STAGE IB                 21                118
  STAGE II                  0                  1
  STAGE IIA                10                 40
  STAGE IIB                 7                 65
  STAGE IIIA               15                 57
  STAGE IIIB                4                  7
  STAGE IV                  7                 18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED    24  50   4   5
  17P GAIN WILD-TYPE 147 228  42  14
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               24                147
  T2               50                228
  T3                4                 42
  T4                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  17P GAIN MUTATED    45  19    18
  17P GAIN WILD-TYPE 288  77    58
D30V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                  45                288
  N1                  19                 77
  N2+N3               18                 58
[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"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    61   7
  17P GAIN WILD-TYPE 288  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     61    7
  17P GAIN WILD-TYPE  288   18
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               61                288
  1                7                 18
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    37  47
  17P GAIN WILD-TYPE 239 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     37   47
  17P GAIN WILD-TYPE  239  193
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               37                239
  MALE                 47                193
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    63  15
  17P GAIN WILD-TYPE 347  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     63   15
  17P GAIN WILD-TYPE  347   45
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                63                347
  YES               15                 45
[1] 2 2
[1] FALSE
D30V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17P GAIN MUTATED                            1
  17P GAIN WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17P GAIN MUTATED                                  20
  17P GAIN WILD-TYPE                                87
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                   54
  17P GAIN WILD-TYPE                                                267
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17P GAIN MUTATED                                            0
  17P GAIN WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  17P GAIN MUTATED                                               1
  17P GAIN WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  17P GAIN MUTATED                                0
  17P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  17P GAIN MUTATED                                    1
  17P GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  17P GAIN MUTATED                              1                             3
  17P GAIN WILD-TYPE                            1                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  17P GAIN MUTATED                                 0
  17P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  17P GAIN MUTATED                                               2
  17P GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17P GAIN MUTATED                              1
  17P GAIN WILD-TYPE                            9
D30V10, multiclass
                                                    clus
vv                                                   17P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               54
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   17P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                267
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
D30V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    59   0   0   8
  17P GAIN WILD-TYPE 285  13   4  18
D30V13, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               59                285
  R1                0                 13
  R2                0                  4
  RX                8                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  1     2
  17P GAIN WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           5    65
  17P GAIN WILD-TYPE                        47   325
D30V14, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  5
  BLACK OR AFRICAN AMERICAN                       5                 47
  WHITE                                          65                325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  61
  17P GAIN WILD-TYPE   7 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   61
  17P GAIN WILD-TYPE    7  323
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               61                323
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   116  72
  17Q GAIN WILD-TYPE 207 109
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               188                316 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                72                109 
$`17Q GAIN MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 TCGA-44-2662 
       19.96         8.02         9.01        26.01        28.41        42.08 
TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       18.31        29.00         9.37        46.72        16.04        17.16 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-8205 
       21.47        41.69        48.62         5.79         7.79        19.69 
TCGA-55-A491 TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-78-7633 TCGA-78-8660 
       20.58        20.65        52.60        82.68        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-L9-A443 
       85.32        13.71         6.12        17.29        16.54         6.35 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
       21.83        27.19         5.29        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 
       45.01        47.05         2.99        14.96        30.02        21.99 
TCGA-05-4430 TCGA-05-4432 TCGA-35-4122 TCGA-38-4628 TCGA-38-4632 TCGA-44-3396 
       25.02        25.02         7.40        49.05        44.61        37.15 
TCGA-44-3919 TCGA-44-6144 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7662 
       33.73        23.77        23.15        23.18        32.45         7.17 
TCGA-44-7667 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-49-4490 
       36.07        12.66         8.55        15.98         9.44        12.66 
TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR4 TCGA-49-AARO TCGA-50-5930 TCGA-50-5931 
       53.29        55.33        28.90       123.58         9.27        14.27 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       78.67        48.46        57.53         3.91        25.55        11.05 
TCGA-50-6594 TCGA-53-7813 TCGA-55-5899 TCGA-55-6642 TCGA-55-6971 TCGA-55-6981 
       12.16        13.94        30.58        80.52        46.03        45.34 
TCGA-55-6982 TCGA-55-7281 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       32.71        28.67         3.91        25.41        18.64        11.28 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 TCGA-55-8208 
       17.65        19.82        29.23        23.08        17.79        22.16 
TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       15.72        13.74        17.72        14.66         1.58        12.33 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       21.40         3.25        15.81        19.99        17.95         4.57 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46R TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       14.60        49.25        56.71        13.61        39.25        40.96 
TCGA-64-1680 TCGA-64-5774 TCGA-67-3770 TCGA-67-3772 TCGA-67-6215 TCGA-69-7760 
       37.02        87.98        20.05        18.84         5.72         6.64 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-71-6725 TCGA-73-4666 
        7.56         6.05         4.41        13.51         8.42        26.30 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-5125 TCGA-75-6214 
       15.35        30.31         9.24        50.33        66.64        36.66 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 
      163.10        27.16        19.27       129.53        19.50        64.90 
TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 
        9.57        88.14        26.53        26.01        10.55       232.18 
TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
      110.50        12.36         5.88        34.39        38.04        32.78 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 
       35.24         4.08         0.79        22.82        31.20        21.47 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 
       11.61        13.91        30.84         3.81        13.64        10.62 
TCGA-91-6835 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
        2.60         7.36        17.46         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 
       18.67        12.39        27.29         2.76        61.48        25.48 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 
       18.12        16.41        14.30        21.60        20.58        19.76 
TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-MN-A4N4 TCGA-MN-A4N5 
       18.67        34.85         1.45        21.57        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-NJ-A4YG 
       86.14        49.35        86.04        41.59        29.46        74.33 
TCGA-NJ-A7XG TCGA-O1-A52J 
       20.28        59.11 

$`17Q GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 
       14.01         9.96        20.05        15.02        15.02        35.28 
TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 
       11.64        14.73        26.30        43.53        38.10        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 TCGA-44-A47F TCGA-49-6761 TCGA-49-AAR0 
       27.78        86.01        29.23        11.08        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-55-1592 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       37.32        40.60        23.05         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       16.93        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 TCGA-91-7771 
       19.59        20.19        13.87        39.09         8.48        16.18 
TCGA-91-A4BC TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
        1.45         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A444 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4390 TCGA-05-4395 
       23.80        10.09        31.23         2.43        37.02         0.00 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4420 TCGA-05-4422 TCGA-05-4426 TCGA-05-4433 
       24.03        19.00        29.98        12.00        26.01        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
        4.96        29.00        22.03         9.04         2.04         0.46 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F 
        5.98         8.68        97.74       120.79        37.71         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        44.42        44.94        42.77         3.19        25.02 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        38.89        34.06        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       28.01        19.56        21.63        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7669 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS 
       19.46        18.87        23.64        15.32        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 
       13.45        76.21        28.11        28.57        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6767 
       32.84         8.81        29.46        29.75        55.89        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ 
       22.26        73.12        62.24         8.55        40.41       221.33 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5936 TCGA-50-5939 
       60.16        47.41        49.28         8.22         8.45        15.12 
TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       60.72        53.16        42.35         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       36.99        36.79        27.25        34.29        30.54        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       38.73        67.89        14.30         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 
       15.25        53.65         3.88        69.34        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       40.54       107.21        70.26        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7728 TCGA-55-7910 TCGA-55-7913 TCGA-55-8085 TCGA-55-8087 
       22.03        23.15        34.19        18.44        29.72        15.19 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 
        5.06        23.64        15.65        29.19        15.42        17.56 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       14.47         0.36        20.28        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-A48Y TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
       17.62        20.71         0.92        39.98        42.38        88.64 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
       47.80        19.53        54.35        67.96        72.30        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       56.81        39.09        81.80        38.37         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
       28.41        51.25        28.47        20.05        14.04        12.66 
TCGA-67-4679 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       14.73         4.64         6.12        22.68        13.61         5.42 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K 
       13.41        14.01        13.45         4.24        26.73        19.43 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 
       23.38         4.31         1.25        11.18        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 
       85.15        49.84       108.66       100.57         5.69        20.58 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95       119.51        38.50        32.09         5.88 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
       22.92       104.19       238.29        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
       39.35        39.75        77.59        93.11        27.09        31.13 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
       20.55        19.89        37.74         4.57        24.33        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       31.04        23.05        14.60        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       26.50        29.46        24.23        26.47        41.36         1.97 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       10.19        12.23        27.68         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-95-A4VP TCGA-97-7546 
        1.18        19.82        22.45        23.61        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8176 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8028 
        5.39        15.39        21.44        20.84        24.56        36.76 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4T2 
       14.53         1.91        18.58        15.65        58.45        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       58.85         5.49        11.05        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        71.05         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        0.49         0.43        19.82        16.87 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.79               0.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            232.18             238.29 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            20.580             22.355 
[1] "0.8 - 232.2 (20.6)" "0.0 - 238.3 (22.4)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         2       42       51        0        22        22
  17Q GAIN WILD-TYPE       3       91       88        1        28        50
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17Q GAIN MUTATED           31          7       13
  17Q GAIN WILD-TYPE         41          4       12
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 42                 91
  STAGE IB                 51                 88
  STAGE II                  0                  1
  STAGE IIA                22                 28
  STAGE IIB                22                 50
  STAGE IIIA               31                 41
  STAGE IIIB                7                  4
  STAGE IV                 13                 12
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED    56 109  16   8
  17Q GAIN WILD-TYPE 115 169  30  11
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               56                115
  T2              109                169
  T3               16                 30
  T4                8                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  17Q GAIN MUTATED   115  36    35
  17Q GAIN WILD-TYPE 218  60    41
D31V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                 115                218
  N1                  36                 60
  N2+N3               35                 41
[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"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   133  13
  17Q GAIN WILD-TYPE 216  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    133   13
  17Q GAIN WILD-TYPE  216   12
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0              133                216
  1               13                 12
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   100  91
  17Q GAIN WILD-TYPE 176 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    100   91
  17Q GAIN WILD-TYPE  176  149
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE              100                176
  MALE                 91                149
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   151  26
  17Q GAIN WILD-TYPE 259  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    151   26
  17Q GAIN WILD-TYPE  259   34
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO               151                259
  YES               26                 34
[1] 2 2
[1] FALSE
D31V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17Q GAIN MUTATED                            5
  17Q GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17Q GAIN MUTATED                                  43
  17Q GAIN WILD-TYPE                                64
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                  125
  17Q GAIN WILD-TYPE                                                196
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17Q GAIN MUTATED                                            1
  17Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  17Q GAIN MUTATED                                               4
  17Q GAIN WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  17Q GAIN MUTATED                                2
  17Q GAIN WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  17Q GAIN MUTATED                                    1
  17Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  17Q GAIN MUTATED                              1                             5
  17Q GAIN WILD-TYPE                            1                            18
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  17Q GAIN MUTATED                                 0
  17Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  17Q GAIN MUTATED                                               3
  17Q GAIN WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17Q GAIN MUTATED                              1
  17Q GAIN WILD-TYPE                            9
D31V10, multiclass
                                                    clus
vv                                                   17Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              125
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     5
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   17Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  64
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                196
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      18
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
D31V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED   121   4   2  17
  17Q GAIN WILD-TYPE 223   9   2   9
D31V13, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0              121                223
  R1                4                  9
  R2                2                  2
  RX               17                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  1     4
  17Q GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          11   148
  17Q GAIN WILD-TYPE                        41   242
D31V14, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  3
  BLACK OR AFRICAN AMERICAN                      11                 41
  WHITE                                         148                242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V15, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     3 134
  17Q GAIN WILD-TYPE   4 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3  134
  17Q GAIN WILD-TYPE    4  250
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              134                250
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    55  35
  18P GAIN WILD-TYPE 268 146
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                90                414 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                35                146 
$`18P GAIN MUTATED`
TCGA-44-2662 TCGA-44-6146 TCGA-44-8119 TCGA-49-6761 TCGA-55-8511 TCGA-55-A4DF 
       42.08        23.93         9.37        11.64        18.15        20.19 
TCGA-64-1677 TCGA-73-4662 TCGA-95-7562 TCGA-95-7947 TCGA-L9-A443 TCGA-L9-A444 
       20.65        82.68         2.86        15.68         6.35        10.09 
TCGA-MP-A4TD TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-5428 
       10.09         2.99        29.98        30.02        25.02        22.03 
TCGA-35-4122 TCGA-44-2657 TCGA-44-2659 TCGA-44-6144 TCGA-44-7672 TCGA-44-8117 
        7.40        44.42        44.94        23.77        23.64        12.66 
TCGA-44-A47A TCGA-49-4487 TCGA-50-5068 TCGA-50-5931 TCGA-50-6591 TCGA-50-6593 
       15.32        28.11        49.28        14.27         3.91        11.05 
TCGA-50-6673 TCGA-50-7109 TCGA-53-7813 TCGA-55-6970 TCGA-55-6980 TCGA-55-7907 
        0.72        10.13        13.94        15.25        69.34        11.28 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8096 TCGA-55-8508 TCGA-55-8615 TCGA-55-A494 
       19.82        23.08        23.64        20.28        14.66        15.81 
TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-64-5775 TCGA-64-5779 
       19.99        14.60        88.64        49.25         2.04        28.41 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-73-4668 TCGA-73-4675 
       13.61         7.56        13.51        14.01        15.35        30.31 
TCGA-73-4676 TCGA-75-5147 TCGA-78-7143 TCGA-78-7147 TCGA-78-7148 TCGA-78-7155 
        9.24        43.82       163.10        19.27        20.58        38.50 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8662 TCGA-86-7701 TCGA-86-7713 
        8.02        26.01        10.55       110.50        31.13        38.04 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8359 
       35.24        37.74         4.08         0.79        22.82        14.60 
TCGA-86-8585 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 
       11.61         3.81        41.36        10.19        12.23         1.18 
TCGA-93-A4JN TCGA-95-7944 TCGA-97-7546 TCGA-97-7554 TCGA-97-8175 TCGA-97-8179 
       23.61        12.39        42.25        25.48        18.12        14.30 
TCGA-97-8552 TCGA-MN-A4N4 TCGA-MP-A4TK TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       20.58        38.63        19.13        19.82        20.28        16.87 

$`18P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        43.53        38.10        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.00        29.23        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       17.16       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        19.69        32.12        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 
       22.65        20.58        19.59        13.87        52.60        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
        8.48        50.24        10.55        85.32        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK 
        1.45         6.12        17.29        16.54        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       24.30        23.80        21.83        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        2.43        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
       24.03        47.05        19.00        14.96        12.00        21.99 
TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       26.01        25.02        24.00         4.96        29.00         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         0.46         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2665 
       37.71        49.05        44.61         4.37        46.98        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
        3.19        25.02        37.15        38.24        38.89        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
       33.73        26.56        33.30        28.37        28.01        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8120 
       22.72        19.46         7.17        36.07        18.87         8.55 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.98         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
      101.72        15.72        60.16        47.41         8.22         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-8457 
       53.16        42.35        25.55        12.16         6.21        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 
       36.79        27.25        34.29        30.54        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       67.89        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6981 TCGA-55-6982 
       40.73        46.03        53.65         3.88        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 
       25.41        18.64        34.19        17.65        18.44        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 
       29.72        15.19         5.06        17.79        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       13.74        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46P 
       17.95         4.57        39.98        42.38        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
       40.96        29.92        56.81        39.09        81.80        37.02 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       38.37        87.98        42.90        51.25        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       20.05        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 
        4.64         6.64         6.12        22.68         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K 
        4.41        13.41        13.45         4.24        26.73        19.43 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7499 
        8.42        23.38        26.30         4.31         1.25        50.33 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       11.18        66.64        77.85        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 
      108.66       100.57        27.16         5.69       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.95       119.51        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       31.20        53.33        39.35       232.18        39.75        77.59 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 
       93.11        27.09        12.36         5.88        34.39        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
       32.78        19.89         4.57        24.33        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       31.20        23.05        21.47        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
       26.47        10.62         1.97         2.60        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
        1.15        16.60        14.27        19.82        22.45        17.46 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        41.82        18.67        27.29         2.76 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       19.89        64.60        63.52        61.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       15.91        18.67         5.39        15.39        16.41        21.60 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        21.57        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV 
       32.48        19.00        14.30        14.53         1.91        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       15.65         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        11.15        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.13         1.64        47.08         0.49         0.43        59.11 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.72               0.00 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            163.10             238.29 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             19.20              22.55 
[1] "0.7 - 163.1 (19.2)" "0.0 - 238.3 (22.5)"
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         3       22       24        0        11        11
  18P GAIN WILD-TYPE       2      111      115        1        39        61
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18P GAIN MUTATED           16          2        3
  18P GAIN WILD-TYPE         56          9       22
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 22                111
  STAGE IB                 24                115
  STAGE II                  0                  1
  STAGE IIA                11                 39
  STAGE IIB                11                 61
  STAGE IIIA               16                 56
  STAGE IIIB                2                  9
  STAGE IV                  3                 22
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED    31  50   7   4
  18P GAIN WILD-TYPE 140 228  39  15
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               31                140
  T2               50                228
  T3                7                 39
  T4                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  18P GAIN MUTATED    60  17    14
  18P GAIN WILD-TYPE 273  79    62
D32V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                  60                273
  N1                  17                 79
  N2+N3               14                 62
[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"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    66   3
  18P GAIN WILD-TYPE 283  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     66    3
  18P GAIN WILD-TYPE  283   22
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               66                283
  1                3                 22
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    44  48
  18P GAIN WILD-TYPE 232 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     44   48
  18P GAIN WILD-TYPE  232  192
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               44                232
  MALE                 48                192
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    74  11
  18P GAIN WILD-TYPE 336  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     74   11
  18P GAIN WILD-TYPE  336   49
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                74                336
  YES               11                 49
[1] 2 2
[1] FALSE
D32V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18P GAIN MUTATED                            5
  18P GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18P GAIN MUTATED                                  15
  18P GAIN WILD-TYPE                                92
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                   58
  18P GAIN WILD-TYPE                                                263
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18P GAIN MUTATED                                            1
  18P GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  18P GAIN MUTATED                                               5
  18P GAIN WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  18P GAIN MUTATED                                0
  18P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  18P GAIN MUTATED                                    1
  18P GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  18P GAIN MUTATED                              1                             3
  18P GAIN WILD-TYPE                            1                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  18P GAIN MUTATED                                 0
  18P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  18P GAIN MUTATED                                               2
  18P GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  18P GAIN MUTATED                              1
  18P GAIN WILD-TYPE                            9
D32V10, multiclass
                                                    clus
vv                                                   18P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               58
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   18P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                263
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
D32V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    63   2   0   7
  18P GAIN WILD-TYPE 281  11   4  19
D32V13, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               63                281
  R1                2                 11
  R2                0                  4
  RX                7                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  1     0
  18P GAIN WILD-TYPE                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           5    76
  18P GAIN WILD-TYPE                        47   314
D32V14, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       5                 47
  WHITE                                          76                314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V15, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  71
  18P GAIN WILD-TYPE   7 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   71
  18P GAIN WILD-TYPE    7  313
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               71                313
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    41  26
  18Q GAIN WILD-TYPE 282 155
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                67                437 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                26                155 
$`18Q GAIN MUTATED`
TCGA-44-8119 TCGA-55-8511 TCGA-55-A4DF TCGA-64-1677 TCGA-95-7562 TCGA-MP-A4TD 
        9.37        18.15        20.19        20.65         2.86        10.09 
TCGA-05-4390 TCGA-05-4415 TCGA-05-4420 TCGA-35-4122 TCGA-44-2659 TCGA-44-6144 
       37.02         2.99        29.98         7.40        44.94        23.77 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7672 TCGA-44-A47A TCGA-49-4510 
       61.28        19.46        36.07        23.64        15.32        29.46 
TCGA-49-AAR2 TCGA-4B-A93V TCGA-50-5931 TCGA-50-6591 TCGA-53-7813 TCGA-55-6970 
       73.12         9.86        14.27         3.91        13.94        15.25 
TCGA-55-7907 TCGA-55-7913 TCGA-55-8089 TCGA-55-8096 TCGA-55-8508 TCGA-55-8615 
       11.28        18.44        23.08        23.64        20.28        14.66 
TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       12.33        15.81        19.99        14.60        88.64        49.25 
TCGA-64-1678 TCGA-64-5779 TCGA-69-7764 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 
       39.09        28.41        13.61         7.56        13.51        14.01 
TCGA-71-6725 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-78-7148 TCGA-78-7155 
        8.42        15.35        30.31         9.24        20.58        38.50 
TCGA-78-7167 TCGA-78-7542 TCGA-86-7955 TCGA-86-8075 TCGA-86-8359 TCGA-86-8585 
       88.14        10.55        35.24        22.82        14.60        11.61 
TCGA-86-A4D0 TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 TCGA-93-A4JN TCGA-97-7546 
        3.81        10.19        12.23         1.18        23.61        42.25 
TCGA-97-7554 TCGA-97-8175 TCGA-97-8552 TCGA-L9-A7SV TCGA-NJ-A55R TCGA-NJ-A7XG 
       25.48        18.12        20.58        18.58        19.82        20.28 
TCGA-S2-AA1A 
       16.87 

$`18Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F 
       27.78        86.01        18.31        29.00        29.23        11.08 
TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
       46.72        16.04        17.16        11.64       156.66        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
       40.60        21.47        41.69        23.05        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       32.12        13.68        16.93        22.65        20.58        19.59 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       17.29        16.54        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       23.80         6.35        10.09        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 
       31.23         2.43        50.07         3.98        45.01         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
       24.03        47.05        19.00        14.96        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
       29.00        22.03         9.04         2.04         0.46         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        4.37        46.98        44.42        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       33.30        28.37        28.01        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 
       23.18        32.45        16.44        22.72         7.17        18.87 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       12.66         8.55        15.98         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       14.07        32.84         8.81        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       55.33        22.26        22.26        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 
       40.41       123.58       221.33       164.12        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       57.53        53.16        42.35        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       34.29        30.54        35.21        38.73        67.89        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 
       14.30        80.52         5.62        42.51        40.73        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
       24.99        40.54       107.21        70.26        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       18.64        34.19        17.65        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       15.19         5.06        17.79        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
       17.72        19.96        26.01        17.10        17.62         1.58 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A57B TCGA-62-8394 
       20.71        21.40         3.25         0.92        17.95         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       39.98        42.38        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        81.80        37.02        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       42.90        51.25        28.47        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
        6.12        22.68         5.42         6.05         4.41        13.41 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 
       13.45         4.24        26.73        19.43        23.38        26.30 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 
        4.31         1.25        50.33        11.18        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         5.69        19.27       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.95       119.51        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 
       22.92         9.57       104.19       238.29        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 
        8.02        53.33        26.01        39.35       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
       37.74         4.08         4.57        24.33         0.79        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 
       31.04        31.20        23.05        21.47        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
       13.64        26.47        10.62        41.36         1.97         2.60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       27.68         7.36         1.15        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       22.45        17.46         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       12.39        27.29         2.76        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       61.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        16.41        14.30        21.60        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        21.63        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30        14.53         1.91        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       11.15        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        59.11 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.18               0.00 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             88.64             238.29 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             18.44              22.45 
[1] "1.2 - 88.6 (18.4)"  "0.0 - 238.3 (22.4)"
[1] "hr=" "1.5"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         2       15       20        0         7         6
  18Q GAIN WILD-TYPE       3      118      119        1        43        66
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18Q GAIN MUTATED           12          2        4
  18Q GAIN WILD-TYPE         60          9       21
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 15                118
  STAGE IB                 20                119
  STAGE II                  0                  1
  STAGE IIA                 7                 43
  STAGE IIB                 6                 66
  STAGE IIIA               12                 60
  STAGE IIIB                2                  9
  STAGE IV                  4                 21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED    20  41   5   3
  18Q GAIN WILD-TYPE 151 237  41  16
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               20                151
  T2               41                237
  T3                5                 41
  T4                3                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  18Q GAIN MUTATED    45  13    11
  18Q GAIN WILD-TYPE 288  83    65
D33V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                  45                288
  N1                  13                 83
  N2+N3               11                 65
[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"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    44   4
  18Q GAIN WILD-TYPE 305  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     44    4
  18Q GAIN WILD-TYPE  305   21
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               44                305
  1                4                 21
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    33  36
  18Q GAIN WILD-TYPE 243 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     33   36
  18Q GAIN WILD-TYPE  243  204
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               33                243
  MALE                 36                204
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    56   8
  18Q GAIN WILD-TYPE 354  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     56    8
  18Q GAIN WILD-TYPE  354   52
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                56                354
  YES                8                 52
[1] 2 2
[1] FALSE
D33V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18Q GAIN MUTATED                            4
  18Q GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18Q GAIN MUTATED                                  11
  18Q GAIN WILD-TYPE                                96
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                   42
  18Q GAIN WILD-TYPE                                                279
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18Q GAIN MUTATED                                            1
  18Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  18Q GAIN MUTATED                                               2
  18Q GAIN WILD-TYPE                                            17
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  18Q GAIN MUTATED                                0
  18Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  18Q GAIN MUTATED                                    1
  18Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  18Q GAIN MUTATED                              0                             5
  18Q GAIN WILD-TYPE                            2                            18
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  18Q GAIN MUTATED                                 0
  18Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  18Q GAIN MUTATED                                               2
  18Q GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  18Q GAIN MUTATED                              1
  18Q GAIN WILD-TYPE                            9
D33V10, multiclass
                                                    clus
vv                                                   18Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               42
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     5
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   18Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      18
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
D33V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    42   1   0   8
  18Q GAIN WILD-TYPE 302  12   4  18
D33V13, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               42                302
  R1                1                 12
  R2                0                  4
  RX                8                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  1     1
  18Q GAIN WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                          11    51
  18Q GAIN WILD-TYPE                        41   339
D33V14, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                      11                 41
  WHITE                                          51                339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  57
  18Q GAIN WILD-TYPE   7 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   57
  18Q GAIN WILD-TYPE    7  327
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               57                327
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    23   9
  19P GAIN WILD-TYPE 300 172
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                32                472 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 9                172 
$`19P GAIN MUTATED`
TCGA-44-2662 TCGA-44-A47F TCGA-50-5935 TCGA-97-8172 TCGA-05-4390 TCGA-05-4424 
       42.08        11.08        21.47        17.92        37.02        30.02 
TCGA-44-2665 TCGA-44-A47A TCGA-50-5049 TCGA-50-6594 TCGA-53-7624 TCGA-55-7907 
       42.77        15.32       101.72        12.16        34.29        11.28 
TCGA-55-8615 TCGA-55-8620 TCGA-62-8399 TCGA-69-7973 TCGA-69-8253 TCGA-73-4675 
       14.66        12.33        88.64         7.56        14.01        30.31 
TCGA-78-7154 TCGA-86-8359 TCGA-86-8585 TCGA-93-A4JN TCGA-95-7944 TCGA-95-8494 
       19.50        14.60        11.61        23.61        12.39         2.76 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 TCGA-97-8179 TCGA-MN-A4N4 TCGA-MP-A4TJ 
       25.48        18.54        18.12        14.30        38.63        11.15 
TCGA-NJ-A55O TCGA-S2-AA1A 
        0.43        16.87 

$`19P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 
       14.73        26.30        43.53        38.10        23.93        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 
       86.01        18.31        29.00        29.23         9.37        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       16.04        17.16        11.64       156.66        37.32        40.60 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       41.69        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
       19.73        17.98        16.93        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       13.68        16.93        22.65        20.58        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        6.12        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       21.40        18.18        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       24.30        23.80         6.35        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       45.01         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       14.96        29.98        12.00        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        2.04         0.46         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.42        44.94         3.19        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.89        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       14.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       30.54        13.94        35.21        38.73        67.89        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       25.41        18.64        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-A48Y 
       19.96        26.01        17.10        17.62         1.58        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       21.40         3.25         0.92        15.81        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        42.38        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       39.25        40.96        29.92        56.81        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       37.02        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       51.25        28.47        20.05        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         5.42         6.05         4.41        13.41 
TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 
       13.51        13.45         4.24        26.73        19.43         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
       23.38        26.30        15.35         4.31         9.24         1.25 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
       50.33        11.18        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
      119.51        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       21.47        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       26.50        29.46         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       19.82        22.45        17.46         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       18.67        27.29        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 
       61.48         0.59        15.91        18.67         5.39        15.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       16.41        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.53         1.91        18.58        15.65         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.49        19.82        20.28        59.11 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.43               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            101.72             238.29 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            17.395             22.010 
[1] "0.4 - 101.7 (17.4)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1"  
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         0        7        9        0         4         3
  19P GAIN WILD-TYPE       5      126      130        1        46        69
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19P GAIN MUTATED            7          0        3
  19P GAIN WILD-TYPE         65         11       22
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  7                126
  STAGE IB                  9                130
  STAGE II                  0                  1
  STAGE IIA                 4                 46
  STAGE IIB                 3                 69
  STAGE IIIA                7                 65
  STAGE IIIB                0                 11
  STAGE IV                  3                 22
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED     9  18   6   0
  19P GAIN WILD-TYPE 162 260  40  19
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                9                162
  T2               18                260
  T3                6                 40
  T4                0                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  19P GAIN MUTATED    19   8     6
  19P GAIN WILD-TYPE 314  88    70
D34V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                  19                314
  N1                   8                 88
  N2+N3                6                 70
[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"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    25   3
  19P GAIN WILD-TYPE 324  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     25    3
  19P GAIN WILD-TYPE  324   22
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               25                324
  1                3                 22
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    15  18
  19P GAIN WILD-TYPE 261 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     15   18
  19P GAIN WILD-TYPE  261  222
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               15                261
  MALE                 18                222
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    27   4
  19P GAIN WILD-TYPE 383  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     27    4
  19P GAIN WILD-TYPE  383   56
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                27                383
  YES                4                 56
[1] 2 2
[1] FALSE
D34V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19P GAIN MUTATED                            3
  19P GAIN WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19P GAIN MUTATED                                   4
  19P GAIN WILD-TYPE                               103
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                   18
  19P GAIN WILD-TYPE                                                303
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19P GAIN MUTATED                                            1
  19P GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  19P GAIN MUTATED                                               0
  19P GAIN WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  19P GAIN MUTATED                                0
  19P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  19P GAIN MUTATED                                    1
  19P GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  19P GAIN MUTATED                              0                             2
  19P GAIN WILD-TYPE                            2                            21
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  19P GAIN MUTATED                                 1
  19P GAIN WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  19P GAIN MUTATED                                               2
  19P GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  19P GAIN MUTATED                              1
  19P GAIN WILD-TYPE                            9
D34V10, multiclass
                                                    clus
vv                                                   19P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               18
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   19P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 103
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                303
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      21
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
D34V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    18   1   0   2
  19P GAIN WILD-TYPE 326  12   4  24
D34V13, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               18                326
  R1                1                 12
  R2                0                  4
  RX                2                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           3    26
  19P GAIN WILD-TYPE                        49   364
D34V14, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       3                 49
  WHITE                                          26                364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  27
  19P GAIN WILD-TYPE   6 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   27
  19P GAIN WILD-TYPE    6  357
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               27                357
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    49  26
  19Q GAIN WILD-TYPE 274 155
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                75                429 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                26                155 
$`19Q GAIN MUTATED`
TCGA-05-4418 TCGA-38-4631 TCGA-44-2662 TCGA-44-6147 TCGA-44-6776 TCGA-44-A47F 
        9.01        11.64        42.08        27.78        86.01        11.08 
TCGA-50-5935 TCGA-95-7043 TCGA-97-8172 TCGA-L9-A443 TCGA-MP-A4TC TCGA-05-4390 
       21.47        16.54        17.92         6.35         2.43        37.02 
TCGA-05-4424 TCGA-35-4122 TCGA-35-5375 TCGA-44-6144 TCGA-44-7660 TCGA-44-7667 
       30.02         7.40         8.68        23.77        19.46        36.07 
TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SS TCGA-49-4510 TCGA-49-6743 
       18.87        15.32         9.44        13.64        29.46        53.29 
TCGA-49-AAR4 TCGA-50-5049 TCGA-50-5936 TCGA-50-6594 TCGA-53-7624 TCGA-53-7813 
       28.90       101.72         8.45        12.16        34.29        13.94 
TCGA-53-A4EZ TCGA-55-6971 TCGA-55-7907 TCGA-55-7913 TCGA-55-8092 TCGA-55-8302 
       35.21        46.03        11.28        18.44         5.06        15.72 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-62-8399 TCGA-62-A46S TCGA-64-5778 
       17.62        14.66        12.33        88.64        54.35        42.90 
TCGA-64-5781 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 
       51.25        22.68        13.61         7.56        13.51        14.01 
TCGA-69-8453 TCGA-73-4675 TCGA-78-7150 TCGA-78-7154 TCGA-86-7713 TCGA-86-8055 
       26.73        30.31        21.90        19.50        38.04         4.08 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8673 TCGA-91-6830 TCGA-93-A4JN 
       21.47        14.60        11.61        28.34         1.97        23.61 
TCGA-95-7944 TCGA-95-A4VP TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8179 
       12.39        19.89        25.48        18.54         5.39        14.30 
TCGA-99-8025 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T7 TCGA-MP-A4TH 
       34.85         1.91        15.65        38.63         5.49        24.36 
TCGA-MP-A4TJ TCGA-NJ-A55O TCGA-S2-AA1A 
       11.15         0.43        16.87 

$`19Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 
       19.96        14.01         9.96         8.02        20.05        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        35.28        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 
       43.53        38.10        23.93        18.31        29.00        29.23 
TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
        9.37        46.72        16.04        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
       37.32        40.60        41.69        23.05        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 
       16.18         1.45         6.12        17.29         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       15.65        21.40        18.18        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       20.68        24.30        23.80        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
        5.29        31.23        10.09        50.07         3.98        45.01 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       29.98        12.00        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        0.46         5.98        97.74       120.79        37.71        49.05 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 
       44.61         4.37        46.98        44.42        44.94        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
        3.19        25.02        37.15        38.24        38.89        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
       33.73        26.56        33.30        28.37        28.01        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7662 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       22.72         7.17        23.64        12.66         8.55        15.98 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
       35.54        14.07        32.84         8.81        29.75        55.89 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 
       55.33        22.26        22.26        73.12        62.24         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       40.41       123.58       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       71.47        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        14.27        78.67        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        38.73        67.89        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 
        5.62        42.51        40.73        15.25        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
       22.03         3.91        23.15        25.41        18.64        34.19 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       17.56        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z 
       19.96        26.01        17.10         1.58        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
        3.25         0.92        15.81        19.99        17.95         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        14.60        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       56.71        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       29.92        56.81        39.09        81.80        37.02        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       87.98         2.04        28.41        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
        6.64         6.12         5.42         6.05         4.41        13.41 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
       13.45         4.24        19.43         8.42        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS 
       15.35         4.31         9.24         1.25        50.33        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
       20.58       129.53        39.95       119.51        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
       20.55        32.78        19.89        35.24        37.74         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
       23.05        13.91        30.84        27.58         0.62        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       29.46         3.81        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       41.36        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 
       17.46         1.08        19.00        41.82        18.67        27.29 
TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
        2.76        42.25        64.60        63.52        61.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       15.91        18.67        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        21.57        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N5 
       32.48        19.00        14.30        14.53        18.58         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       41.59        29.46        11.05        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       19.82        20.28        59.11 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.43               0.00 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            101.72             238.29 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             17.92              22.26 
[1] "0.4 - 101.7 (17.9)" "0.0 - 238.3 (22.3)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         1       18       22        0         9         7
  19Q GAIN WILD-TYPE       4      115      117        1        41        65
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19Q GAIN MUTATED           15          1        5
  19Q GAIN WILD-TYPE         57         10       20
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 18                115
  STAGE IB                 22                117
  STAGE II                  0                  1
  STAGE IIA                 9                 41
  STAGE IIB                 7                 65
  STAGE IIIA               15                 57
  STAGE IIIB                1                 10
  STAGE IV                  5                 20
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED    25  40  12   1
  19Q GAIN WILD-TYPE 146 238  34  18
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               25                146
  T2               40                238
  T3               12                 34
  T4                1                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  19Q GAIN MUTATED    50  12    15
  19Q GAIN WILD-TYPE 283  84    61
D35V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                  50                283
  N1                  12                 84
  N2+N3               15                 61
[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"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    51   5
  19Q GAIN WILD-TYPE 298  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     51    5
  19Q GAIN WILD-TYPE  298   20
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               51                298
  1                5                 20
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    34  44
  19Q GAIN WILD-TYPE 242 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     34   44
  19Q GAIN WILD-TYPE  242  196
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               34                242
  MALE                 44                196
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    65   8
  19Q GAIN WILD-TYPE 345  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     65    8
  19Q GAIN WILD-TYPE  345   52
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                65                345
  YES                8                 52
[1] 2 2
[1] FALSE
D35V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19Q GAIN MUTATED                            5
  19Q GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19Q GAIN MUTATED                                   9
  19Q GAIN WILD-TYPE                                98
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                   49
  19Q GAIN WILD-TYPE                                                272
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19Q GAIN MUTATED                                            1
  19Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  19Q GAIN MUTATED                                               3
  19Q GAIN WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  19Q GAIN MUTATED                                1
  19Q GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  19Q GAIN MUTATED                                    1
  19Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  19Q GAIN MUTATED                              0                             4
  19Q GAIN WILD-TYPE                            2                            19
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  19Q GAIN MUTATED                                 1
  19Q GAIN WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  19Q GAIN MUTATED                                               1
  19Q GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  19Q GAIN MUTATED                              3
  19Q GAIN WILD-TYPE                            7
D35V10, multiclass
                                                    clus
vv                                                   19Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               49
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   19Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                272
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      19
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
D35V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    45   2   0   4
  19Q GAIN WILD-TYPE 299  11   4  22
D35V13, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               45                299
  R1                2                 11
  R2                0                  4
  RX                4                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                          10    60
  19Q GAIN WILD-TYPE                        42   330
D35V14, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                      10                 42
  WHITE                                          60                330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  61
  19Q GAIN WILD-TYPE   5 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   61
  19Q GAIN WILD-TYPE    5  323
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               61                323
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   111  61
  20P GAIN WILD-TYPE 212 120
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               172                332 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                120 
$`20P GAIN MUTATED`
TCGA-05-4402 TCGA-05-5420 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-6147 
        8.02        15.02        28.41        11.64        14.73        27.78 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5935 
       29.23         9.37        11.08       156.66        37.32        21.47 
TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 
       23.05         5.79         7.79         7.99        23.18        21.44 
TCGA-55-8205 TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 
       19.69        20.58        20.19        20.65        52.60        82.68 
TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-MN-A4N1 TCGA-05-4249 
       13.71         1.45         6.12        16.54        27.19        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4417 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 
        3.98        45.01        14.96        30.02        25.02        25.02 
TCGA-05-5425 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-44-2657 
       29.00         8.68        97.74        37.71        49.05        44.42 
TCGA-44-3917 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 
       38.89        28.37        28.01        23.77        21.63        23.18 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       61.28        19.46         7.17        36.07        18.87        23.64 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 TCGA-49-4506 
       15.98         9.44        13.64        13.45        35.54        32.84 
TCGA-49-4510 TCGA-49-6767 TCGA-49-AAR9 TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 
       29.46        22.26         8.55         9.86        71.47       101.72 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 
       47.41        49.28        14.27        48.46        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-53-7813 
        3.91        25.55         6.21         0.72        10.13        13.94 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 
       67.89        30.58        14.30        80.52        40.73        15.25 
TCGA-55-6972 TCGA-55-7574 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       53.65        32.71        18.44        29.23        29.72        15.19 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 
       23.64        15.65        29.19        22.16        15.72        13.74 
TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Z TCGA-55-A493 
       20.28        17.10        17.62        14.66        21.40         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8399 TCGA-62-8402 TCGA-64-5775 
       15.81        19.99         4.57        88.64        49.25         2.04 
TCGA-67-3771 TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 TCGA-69-7978 TCGA-69-7979 
       20.05        18.84        22.68        13.61         4.41        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-71-6725 TCGA-73-4668 TCGA-73-4677 TCGA-73-A9RS 
       13.51        14.01         8.42        15.35         1.25        11.18 
TCGA-75-6206 TCGA-75-7027 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 
       85.15       100.57       119.51        19.50        38.50        64.90 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 
      238.29        88.14        26.53         8.02        10.55       232.18 
TCGA-83-5908 TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 
       27.09        38.04        35.24        37.74         4.08        24.33 
TCGA-86-8075 TCGA-86-8585 TCGA-86-8669 TCGA-91-6829 TCGA-91-6840 TCGA-91-6847 
       22.82        11.61        30.84        41.36        12.23        27.68 
TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-8494 
        1.18        23.61         1.08        19.00        18.67         2.76 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 
       42.25        61.48        18.54         5.39        18.12        14.30 
TCGA-97-8552 TCGA-97-A4M1 TCGA-99-8025 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N5 
       20.58        19.76        34.85         1.91        15.65         2.76 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
       49.35        37.35        58.85         5.49        29.46        11.05 
TCGA-MP-A4TK TCGA-NJ-A4YP TCGA-NJ-A55R TCGA-S2-AA1A 
       19.13         1.64        19.82        16.87 

$`20P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       15.02        35.28        26.30        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-49-4501 TCGA-49-6742 
       23.93        86.01        18.31        29.00        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-6597 TCGA-55-1595 TCGA-55-7573 
       17.16        11.64        40.60        41.69        48.62        16.01 
TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       14.53         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 
       32.12        18.15        13.68        16.93        22.65        19.59 
TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       13.87        39.09         8.48        50.24        10.55        85.32 
TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       16.18        17.29         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        21.83         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       31.23         2.43        10.09        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
       47.05        19.00         2.99        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       26.01        24.00         4.96        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F 
        0.46         7.40         5.98       120.79        44.61         4.37 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       46.98        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6145 
       38.24        34.06        33.73        26.56        33.30        19.56 
TCGA-44-6148 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-8117 TCGA-44-8120 
       23.15        32.45        16.44        22.72        12.66         8.55 
TCGA-44-A47A TCGA-44-A47G TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       15.32        11.54        76.21        28.11        28.57        12.66 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
       14.07         8.81        29.75        55.89        53.29        55.33 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO 
       22.26        73.12        62.24        28.90        40.41       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 
      221.33       164.12        20.52        15.72        60.16         8.22 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
        9.27        78.67         8.45        15.12        60.72        57.53 
TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       11.05        12.16        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6712 TCGA-55-6968 TCGA-55-6971 
       30.54        35.21        38.73         5.62        42.51        46.03 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
       40.54       107.21        70.26        28.67        20.02        27.09 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       22.03         3.91        23.15        25.41        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       34.19        17.65        19.82        23.08         5.06        17.79 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 
       15.42        17.56        14.47         0.36        17.72        19.96 
TCGA-55-8513 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A57B 
       26.01         1.58        12.33        20.71         3.25        17.95 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       39.98        42.38        14.60        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       29.92        56.81        39.09        81.80        37.02        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       87.98        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 
        6.12         5.42         7.56         6.05        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
       26.73        19.43        23.38        26.30         4.31        30.31 
TCGA-73-4676 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 
        9.24        50.33        66.64        77.85        43.82        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       36.66       108.66       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 
       20.58       129.53        21.90        39.95        32.09         5.88 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
       22.92         9.57       104.19        31.20        53.33        26.01 
TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 
       39.35        39.75        77.59       110.50        93.11        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        34.39        20.55        32.78        19.89 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        4.57         0.79        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       21.47        14.60        13.91        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       26.50        29.46         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 
       10.62         1.97        10.19         2.60         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 
       16.60        14.27        19.82        22.45        17.46        41.82 
TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 
       12.39        27.29        19.89        64.60        63.52        25.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
        0.59        15.91        18.67        15.39        16.41        21.60 
TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       21.44        20.84        18.67        24.56        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        21.63        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
       14.30        14.53        18.58        38.63        86.14        58.45 
TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 
       86.04        41.59        24.36        14.10        11.15        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        74.33         0.13        47.08         0.49         0.43 
TCGA-NJ-A7XG TCGA-O1-A52J 
       20.28        59.11 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.72               0.00 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            238.29             221.33 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             20.58              22.03 
[1] "0.7 - 238.3 (20.6)" "0.0 - 221.3 (22.0)"
[1] "hr=" "1"  
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         3       47       55        0        15        23
  20P GAIN WILD-TYPE       2       86       84        1        35        49
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20P GAIN MUTATED           19          3        7
  20P GAIN WILD-TYPE         53          8       18
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 47                 86
  STAGE IB                 55                 84
  STAGE II                  0                  1
  STAGE IIA                15                 35
  STAGE IIB                23                 49
  STAGE IIIA               19                 53
  STAGE IIIB                3                  8
  STAGE IV                  7                 18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED    56 101  14   3
  20P GAIN WILD-TYPE 115 177  32  16
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               56                115
  T2              101                177
  T3               14                 32
  T4                3                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  20P GAIN MUTATED   123  26    20
  20P GAIN WILD-TYPE 210  70    56
D36V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                 123                210
  N1                  26                 70
  N2+N3               20                 56
[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"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   109   7
  20P GAIN WILD-TYPE 240  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    109    7
  20P GAIN WILD-TYPE  240   18
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              109                240
  1                7                 18
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    92  83
  20P GAIN WILD-TYPE 184 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     92   83
  20P GAIN WILD-TYPE  184  157
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               92                184
  MALE                 83                157
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   139  22
  20P GAIN WILD-TYPE 271  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    139   22
  20P GAIN WILD-TYPE  271   38
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               139                271
  YES               22                 38
[1] 2 2
[1] FALSE
D36V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20P GAIN MUTATED                            5
  20P GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20P GAIN MUTATED                                  25
  20P GAIN WILD-TYPE                                82
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                  123
  20P GAIN WILD-TYPE                                                198
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20P GAIN MUTATED                                            2
  20P GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20P GAIN MUTATED                                               6
  20P GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  20P GAIN MUTATED                                0
  20P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  20P GAIN MUTATED                                    2
  20P GAIN WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  20P GAIN MUTATED                              0                             9
  20P GAIN WILD-TYPE                            2                            14
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  20P GAIN MUTATED                                 0
  20P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  20P GAIN MUTATED                                               2
  20P GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  20P GAIN MUTATED                              1
  20P GAIN WILD-TYPE                            9
D36V10, multiclass
                                                    clus
vv                                                   20P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              123
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     9
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   20P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                198
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      14
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
D36V12, continuous
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   104   6   2   9
  20P GAIN WILD-TYPE 240   7   2  17
D36V13, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              104                240
  R1                6                  7
  R2                2                  2
  RX                9                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  1     4
  20P GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          23   129
  20P GAIN WILD-TYPE                        29   261
D36V14, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  3
  BLACK OR AFRICAN AMERICAN                      23                 29
  WHITE                                         129                261
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1 136
  20P GAIN WILD-TYPE   6 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1  136
  20P GAIN WILD-TYPE    6  248
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              136                248
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   126  71
  20Q GAIN WILD-TYPE 197 110
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               197                307 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                71                110 
$`20Q GAIN MUTATED`
TCGA-05-5420 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 
       15.02        28.41        11.64        14.73        42.08        27.78 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-AAR0 TCGA-49-AARN 
       29.00        29.23         9.37        11.08       156.66        37.32 
TCGA-50-5935 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 
       21.47        23.05         5.79         7.79         7.99        23.18 
TCGA-55-7726 TCGA-55-8205 TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 
       21.44        19.69        20.58        20.19        20.65        52.60 
TCGA-78-8660 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 
       10.55        13.71        16.18         1.45         6.12        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-05-4250 TCGA-05-4389 
        2.86        15.68        10.09        27.19         3.98        45.01 
TCGA-05-4397 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 
       24.03        14.96        29.98        30.02        25.02        25.02 
TCGA-05-5423 TCGA-05-5425 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
        4.96        29.00         8.68        97.74        37.71        49.05 
TCGA-44-2657 TCGA-44-3917 TCGA-44-5645 TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 
       44.42        38.89        28.01        23.77        21.63        23.18 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       61.28        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A4SU TCGA-49-4487 TCGA-49-4494 
       12.66        15.98        15.32        13.45        28.11        35.54 
TCGA-49-4506 TCGA-49-4510 TCGA-49-6767 TCGA-49-AAR9 TCGA-49-AARQ TCGA-4B-A93V 
       32.84        29.46        22.26         8.55       221.33         9.86 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 
       47.41        49.28        14.27        48.46        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-53-7813 
        3.91        25.55         6.21         0.72        10.13        13.94 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       38.73        67.89        14.30        80.52         5.62        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-7995 
       15.25        53.65        11.28        34.19        18.44        29.23 
TCGA-55-8085 TCGA-55-8092 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8302 
       29.72         5.06        23.64        29.19        22.16        15.72 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.36        13.74        20.28        17.10        17.62        14.66 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8399 
       12.33        21.40         0.92        19.99         4.57        88.64 
TCGA-62-8402 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-67-3771 
       49.25        38.37        87.98         2.04        51.25        20.05 
TCGA-67-3772 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7978 TCGA-69-7979 
       18.84         6.12        22.68        13.61         4.41        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 
       13.51        14.01         4.24         8.42        26.30        15.35 
TCGA-73-4670 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5125 TCGA-75-6206 TCGA-75-6214 
        4.31         1.25        11.18        66.64        85.15        36.66 
TCGA-75-7027 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7163 
      100.57       119.51        19.50        38.50        64.90       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 
       88.14        26.53        31.20         8.02        10.55       232.18 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       27.09        12.36        38.04        35.24        37.74         4.08 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8585 TCGA-86-8669 TCGA-91-6829 
       24.33        22.82        31.20        11.61        30.84        41.36 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JO 
        2.60        12.23        27.68         1.18        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-8494 TCGA-97-7546 TCGA-97-7553 
       19.00        41.82        18.67         2.76        42.25        61.48 
TCGA-97-7937 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 
       18.54        18.12        16.41        14.30        20.58        19.76 
TCGA-99-8025 TCGA-L4-A4E5 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       34.85        19.00        15.65        38.63         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
       49.35        37.35        58.85         5.49        29.46        11.05 
TCGA-MP-A4TK TCGA-NJ-A4YP TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       19.13         1.64        19.82        59.11        16.87 

$`20Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       26.01        15.02        35.28        26.30        43.53        38.10 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       23.93        86.01        18.31        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-6597 TCGA-55-1595 TCGA-55-7573 TCGA-55-7725 
       11.64        40.60        41.69        48.62        16.01        14.53 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 
        6.15        19.66        19.73        17.98        16.93        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-67-6217 
       18.15        13.68        16.93        22.65        19.59        13.87 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-93-A4JQ 
       82.68        39.09         8.48        50.24        85.32        17.29 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.65        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 
       17.75        20.68        24.30        23.80         6.35        21.83 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4390 
        5.29        31.23         2.43        10.09        50.07        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 
        0.00        47.05        19.00         2.99        12.00        21.99 
TCGA-05-4426 TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       26.01        24.00        22.03         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
        7.40         5.98       120.79        44.61         4.37        46.98 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.94        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 
       34.06        33.73        26.56        33.30        28.37        19.56 
TCGA-44-6148 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-8120 TCGA-44-A47B 
       23.15        32.45        16.44        22.72         8.55         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 
       11.54        13.64        76.21        28.57        12.66        14.07 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV 
        8.81        29.75        55.89        53.29        55.33        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR 
       73.12        62.24        28.90        40.41       123.58       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 
       20.52        71.47       101.72        15.72        60.16         8.22 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
        9.27        78.67         8.45        15.12        60.72        57.53 
TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       11.05        12.16        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-6975 
       30.54        35.21        30.58        42.51        46.03         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
       22.03         3.91        23.15        25.41        18.64        17.65 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8097 TCGA-55-8299 
       19.82        15.19        23.08        17.79        15.65        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8616 
       17.56        14.47        17.72        19.96        26.01         1.58 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
       20.71         3.25        15.81        17.95        39.98        42.38 
TCGA-62-8398 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       14.60        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       39.09        81.80        37.02        42.90        28.41        28.47 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8254 TCGA-69-8453 
        6.64         5.42         7.56         6.05        13.45        26.73 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-5146 
       19.43        23.38        30.31         9.24        50.33        77.85 
TCGA-75-5147 TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       43.82        49.84       108.66       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 
       19.27        20.58       129.53        21.90        39.95        32.09 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7537 TCGA-78-7539 
        5.88        22.92         9.57       104.19        53.33        26.01 
TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 
       39.35        39.75        77.59       110.50        93.11         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8056 
       31.13        34.39        20.55        32.78        19.89         4.57 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
        0.79        32.65        31.04        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
        3.81        24.23        13.64        26.47        10.62         1.97 
TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       10.19         7.36         1.15        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7547 
       22.45        17.46        12.39        27.29        19.89        64.60 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       63.52        25.48         0.59        15.91        18.67         5.39 
TCGA-97-8176 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       15.39        21.60        21.44        20.84        18.67        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        21.57        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MP-A4SW 
       32.48        14.30        14.53         1.91        18.58        58.45 
TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 
       86.04        41.59        24.36        14.10        11.15        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        74.33         0.13        47.08         0.49         0.43 
TCGA-NJ-A7XG 
       20.28 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.36               0.00 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            238.29             164.12 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             20.58              22.03 
[1] "0.4 - 238.3 (20.6)" "0.0 - 164.1 (22.0)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         5       51       59        0        21        31
  20Q GAIN WILD-TYPE       0       82       80        1        29        41
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20Q GAIN MUTATED           22          3        8
  20Q GAIN WILD-TYPE         50          8       17
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   5                  0
  STAGE IA                 51                 82
  STAGE IB                 59                 80
  STAGE II                  0                  1
  STAGE IIA                21                 29
  STAGE IIB                31                 41
  STAGE IIIA               22                 50
  STAGE IIIB                3                  8
  STAGE IV                  8                 17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED    64 115  18   3
  20Q GAIN WILD-TYPE 107 163  28  16
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               64                107
  T2              115                163
  T3               18                 28
  T4                3                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  20Q GAIN MUTATED   139  35    22
  20Q GAIN WILD-TYPE 194  61    54
D37V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                 139                194
  N1                  35                 61
  N2+N3               22                 54
[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"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   127   8
  20Q GAIN WILD-TYPE 222  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    127    8
  20Q GAIN WILD-TYPE  222   17
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              127                222
  1                8                 17
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   102  99
  20Q GAIN WILD-TYPE 174 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    102   99
  20Q GAIN WILD-TYPE  174  141
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              102                174
  MALE                 99                141
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   159  24
  20Q GAIN WILD-TYPE 251  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    159   24
  20Q GAIN WILD-TYPE  251   36
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               159                251
  YES               24                 36
[1] 2 2
[1] FALSE
D37V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20Q GAIN MUTATED                            6
  20Q GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20Q GAIN MUTATED                                  30
  20Q GAIN WILD-TYPE                                77
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                  142
  20Q GAIN WILD-TYPE                                                179
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20Q GAIN MUTATED                                            2
  20Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20Q GAIN MUTATED                                               6
  20Q GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  20Q GAIN MUTATED                                0
  20Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  20Q GAIN MUTATED                                    2
  20Q GAIN WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  20Q GAIN MUTATED                              0                             9
  20Q GAIN WILD-TYPE                            2                            14
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  20Q GAIN MUTATED                                 0
  20Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  20Q GAIN MUTATED                                               3
  20Q GAIN WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  20Q GAIN MUTATED                              1
  20Q GAIN WILD-TYPE                            9
D37V10, multiclass
                                                    clus
vv                                                   20Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              142
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     9
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   20Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                179
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      14
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
D37V12, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   127   5   2  10
  20Q GAIN WILD-TYPE 217   8   2  16
D37V13, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              127                217
  R1                5                  8
  R2                2                  2
  RX               10                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  1     4
  20Q GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          24   148
  20Q GAIN WILD-TYPE                        28   242
D37V14, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  3
  BLACK OR AFRICAN AMERICAN                      24                 28
  WHITE                                         148                242
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 152
  20Q GAIN WILD-TYPE   4 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  152
  20Q GAIN WILD-TYPE    4  232
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              152                232
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    57  40
  21Q GAIN WILD-TYPE 266 141
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                97                407 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                40                141 
$`21Q GAIN MUTATED`
TCGA-05-4405 TCGA-05-4418 TCGA-38-4629 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 
       20.05         9.01        28.41        14.73        42.08        27.78 
TCGA-49-4501 TCGA-49-6742 TCGA-50-6597 TCGA-55-1595 TCGA-55-7914 TCGA-55-8207 
       46.72        16.04        41.69        48.62         6.15        32.12 
TCGA-55-8511 TCGA-67-6217 TCGA-80-5611 TCGA-97-A4LX TCGA-L9-A444 TCGA-MN-A4N1 
       18.15        13.87        85.32        20.19        10.09        27.19 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4415 TCGA-05-5423 TCGA-05-5428 TCGA-38-4628 
       31.23         2.43         2.99         4.96        22.03        49.05 
TCGA-44-2657 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-A47A TCGA-49-4487 
       44.42        21.63        23.18        32.45        15.32        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4512 TCGA-49-6743 TCGA-49-AAQV 
       28.57        12.66        14.07        29.75        53.29        22.26 
TCGA-50-5049 TCGA-50-5931 TCGA-50-5941 TCGA-50-6594 TCGA-50-6673 TCGA-50-8457 
      101.72        14.27        48.46        12.16         0.72        36.99 
TCGA-53-7626 TCGA-55-6642 TCGA-55-6980 TCGA-55-6981 TCGA-55-7727 TCGA-55-8206 
       30.54        80.52        69.34        45.34         3.91        29.19 
TCGA-55-8208 TCGA-55-8615 TCGA-55-A48Z TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 
       22.16        14.66        21.40        17.95         4.57        14.60 
TCGA-62-8399 TCGA-62-A46R TCGA-64-1678 TCGA-64-1680 TCGA-67-3771 TCGA-69-8253 
       88.64        56.71        39.09        37.02        20.05        14.01 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4677 TCGA-73-7499 TCGA-75-5147 TCGA-75-6212 
       19.43         8.42         1.25        50.33        43.82        49.84 
TCGA-75-6214 TCGA-78-7147 TCGA-78-7155 TCGA-78-7163 TCGA-78-7535 TCGA-78-7539 
       36.66        19.27        38.50       238.29        31.20        26.01 
TCGA-78-7542 TCGA-78-8662 TCGA-86-6562 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 
       10.55       110.50        12.36        22.82        31.20        21.47 
TCGA-91-8496 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7944 TCGA-97-7546 
       16.60         1.18        23.61        19.00        12.39        42.25 
TCGA-97-7553 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       61.48        16.41        14.30        20.58        21.44        19.76 
TCGA-J2-A4AD TCGA-MN-A4N5 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-NJ-A4YG TCGA-O1-A52J 
       18.08         2.76        58.85         5.49        74.33        59.11 
TCGA-S2-AA1A 
       16.87 

$`21Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         8.02        26.01        15.02 
TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       15.02        35.28        11.64        26.30        43.53        38.10 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 
       23.93        86.01        18.31        29.00        29.23         9.37 
TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       11.08        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       21.47        23.05         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       23.18        14.53        21.44        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       16.93        19.69        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 
       19.59        20.19        20.65        52.60        82.68        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
        8.48        50.24        10.55        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        6.12        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       21.40        18.18        17.92        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TD 
       24.30        23.80         6.35        21.83         5.29        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       47.05        19.00        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5425 
       21.99        26.01        25.02        25.02        24.00        29.00 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
        9.04         2.04         0.46         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
       97.74       120.79        37.71        44.61         4.37        46.98 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.94        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.89        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6778 TCGA-44-6779 
       28.01        23.77        19.56        23.15        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       12.66         8.55        15.98         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       13.45        76.21        35.54        32.84         8.81        29.46 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.89        55.33        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
        8.22         9.27        78.67         8.45        15.12        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
        6.21        10.13        36.79        27.25        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
       35.21        38.73        67.89        30.58        14.30         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 
       28.67        20.02        27.09        32.71        22.03        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       25.41        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       17.79        23.64        15.65        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       26.01        17.10        17.62         1.58        12.33        20.71 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
        3.25         0.92        15.81        19.99        39.98        42.38 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        47.80        19.53        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       28.47        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       13.45         4.24        26.73        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 
        4.31        30.31         9.24        11.18        66.64        77.85 
TCGA-75-6206 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       85.15       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 
       88.14        26.53         8.02        53.33        39.35       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
       39.75        77.59        93.11        27.09         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
       37.74         4.08         4.57        24.33         0.79        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.04        23.05        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       27.58         0.62        28.34        26.50        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7039 
       14.27        19.82        22.45        17.46         1.08        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       18.67        27.29         2.76        19.89        64.60        63.52 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       18.12        15.39        21.60        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        21.63        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV 
       32.48        19.00        14.30        14.53         1.91        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       15.65        38.63        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       86.04        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP 
       11.15        19.13        73.91        71.05         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       47.08         0.49         0.43        19.82        20.28 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.72               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            238.29             232.18 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             22.16              21.47 
[1] "0.7 - 238.3 (22.2)" "0.0 - 232.2 (21.5)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         2       23       29        1        10         7
  21Q GAIN WILD-TYPE       3      110      110        0        40        65
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  21Q GAIN MUTATED           16          3        5
  21Q GAIN WILD-TYPE         56          8       20
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 23                110
  STAGE IB                 29                110
  STAGE II                  1                  0
  STAGE IIA                10                 40
  STAGE IIB                 7                 65
  STAGE IIIA               16                 56
  STAGE IIIB                3                  8
  STAGE IV                  5                 20
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED    36  53   6   2
  21Q GAIN WILD-TYPE 135 225  40  17
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               36                135
  T2               53                225
  T3                6                 40
  T4                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  21Q GAIN MUTATED    57  15    21
  21Q GAIN WILD-TYPE 276  81    55
D38V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                  57                276
  N1                  15                 81
  N2+N3               21                 55
[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"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    68   5
  21Q GAIN WILD-TYPE 281  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     68    5
  21Q GAIN WILD-TYPE  281   20
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               68                281
  1                5                 20
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    62  36
  21Q GAIN WILD-TYPE 214 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     62   36
  21Q GAIN WILD-TYPE  214  204
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               62                214
  MALE                 36                204
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    80  12
  21Q GAIN WILD-TYPE 330  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     80   12
  21Q GAIN WILD-TYPE  330   48
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                80                330
  YES               12                 48
[1] 2 2
[1] FALSE
D38V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  21Q GAIN MUTATED                            4
  21Q GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  21Q GAIN MUTATED                                  21
  21Q GAIN WILD-TYPE                                86
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                   60
  21Q GAIN WILD-TYPE                                                261
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  21Q GAIN MUTATED                                            1
  21Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  21Q GAIN MUTATED                                               4
  21Q GAIN WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  21Q GAIN MUTATED                                2
  21Q GAIN WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  21Q GAIN MUTATED                                    1
  21Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  21Q GAIN MUTATED                              0                             3
  21Q GAIN WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  21Q GAIN MUTATED                                 0
  21Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  21Q GAIN MUTATED                                               1
  21Q GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  21Q GAIN MUTATED                              1
  21Q GAIN WILD-TYPE                            9
D38V10, multiclass
                                                    clus
vv                                                   21Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               60
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   21Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                261
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
D38V12, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    67   2   0   6
  21Q GAIN WILD-TYPE 277  11   4  20
D38V13, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               67                277
  R1                2                 11
  R2                0                  4
  RX                6                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     3
  21Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           9    74
  21Q GAIN WILD-TYPE                        43   316
D38V14, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                       9                 43
  WHITE                                          74                316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  72
  21Q GAIN WILD-TYPE   6 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   72
  21Q GAIN WILD-TYPE    6  312
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               72                312
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    31  28
  22Q GAIN WILD-TYPE 292 153
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                59                445 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                28                153 
$`22Q GAIN MUTATED`
TCGA-05-4434 TCGA-44-7670 TCGA-44-A47F TCGA-49-6742 TCGA-55-1592 TCGA-55-7724 
       15.02        29.00        11.08        16.04        23.05        23.18 
TCGA-55-7726 TCGA-55-8091 TCGA-55-8204 TCGA-55-A491 TCGA-05-4420 TCGA-38-4625 
       21.44        19.73        16.93        20.58        29.98        97.74 
TCGA-38-A44F TCGA-44-3398 TCGA-44-6777 TCGA-44-6779 TCGA-44-7662 TCGA-44-A47A 
        4.37        38.24        32.45        16.44         7.17        15.32 
TCGA-49-4488 TCGA-49-4490 TCGA-49-6743 TCGA-50-5931 TCGA-50-5944 TCGA-50-6594 
       28.57        12.66        53.29        14.27        57.53        12.16 
TCGA-55-1596 TCGA-55-6712 TCGA-55-6981 TCGA-55-6982 TCGA-55-7907 TCGA-55-8096 
       67.89         5.62        45.34        32.71        11.28        23.64 
TCGA-55-8208 TCGA-55-8506 TCGA-55-8514 TCGA-55-8614 TCGA-55-A57B TCGA-62-8397 
       22.16         0.36        17.10        17.62        17.95        42.38 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-67-3770 TCGA-67-3771 TCGA-73-4675 
       14.60        49.25        47.80        20.05        20.05        30.31 
TCGA-75-6212 TCGA-78-7150 TCGA-78-7154 TCGA-78-8662 TCGA-86-6562 TCGA-86-7713 
       49.84        21.90        19.50       110.50        12.36        38.04 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8280 TCGA-91-6847 TCGA-95-7944 TCGA-97-8174 
        4.08        24.33        23.05        27.68        12.39         5.39 
TCGA-97-8552 TCGA-99-8033 TCGA-J2-A4AE TCGA-MP-A4SW TCGA-MP-A4T7 
       20.58        21.57        35.47        58.45         5.49 

$`22Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       26.01        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 
       26.30        43.53        38.10        42.08        23.93        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6745 
       86.01        18.31        29.23         9.37        46.72        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       11.64       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 
       48.62         5.79         7.79         7.99        16.01        14.53 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
        6.15        19.66        17.98        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       13.68        16.93        22.65        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       24.30        23.80         6.35        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        2.99        14.96        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
        9.04         2.04         0.46         7.40         5.98         8.68 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 
      120.79        37.71        49.05        44.61        46.98        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 
       44.94        42.77         3.19        25.02        37.15        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 
       23.77        19.56        23.15        21.63        23.18        61.28 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       22.72        19.46        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
        8.55        15.98         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       76.21        28.11        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV 
       29.46        29.75        55.89        55.33        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       73.12        62.24        28.90         8.55        40.41       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      221.33       164.12         9.86        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
       78.67         8.45        15.12        48.46        60.72        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 
       42.35         3.91        25.55        11.05         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94        35.21        38.73        30.58        14.30        80.52 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       69.34        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       23.15        25.41        18.64        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       17.79        15.65        29.19        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       14.47        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8399 
        0.92        15.81        19.99         4.57        39.98        88.64 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       39.25        40.96        29.92        56.81        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       37.02        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       51.25        28.47        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 
       14.01        13.45         4.24        26.73        19.43         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
       23.38        26.30        15.35         4.31         9.24         1.25 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
       50.33        11.18        66.64        77.85        43.82        85.15 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
       19.27        20.58       129.53        39.95       119.51        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
       93.11        27.09         5.88        31.13        34.39        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8074 
       32.78        19.89        35.24        37.74         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
       22.82        32.65        31.04        31.20        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       11.61        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       26.50        29.46         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       18.67        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       18.67        18.12        15.39        16.41        14.30        21.60 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
       36.76         1.45        21.63        18.08        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.30        14.53         1.91        18.58        15.65        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        86.14        49.35        37.35        86.04        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.36               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            110.50             238.29 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             21.44              21.63 
[1] "0.4 - 110.5 (21.4)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.5"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1       12       19        0         9         9
  22Q GAIN WILD-TYPE       4      121      120        1        41        63
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  22Q GAIN MUTATED            9          0        3
  22Q GAIN WILD-TYPE         63         11       22
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 12                121
  STAGE IB                 19                120
  STAGE II                  0                  1
  STAGE IIA                 9                 41
  STAGE IIB                 9                 63
  STAGE IIIA                9                 63
  STAGE IIIB                0                 11
  STAGE IV                  3                 22
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED    15  39   6   1
  22Q GAIN WILD-TYPE 156 239  40  18
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               15                156
  T2               39                239
  T3                6                 40
  T4                1                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  22Q GAIN MUTATED    37  15     8
  22Q GAIN WILD-TYPE 296  81    68
D39V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                  37                296
  N1                  15                 81
  N2+N3                8                 68
[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"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    39   3
  22Q GAIN WILD-TYPE 310  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     39    3
  22Q GAIN WILD-TYPE  310   22
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               39                310
  1                3                 22
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    39  23
  22Q GAIN WILD-TYPE 237 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     39   23
  22Q GAIN WILD-TYPE  237  217
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               39                237
  MALE                 23                217
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    51   5
  22Q GAIN WILD-TYPE 359  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     51    5
  22Q GAIN WILD-TYPE  359   55
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                51                359
  YES                5                 55
[1] 2 2
[1] FALSE
D39V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  22Q GAIN MUTATED                            1
  22Q GAIN WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  22Q GAIN MUTATED                                   8
  22Q GAIN WILD-TYPE                                99
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                   46
  22Q GAIN WILD-TYPE                                                275
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  22Q GAIN MUTATED                                            0
  22Q GAIN WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  22Q GAIN MUTATED                                               3
  22Q GAIN WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  22Q GAIN MUTATED                                1
  22Q GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  22Q GAIN MUTATED                                    1
  22Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  22Q GAIN MUTATED                              0                             1
  22Q GAIN WILD-TYPE                            2                            22
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  22Q GAIN MUTATED                                 0
  22Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  22Q GAIN MUTATED                                               0
  22Q GAIN WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  22Q GAIN MUTATED                              1
  22Q GAIN WILD-TYPE                            9
D39V10, multiclass
                                                    clus
vv                                                   22Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               46
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     1
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   22Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                275
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
D39V12, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    45   1   1   2
  22Q GAIN WILD-TYPE 299  12   3  24
D39V13, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               45                299
  R1                1                 12
  R2                1                  3
  RX                2                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     1
  22Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           4    49
  22Q GAIN WILD-TYPE                        48   341
D39V14, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                       4                 48
  WHITE                                          49                341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  44
  22Q GAIN WILD-TYPE   6 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   44
  22Q GAIN WILD-TYPE    6  340
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               44                340
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    31  20
  XP GAIN WILD-TYPE 292 161
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               51               453 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               20               161 
$`XP GAIN MUTATED`
TCGA-05-4434 TCGA-44-2655 TCGA-55-A491 TCGA-05-4397 TCGA-05-5423 TCGA-35-5375 
       15.02        43.53        20.58        24.03         4.96         8.68 
TCGA-44-5645 TCGA-44-8117 TCGA-44-A47A TCGA-44-A4SU TCGA-49-AAR9 TCGA-4B-A93V 
       28.01        12.66        15.32        13.45         8.55         9.86 
TCGA-50-5066 TCGA-50-5933 TCGA-50-6591 TCGA-55-6543 TCGA-55-6712 TCGA-55-6970 
       47.41        78.67         3.91        14.30         5.62        15.25 
TCGA-55-6987 TCGA-55-7576 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8094 
       70.26        22.03        11.28        34.19        29.23        17.79 
TCGA-55-8096 TCGA-55-8615 TCGA-55-A494 TCGA-62-8394 TCGA-64-1680 TCGA-64-5775 
       23.64        14.66        15.81         4.57        37.02         2.04 
TCGA-67-6215 TCGA-69-7973 TCGA-69-7980 TCGA-73-4676 TCGA-73-4677 TCGA-75-6206 
        5.72         7.56        13.51         9.24         1.25        85.15 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 TCGA-78-7163 TCGA-78-7220 TCGA-78-7536 
      129.53        19.50        38.50       238.29        26.53         8.02 
TCGA-78-7539 TCGA-78-8640 TCGA-91-8499 TCGA-93-A4JN TCGA-97-7554 TCGA-97-8179 
       26.01       232.18         1.18        23.61        25.48        14.30 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-NJ-A7XG 
        1.91        18.58        20.28 

$`XP GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       26.01        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       26.30        38.10        42.08        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       16.04        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       21.47        41.69        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       19.66        19.73        17.98        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF 
       18.15        13.68        16.93        22.65        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        6.12        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       20.68        24.30        23.80         6.35        10.09        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       27.19         5.29        31.23         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 
        3.98        45.01        37.02         0.00        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 
       26.01        25.02        25.02        24.00        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
        9.04         2.04         0.46         7.40         5.98        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       38.24        38.89        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.37        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       36.07        18.87        23.64         8.55        15.98         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       55.89        53.29        55.33        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90        40.41       123.58       221.33       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 
       20.52        71.47       101.72        15.72        60.16        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        8.22         9.27        14.27         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 
       60.72        57.53        53.16        42.35        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 
       67.89        30.58        80.52        42.51        40.73        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
       24.99        40.54       107.21        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
       32.71         3.91        23.15        25.41        18.64        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       18.44        19.82        29.72        15.19        23.08         5.06 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       26.01        17.10        17.62         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 
       21.40         3.25         0.92        19.99        17.95        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        39.09        81.80        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       87.98        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 
       20.05        18.84        14.04        12.66        14.73         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
        6.64         6.12        22.68        13.61         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        4.41        13.41        14.01        13.45         4.24        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       19.43         8.42        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
       30.31        50.33        11.18        66.64        77.85        43.82 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        20.58        21.90        39.95       119.51 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
       88.14        31.20        53.33        39.35        10.55        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       28.34        26.50        29.46         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       19.82        22.45        17.46         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        61.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       18.67         5.39        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       34.85        36.76         1.45        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A8F4 
       35.47        32.48        19.00        14.30        14.53        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       24.36        14.10        11.15        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       74.33         0.13         1.64        47.08         0.49         0.43 
TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        59.11        16.87 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             1.18              0.00 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           238.29            221.33 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            15.81             22.03 
[1] "1.2 - 238.3 (15.8)" "0.0 - 221.3 (22.0)"
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         1       10       11        0         7         3
  XP GAIN WILD-TYPE       4      123      128        1        43        69
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XP GAIN MUTATED           10          3        7
  XP GAIN WILD-TYPE         62          8       18
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                10               123
  STAGE IB                11               128
  STAGE II                 0                 1
  STAGE IIA                7                43
  STAGE IIB                3                69
  STAGE IIIA              10                62
  STAGE IIIB               3                 8
  STAGE IV                 7                18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP GAIN MUTATED    12  31   4   6
  XP GAIN WILD-TYPE 159 247  42  13
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              12               159
  T2              31               247
  T3               4                42
  T4               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  XP GAIN MUTATED    30   9    13
  XP GAIN WILD-TYPE 303  87    63
D40V5, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  N0                 30               303
  N1                  9                87
  N2+N3              13                63
[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"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    33   7
  XP GAIN WILD-TYPE 316  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     33    7
  XP GAIN WILD-TYPE  316   18
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              33               316
  1               7                18
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    24  29
  XP GAIN WILD-TYPE 252 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     24   29
  XP GAIN WILD-TYPE  252  211
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              24               252
  MALE                29               211
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    38   8
  XP GAIN WILD-TYPE 372  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     38    8
  XP GAIN WILD-TYPE  372   52
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               38               372
  YES               8                52
[1] 2 2
[1] FALSE
D40V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XP GAIN MUTATED                            2
  XP GAIN WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XP GAIN MUTATED                                  11
  XP GAIN WILD-TYPE                                96
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XP GAIN MUTATED                                                   37
  XP GAIN WILD-TYPE                                                284
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XP GAIN MUTATED                                            1
  XP GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  XP GAIN MUTATED                                               0
  XP GAIN WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  XP GAIN MUTATED                                0
  XP GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  XP GAIN MUTATED                                    0
  XP GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  XP GAIN MUTATED                              0                             2
  XP GAIN WILD-TYPE                            2                            21
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  XP GAIN MUTATED                                 0
  XP GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  XP GAIN MUTATED                                               0
  XP GAIN WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  XP GAIN MUTATED                              0
  XP GAIN WILD-TYPE                           10
D40V10, multiclass
                                                    clus
vv                                                   XP GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              37
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   XP GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
D40V12, continuous
                   vv
clus                 R0  R1  R2  RX
  XP GAIN MUTATED    35   3   1   2
  XP GAIN WILD-TYPE 309  10   3  24
D40V13, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              35               309
  R1               3                10
  R2               1                 3
  RX               2                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  0     0
  XP GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                           9    37
  XP GAIN WILD-TYPE                        43   353
D40V14, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      9                43
  WHITE                                         37               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0  36
  XP GAIN WILD-TYPE   7 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   36
  XP GAIN WILD-TYPE    7  348
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              36               348
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    54  29
  XQ GAIN WILD-TYPE 269 152
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               83               421 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               29               152 
$`XQ GAIN MUTATED`
TCGA-05-4405 TCGA-05-4434 TCGA-44-2655 TCGA-55-7726 TCGA-95-7043 TCGA-97-8172 
       20.05        15.02        43.53        21.44        16.54        17.92 
TCGA-05-4397 TCGA-05-4426 TCGA-05-5423 TCGA-35-5375 TCGA-44-2659 TCGA-44-5645 
       24.03        26.01         4.96         8.68        44.94        28.01 
TCGA-44-6778 TCGA-44-8117 TCGA-44-A47A TCGA-44-A4SU TCGA-49-6767 TCGA-49-AARQ 
       61.28        12.66        15.32        13.45        22.26       221.33 
TCGA-4B-A93V TCGA-50-5066 TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6591 
        9.86        47.41        78.67        48.46        53.16         3.91 
TCGA-50-7109 TCGA-53-7626 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6970 
       10.13        30.54        30.58        14.30         5.62        15.25 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 
       70.26        28.67        11.28        34.19        19.82        29.23 
TCGA-55-8094 TCGA-55-8096 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8399 
       17.79        23.64        15.81        17.95         4.57        88.64 
TCGA-64-1676 TCGA-64-1680 TCGA-64-5775 TCGA-67-4679 TCGA-67-6215 TCGA-69-7980 
       56.81        37.02         2.04        14.73         5.72        13.51 
TCGA-71-6725 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 
        8.42        26.30         4.31         9.24         1.25        66.64 
TCGA-75-6206 TCGA-75-7025 TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 TCGA-78-7163 
       85.15       108.66       129.53        19.50        38.50       238.29 
TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-86-8055 TCGA-86-8075 
       31.20        26.01        10.55       232.18         4.08        22.82 
TCGA-86-8358 TCGA-86-A4P7 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JO TCGA-97-7554 
       21.47        13.64         1.18        23.61         1.08        25.48 
TCGA-97-7937 TCGA-97-8179 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4T4 
       18.54        14.30         1.91        18.58        38.63        86.04 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-S2-AA1A 
       14.10        19.13         0.49        20.28        16.87 

$`XQ GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       17.16        11.64       156.66        37.32        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       41.69        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       16.01        23.18        14.53         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       17.29         2.86        15.68        15.65        21.40        18.18 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
        6.35        10.09        21.83        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
        0.00        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       12.00        30.02        21.99        25.02        25.02        24.00 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
       29.00        22.03         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        5.98        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        4.37        46.98        44.42        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       33.30        28.37        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       23.18        32.45        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       36.07        18.87        23.64         8.55        15.98         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       55.89        53.29        55.33        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-50-5044 
       28.90         8.55        40.41       123.58       164.12        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 
       71.47       101.72        15.72        60.16        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
        9.27        14.27         8.45        15.12        60.72        57.53 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       42.35        25.55        11.05        12.16         6.21         0.72 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
       36.99        36.79        27.25        34.29        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 
       38.73        67.89        80.52        42.51        40.73        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       24.99        40.54       107.21        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
       22.03         3.91        23.15        25.41        18.64        17.65 
TCGA-55-7913 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8097 
       18.44        29.72        15.19        23.08         5.06        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
       21.40         3.25         0.92        19.99        39.98        42.38 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       39.09        81.80        38.37        87.98        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       51.25        28.47        20.05        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
       12.66         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
        5.42         7.56         6.05         4.41        13.41        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4668 
       13.45         4.24        26.73        19.43        23.38        15.35 
TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 
       30.31        50.33        11.18        77.85        43.82        49.84 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       36.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
       20.58        21.90        39.95       119.51        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 
       64.90        22.92         9.57       104.19        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
        8.02        53.33        39.35        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57        24.33         0.79        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
        0.62        28.34        26.50        29.46         3.81        24.23 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       19.82        22.45        17.46        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       63.52        61.48         0.59        15.91        18.67         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       18.12        15.39        16.41        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        21.57        21.63        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       19.00        14.30        14.53        15.65         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       58.45        49.35        37.35        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        11.05        24.36        11.15        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       74.33         0.13         1.64        47.08         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.49              0.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           238.29            164.12 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            19.82             21.99 
[1] "0.5 - 238.3 (19.8)" "0.0 - 164.1 (22.0)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         2       20       22        0        10         8
  XQ GAIN WILD-TYPE       3      113      117        1        40        64
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XQ GAIN MUTATED            9          3        9
  XQ GAIN WILD-TYPE         63          8       16
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                20               113
  STAGE IB                22               117
  STAGE II                 0                 1
  STAGE IIA               10                40
  STAGE IIB                8                64
  STAGE IIIA               9                63
  STAGE IIIB               3                 8
  STAGE IV                 9                16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED    26  49   5   6
  XQ GAIN WILD-TYPE 145 229  41  13
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              26               145
  T2              49               229
  T3               5                41
  T4               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  XQ GAIN MUTATED    56  17    12
  XQ GAIN WILD-TYPE 277  79    64
D41V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                 56               277
  N1                 17                79
  N2+N3              12                64
[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"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    57   9
  XQ GAIN WILD-TYPE 292  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     57    9
  XQ GAIN WILD-TYPE  292   16
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              57               292
  1               9                16
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    42  44
  XQ GAIN WILD-TYPE 234 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     42   44
  XQ GAIN WILD-TYPE  234  196
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              42               234
  MALE                44               196
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    67   7
  XQ GAIN WILD-TYPE 343  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     67    7
  XQ GAIN WILD-TYPE  343   53
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               67               343
  YES               7                53
[1] 2 2
[1] FALSE
D41V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XQ GAIN MUTATED                            3
  XQ GAIN WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XQ GAIN MUTATED                                  15
  XQ GAIN WILD-TYPE                                92
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                   61
  XQ GAIN WILD-TYPE                                                260
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XQ GAIN MUTATED                                            2
  XQ GAIN WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  XQ GAIN MUTATED                                               0
  XQ GAIN WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  XQ GAIN MUTATED                                0
  XQ GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  XQ GAIN MUTATED                                    1
  XQ GAIN WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  XQ GAIN MUTATED                              0                             4
  XQ GAIN WILD-TYPE                            2                            19
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  XQ GAIN MUTATED                                 0
  XQ GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  XQ GAIN MUTATED                                               0
  XQ GAIN WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  XQ GAIN MUTATED                              0
  XQ GAIN WILD-TYPE                           10
D41V10, multiclass
                                                    clus
vv                                                   XQ GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              61
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   XQ GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               260
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     19
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                      10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
D41V12, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    59   3   1   4
  XQ GAIN WILD-TYPE 285  10   3  22
D41V13, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              59               285
  R1               3                10
  R2               1                 3
  RX               4                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     1
  XQ GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          11    61
  XQ GAIN WILD-TYPE                        41   329
D41V14, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                     11                41
  WHITE                                         61               329
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  57
  XQ GAIN WILD-TYPE   7 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   57
  XQ GAIN WILD-TYPE    7  327
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              57               327
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    45  35
  1P LOSS WILD-TYPE 278 146
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               80               424 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               35               146 
$`1P LOSS MUTATED`
TCGA-05-4396 TCGA-05-5420 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-55-8090 
        9.96        15.02        11.08        17.16        11.64        19.66 
TCGA-55-8203 TCGA-55-8205 TCGA-55-A492 TCGA-95-7043 TCGA-97-8172 TCGA-MP-A4TD 
       17.98        19.69        19.59        16.54        17.92        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 
       50.07         3.98        37.02        47.05         2.99        14.96 
TCGA-05-4422 TCGA-38-4628 TCGA-44-2668 TCGA-44-3918 TCGA-44-5643 TCGA-44-6144 
       12.00        49.05        25.02        34.06        33.30        23.77 
TCGA-44-7660 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-AARE TCGA-50-5051 
       19.46        35.54        32.84         8.81        40.41        15.72 
TCGA-50-5936 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-53-7626 TCGA-55-1596 
        8.45        12.16         6.21        10.13        30.54        67.89 
TCGA-55-6972 TCGA-55-6986 TCGA-55-7283 TCGA-55-7913 TCGA-55-8507 TCGA-55-8508 
       53.65       107.21        20.02        18.44        13.74        20.28 
TCGA-55-8615 TCGA-55-A48Y TCGA-62-8398 TCGA-62-8402 TCGA-62-A46S TCGA-62-A46U 
       14.66        20.71        14.60        49.25        54.35        67.96 
TCGA-64-5774 TCGA-64-5778 TCGA-69-7761 TCGA-69-7973 TCGA-73-4659 TCGA-73-4666 
       87.98        42.90         6.12         7.56        23.38        26.30 
TCGA-73-4675 TCGA-73-4677 TCGA-73-A9RS TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 
       30.31         1.25        11.18       100.57         5.69        20.58 
TCGA-78-7149 TCGA-78-7153 TCGA-78-7159 TCGA-78-7160 TCGA-80-5608 TCGA-86-6562 
      129.53       119.51        64.90        22.92        93.11        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-8278 TCGA-86-8669 TCGA-86-A4JF TCGA-91-8499 
        5.88        31.13        31.04        30.84        24.23         1.18 
TCGA-95-7567 TCGA-95-A4VP TCGA-97-7554 TCGA-97-8174 TCGA-MP-A4T7 TCGA-MP-A4TJ 
       18.67        19.89        25.48         5.39         5.49        11.15 
TCGA-NJ-A4YQ TCGA-NJ-A7XG 
       47.08        20.28 

$`1P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       43.53        38.10        42.08        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 
       18.31        29.00        29.23         9.37        46.72        16.04 
TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
      156.66        37.32        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8204 TCGA-55-8207 
       14.53        21.44         6.15        19.73        16.93        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF 
       18.15        13.68        16.93        22.65        20.58        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
        6.12        17.29         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       18.18        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       23.80         6.35        10.09        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 
       31.23         2.43        45.01         0.00        24.03        19.00 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       29.98        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        0.46         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       37.71        44.61         4.37        46.98        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 
       42.77         3.19        37.15        38.24        38.89        33.73 
TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       26.56        28.37        28.01        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 
       23.18        32.45        61.28        16.44        22.72         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
       28.11        28.57        12.66        14.07        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       55.89        53.29        55.33        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90         8.55       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
        9.86        20.52        71.47       101.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 
       49.28         8.22         9.27        14.27        78.67        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       25.55        11.05         0.72        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 
       34.29        13.94        35.21        38.73        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       40.54        70.26        28.67        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        3.91        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 
       15.42        17.56        15.72        14.47         0.36        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 
       19.96        26.01        17.10        17.62         1.58        12.33 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       21.40         3.25         0.92        15.81        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
        4.57        39.98        42.38        88.64        47.80        19.53 
TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       56.71        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
       56.81        39.09        81.80        37.02        38.37         2.04 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       28.41        51.25        28.47        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         5.42         6.05         4.41        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K 
       13.51        14.01        13.45         4.24        26.73        19.43 
TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-7499 TCGA-75-5125 
        8.42        15.35         4.31         9.24        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
      163.10        27.16        19.27        21.90        39.95        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       38.50        32.09         5.88         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       27.09        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       22.82        32.65        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       11.61        13.91        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46         3.81        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
        1.15        16.60        14.27        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 
       23.61         1.08        19.00        41.82        12.39        27.29 
TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
        2.76        42.25        64.60        63.52        61.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.59        15.91        18.67        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        18.58        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05        74.33         0.13         1.64         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82        59.11        16.87 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.18              0.00 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           129.53            238.29 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           19.955            22.010 
[1] "1.2 - 129.5 (20.0)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1.3"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         0       16       16        0         7        10
  1P LOSS WILD-TYPE       5      117      123        1        43        62
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1P LOSS MUTATED           22          4        4
  1P LOSS WILD-TYPE         50          7       21
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                16               117
  STAGE IB                16               123
  STAGE II                 0                 1
  STAGE IIA                7                43
  STAGE IIB               10                62
  STAGE IIIA              22                50
  STAGE IIIB               4                 7
  STAGE IV                 4                21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED    20  45   9   6
  1P LOSS WILD-TYPE 151 233  37  13
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              20               151
  T2              45               233
  T3               9                37
  T4               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  1P LOSS MUTATED    41  17    21
  1P LOSS WILD-TYPE 292  79    55
D42V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                 41               292
  N1                 17                79
  N2+N3              21                55
[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"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    64   4
  1P LOSS WILD-TYPE 285  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     64    4
  1P LOSS WILD-TYPE  285   21
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              64               285
  1               4                21
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    39  41
  1P LOSS WILD-TYPE 237 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     39   41
  1P LOSS WILD-TYPE  237  199
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              39               237
  MALE                41               199
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    68   7
  1P LOSS WILD-TYPE 342  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     68    7
  1P LOSS WILD-TYPE  342   53
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               68               342
  YES               7                53
[1] 2 2
[1] FALSE
D42V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1P LOSS MUTATED                            3
  1P LOSS WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1P LOSS MUTATED                                  19
  1P LOSS WILD-TYPE                                88
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                   48
  1P LOSS WILD-TYPE                                                273
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1P LOSS MUTATED                                            0
  1P LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1P LOSS MUTATED                                               3
  1P LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1P LOSS MUTATED                                0
  1P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  1P LOSS MUTATED                                    0
  1P LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  1P LOSS MUTATED                              0                             4
  1P LOSS WILD-TYPE                            2                            19
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  1P LOSS MUTATED                                 1
  1P LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  1P LOSS MUTATED                                               0
  1P LOSS WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  1P LOSS MUTATED                              2
  1P LOSS WILD-TYPE                            8
D42V10, multiclass
                                                    clus
vv                                                   1P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              48
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   1P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 88
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               273
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     19
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
D42V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    54   1   1   4
  1P LOSS WILD-TYPE 290  12   3  22
D42V13, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              54               290
  R1               1                12
  R2               1                 3
  RX               4                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           7    59
  1P LOSS WILD-TYPE                        45   331
D42V14, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      7                45
  WHITE                                         59               331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  57
  1P LOSS WILD-TYPE   7 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   57
  1P LOSS WILD-TYPE    7  327
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              57               327
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    16  12
  1Q LOSS WILD-TYPE 307 169
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               476 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               169 
$`1Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4427 TCGA-49-6745 TCGA-49-6761 TCGA-55-8090 TCGA-55-8205 
        9.96        26.01        17.16        11.64        19.66        19.69 
TCGA-95-7043 TCGA-05-4422 TCGA-44-5643 TCGA-44-7660 TCGA-49-4507 TCGA-50-5936 
       16.54        12.00        33.30        19.46         8.81         8.45 
TCGA-50-6594 TCGA-50-7109 TCGA-55-6986 TCGA-55-8507 TCGA-55-8620 TCGA-62-8402 
       12.16        10.13       107.21        13.74        12.33        49.25 
TCGA-64-5774 TCGA-64-5778 TCGA-73-4666 TCGA-75-7027 TCGA-78-7146 TCGA-86-6851 
       87.98        42.90        26.30       100.57         5.69         5.88 
TCGA-86-8278 TCGA-91-8499 TCGA-97-8174 TCGA-MP-A4TF 
       31.04         1.18         5.39        11.05 

$`1Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 
       19.96        14.01         8.02        20.05         9.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       43.53        38.10        42.08        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 
       23.18        14.53        21.44         6.15        19.73        17.98 
TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       16.93        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 
       13.71        16.18         1.45         6.12        17.29         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       10.09        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
        4.96        29.00        22.03         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       49.05        44.61         4.37        46.98        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       34.06        33.73        26.56        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       16.44        22.72         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       35.54        14.07        32.84        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       53.29        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        40.41       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        9.86        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
        3.91        25.55        11.05         6.21         0.72        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       38.73        67.89        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        3.91        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
       14.66         1.58        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        19.99        17.95         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
       56.81        39.09        81.80        37.02        38.37         2.04 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       28.41        51.25        28.47        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 
       26.73        19.43         8.42        23.38        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 
       30.31         9.24         1.25        50.33        11.18        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        22.82        32.65        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
        0.62        28.34        26.50        29.46         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
       14.27        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 
       18.54         0.59        15.91        18.67        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        21.63        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.30        14.53         1.91        18.58        15.65        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
       58.85         5.49        41.59        29.46        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       11.15        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        47.08         0.49         0.43        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.18              0.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           107.21            238.29 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            15.14             22.01 
[1] "1.2 - 107.2 (15.1)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1.4"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        5        6        0         4         2
  1Q LOSS WILD-TYPE       5      128      133        1        46        70
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1Q LOSS MUTATED            8          1        2
  1Q LOSS WILD-TYPE         64         10       23
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 5               128
  STAGE IB                 6               133
  STAGE II                 0                 1
  STAGE IIA                4                46
  STAGE IIB                2                70
  STAGE IIIA               8                64
  STAGE IIIB               1                10
  STAGE IV                 2                23
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED     9  16   2   1
  1Q LOSS WILD-TYPE 162 262  44  18
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               9               162
  T2              16               262
  T3               2                44
  T4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  1Q LOSS MUTATED    15   6     7
  1Q LOSS WILD-TYPE 318  90    69
D43V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0                 15               318
  N1                  6                90
  N2+N3               7                69
[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"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    21   2
  1Q LOSS WILD-TYPE 328  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     21    2
  1Q LOSS WILD-TYPE  328   23
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              21               328
  1               2                23
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    14  14
  1Q LOSS WILD-TYPE 262 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14   14
  1Q LOSS WILD-TYPE  262  226
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              14               262
  MALE                14               226
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    22   4
  1Q LOSS WILD-TYPE 388  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     22    4
  1Q LOSS WILD-TYPE  388   56
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               22               388
  YES               4                56
[1] 2 2
[1] FALSE
D43V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1Q LOSS MUTATED                            0
  1Q LOSS WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1Q LOSS MUTATED                                   7
  1Q LOSS WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                   17
  1Q LOSS WILD-TYPE                                                304
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1Q LOSS MUTATED                                            0
  1Q LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1Q LOSS MUTATED                                               2
  1Q LOSS WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1Q LOSS MUTATED                                0
  1Q LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  1Q LOSS MUTATED                                    0
  1Q LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  1Q LOSS MUTATED                              0                             1
  1Q LOSS WILD-TYPE                            2                            22
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  1Q LOSS MUTATED                                 0
  1Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  1Q LOSS MUTATED                                               0
  1Q LOSS WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  1Q LOSS MUTATED                              1
  1Q LOSS WILD-TYPE                            9
D43V10, multiclass
                                                    clus
vv                                                   1Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   1Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               304
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
D43V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    17   0   0   0
  1Q LOSS WILD-TYPE 327  13   4  26
D43V13, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              17               327
  R1               0                13
  R2               0                 4
  RX               0                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     0
  1Q LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           2    22
  1Q LOSS WILD-TYPE                        50   368
D43V14, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                50
  WHITE                                         22               368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  21
  1Q LOSS WILD-TYPE   7 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   21
  1Q LOSS WILD-TYPE    7  363
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              21               363
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    15   7
  2P LOSS WILD-TYPE 308 174
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               22               482 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7               174 
$`2P LOSS MUTATED`
TCGA-55-7726 TCGA-97-8172 TCGA-MP-A4T8 TCGA-44-2665 TCGA-44-6778 TCGA-50-5936 
       21.44        17.92         5.29        42.77        61.28         8.45 
TCGA-50-6591 TCGA-50-7109 TCGA-55-6986 TCGA-55-8097 TCGA-62-8397 TCGA-62-A471 
        3.91        10.13       107.21        15.65        42.38        40.96 
TCGA-64-1676 TCGA-67-3772 TCGA-71-6725 TCGA-73-7499 TCGA-78-7153 TCGA-78-7220 
       56.81        18.84         8.42        50.33       119.51        26.53 
TCGA-86-8074 TCGA-97-7937 TCGA-97-8174 TCGA-L4-A4E5 
        0.79        18.54         5.39        19.00 

$`2P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 
       27.78        86.01        18.31        29.00        29.23         9.37 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       11.08        46.72        16.04        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       37.32        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 
       15.68        15.65        21.40        18.18        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       17.75        20.68        24.30        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       21.83        27.19        31.23         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
        3.98        45.01        37.02         0.00        24.03        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
       29.00        22.03         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2666 
       44.61         4.37        46.98        44.42        44.94         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       25.02        37.15        38.24        38.89        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       23.15        21.63        23.18        32.45        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       53.29        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        40.41       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        9.86        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
       25.55        11.05        12.16         6.21         0.72        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       38.73        67.89        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        3.91        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 
       23.08         5.06        17.79        23.64        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        19.99        17.95         4.57        39.98 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 
       54.35        67.96        72.30        13.61        39.25        29.92 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       39.09        81.80        37.02        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       42.90        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       26.73        19.43        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        11.18        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       24.33        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
        0.62        28.34        26.50        29.46         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 
       25.48         0.59        15.91        18.67        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       21.57        21.63        18.08        35.47        32.48        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        18.58        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       11.15        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        47.08         0.49         0.43        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.79              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           119.51            238.29 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            18.92             21.73 
[1] "0.8 - 119.5 (18.9)" "0.0 - 238.3 (21.7)"
[1] "hr=" "1.3"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         1        5        9        0         2         3
  2P LOSS WILD-TYPE       4      128      130        1        48        69
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2P LOSS MUTATED            3          0        1
  2P LOSS WILD-TYPE         69         11       24
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 5               128
  STAGE IB                 9               130
  STAGE II                 0                 1
  STAGE IIA                2                48
  STAGE IIB                3                69
  STAGE IIIA               3                69
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     7  16   1   0
  2P LOSS WILD-TYPE 164 262  45  19
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               7               164
  T2              16               262
  T3               1                45
  T4               0                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  2P LOSS MUTATED    18   3     3
  2P LOSS WILD-TYPE 315  93    73
D44V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0                 18               315
  N1                  3                93
  N2+N3               3                73
[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"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    19   1
  2P LOSS WILD-TYPE 330  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     19    1
  2P LOSS WILD-TYPE  330   24
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              19               330
  1               1                24
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    15   9
  2P LOSS WILD-TYPE 261 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     15    9
  2P LOSS WILD-TYPE  261  231
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              15               261
  MALE                 9               231
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    20   1
  2P LOSS WILD-TYPE 390  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     20    1
  2P LOSS WILD-TYPE  390   59
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               20               390
  YES               1                59
[1] 2 2
[1] FALSE
D44V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2P LOSS MUTATED                            1
  2P LOSS WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2P LOSS MUTATED                                   5
  2P LOSS WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                   13
  2P LOSS WILD-TYPE                                                308
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2P LOSS MUTATED                                            0
  2P LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  2P LOSS MUTATED                                               1
  2P LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  2P LOSS MUTATED                                0
  2P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  2P LOSS MUTATED                                    1
  2P LOSS WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  2P LOSS MUTATED                              0                             2
  2P LOSS WILD-TYPE                            2                            21
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  2P LOSS MUTATED                                 0
  2P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  2P LOSS MUTATED                                               0
  2P LOSS WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  2P LOSS MUTATED                              1
  2P LOSS WILD-TYPE                            9
D44V10, multiclass
                                                    clus
vv                                                   2P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   2P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               308
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
D44V12, continuous
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    13   0   0   2
  2P LOSS WILD-TYPE 331  13   4  24
D44V13, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              13               331
  R1               0                13
  R2               0                 4
  RX               2                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           1    19
  2P LOSS WILD-TYPE                        51   371
D44V14, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      1                51
  WHITE                                         19               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  17
  2P LOSS WILD-TYPE   7 367
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   17
  2P LOSS WILD-TYPE    7  367
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              17               367
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    19   5
  2Q LOSS WILD-TYPE 304 176
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               24               480 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5               176 
$`2Q LOSS MUTATED`
TCGA-55-1595 TCGA-97-8172 TCGA-MP-A4T8 TCGA-44-2656 TCGA-44-6778 TCGA-49-AARO 
       48.62        17.92         5.29        46.98        61.28       123.58 
TCGA-50-5936 TCGA-50-5946 TCGA-50-6591 TCGA-55-6986 TCGA-55-8097 TCGA-62-8397 
        8.45        53.16         3.91       107.21        15.65        42.38 
TCGA-64-1676 TCGA-67-3772 TCGA-69-7760 TCGA-71-6725 TCGA-73-7499 TCGA-75-5125 
       56.81        18.84         6.64         8.42        50.33        66.64 
TCGA-75-5147 TCGA-78-7153 TCGA-86-8054 TCGA-86-8074 TCGA-97-7554 TCGA-L4-A4E5 
       43.82       119.51        37.74         0.79        25.48        19.00 

$`2Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 
       27.78        86.01        18.31        29.00        29.23         9.37 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       11.08        46.72        16.04        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 
       37.32        40.60        21.47        41.69        23.05         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 
       15.68        15.65        21.40        18.18        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       17.75        20.68        24.30        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       21.83        27.19        31.23         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
        3.98        45.01        37.02         0.00        24.03        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
       29.00        22.03         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 
       44.61         4.37        44.42        44.94        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       25.02        37.15        38.24        38.89        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       23.15        21.63        23.18        32.45        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       53.29        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       28.90         8.55        40.41       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 
       49.28         8.22         9.27        14.27        78.67        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 
       48.46        60.72        57.53        42.35        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       67.89        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 
       45.34        32.71        92.81        24.99        40.54        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       23.15        25.41        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
        5.06        17.79        23.64        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
       15.81        19.99        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       39.09        81.80        37.02        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       42.90        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
       14.04        12.66        14.73         5.72         4.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
       13.41        13.51        14.01        13.45         4.24        26.73 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       19.43        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 
        9.24         1.25        11.18        77.85        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
       19.27        20.58       129.53        21.90        39.95        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
       35.24         4.08         4.57        24.33        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       29.46         3.81        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        61.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       24.56        34.85        36.76         1.45        21.57        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       18.08        35.47        32.48        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       18.58        15.65        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       29.46        11.05        24.36        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.49         0.43        19.82        20.28        59.11        16.87 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.79              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           123.58            238.29 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            40.06             21.52 
[1] "0.8 - 123.6 (40.1)" "0.0 - 238.3 (21.5)"
[1] "hr=" "2.6"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         1        6        9        0         1         4
  2Q LOSS WILD-TYPE       4      127      130        1        49        68
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2Q LOSS MUTATED            3          0        1
  2Q LOSS WILD-TYPE         69         11       24
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 6               127
  STAGE IB                 9               130
  STAGE II                 0                 1
  STAGE IIA                1                49
  STAGE IIB                4                68
  STAGE IIIA               3                69
  STAGE IIIB               0                11
  STAGE IV                 1                24
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     8  15   2   0
  2Q LOSS WILD-TYPE 163 263  44  19
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               8               163
  T2              15               263
  T3               2                44
  T4               0                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  2Q LOSS MUTATED    19   3     3
  2Q LOSS WILD-TYPE 314  93    73
D45V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                 19               314
  N1                  3                93
  N2+N3               3                73
[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"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    20   1
  2Q LOSS WILD-TYPE 329  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     20    1
  2Q LOSS WILD-TYPE  329   24
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              20               329
  1               1                24
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    16   9
  2Q LOSS WILD-TYPE 260 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     16    9
  2Q LOSS WILD-TYPE  260  231
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              16               260
  MALE                 9               231
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    22   1
  2Q LOSS WILD-TYPE 388  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     22    1
  2Q LOSS WILD-TYPE  388   59
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               22               388
  YES               1                59
[1] 2 2
[1] FALSE
D45V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2Q LOSS MUTATED                            2
  2Q LOSS WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2Q LOSS MUTATED                                   5
  2Q LOSS WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                   12
  2Q LOSS WILD-TYPE                                                309
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2Q LOSS MUTATED                                            0
  2Q LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  2Q LOSS MUTATED                                               1
  2Q LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  2Q LOSS MUTATED                                1
  2Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  2Q LOSS MUTATED                                    0
  2Q LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  2Q LOSS MUTATED                              0                             3
  2Q LOSS WILD-TYPE                            2                            20
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  2Q LOSS MUTATED                                 0
  2Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  2Q LOSS MUTATED                                               0
  2Q LOSS WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  2Q LOSS MUTATED                              1
  2Q LOSS WILD-TYPE                            9
D45V10, multiclass
                                                    clus
vv                                                   2Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              12
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   2Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               309
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
D45V12, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    14   0   0   1
  2Q LOSS WILD-TYPE 330  13   4  25
D45V13, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              14               330
  R1               0                13
  R2               0                 4
  RX               1                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     2
  2Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           2    17
  2Q LOSS WILD-TYPE                        50   373
D45V14, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                      2                50
  WHITE                                         17               373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  17
  2Q LOSS WILD-TYPE   7 367
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   17
  2Q LOSS WILD-TYPE    7  367
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              17               367
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   135  73
  3P LOSS WILD-TYPE 188 108
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              208               296 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               73               108 
$`3P LOSS MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-5420 TCGA-38-6178 TCGA-44-6147 TCGA-44-6776 
       19.96         8.02        15.02        14.73        27.78        86.01 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-7573 
      156.66        40.60        21.47        41.69        48.62        16.01 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8204 TCGA-55-A491 
       23.18        21.44         6.15        19.66        16.93        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-8660 
       19.59        20.19        13.87        82.68        39.09        10.55 
TCGA-91-A4BC TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-97-A4LX TCGA-97-A4M7 
        1.45        16.54        15.68        15.65        20.19        20.68 
TCGA-J2-8192 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 
       24.30         5.29         2.43        10.09        50.07        45.01 
TCGA-05-4390 TCGA-05-4397 TCGA-05-4415 TCGA-05-4432 TCGA-05-5425 TCGA-05-5715 
       37.02        24.03         2.99        25.02        29.00         2.04 
TCGA-35-4122 TCGA-38-4627 TCGA-38-4628 TCGA-44-2656 TCGA-44-2657 TCGA-44-2668 
        7.40        37.71        49.05        46.98        44.42        25.02 
TCGA-44-3917 TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 
       38.89        23.77        19.56        21.63        61.28        16.44 
TCGA-44-7660 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-49-4505 
       19.46        23.64        12.66         8.55        15.98        14.07 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 
       32.84        29.46        55.89        55.33        22.26        73.12 
TCGA-50-5049 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 
      101.72        49.28         8.22        14.27         8.45        15.12 
TCGA-50-5941 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       48.46         3.91        11.05        12.16         6.21         0.72 
TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 TCGA-55-6968 TCGA-55-6975 
       34.29        30.54        38.73        67.89        42.51         3.88 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 
       32.71        92.81        40.54        20.02        27.09        22.03 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-8094 TCGA-55-8206 
        3.91        11.28        34.19        18.44        17.79        29.19 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.36        13.74        20.28        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
        1.58        12.33        21.40        19.99         4.57        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46Y 
       14.60        88.64        47.80        19.53        56.71        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 
       39.25        40.96        56.81        39.09        87.98        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-69-7763 
       51.25        28.47        20.05        20.05        18.84        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 
       13.61         5.42         7.56        13.41        14.01         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS 
       23.38        26.30         4.31        30.31        50.33        11.18 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 
       77.85        43.82        36.66       100.57         5.69        20.58 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
       64.90        22.92        88.14        26.53        31.20         8.02 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       26.01        10.55       232.18        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 
        5.88        31.13        38.04        19.89        37.74        24.33 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 
       31.04        23.05        21.47        11.61        30.84         3.81 
TCGA-86-A4JF TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 
       24.23        41.36         1.97        10.19         2.60        27.68 
TCGA-91-8499 TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-A4VP 
        1.18        17.46        41.82        18.67        27.29        19.89 
TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M0 
       42.25        25.48        18.54         5.39        16.41        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A50W 
       19.76        20.84        18.67        32.48        19.00        14.53 
TCGA-L9-A7SV TCGA-MP-A4T6 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YF 
       18.58        58.85        11.05        14.10        11.15        71.05 
TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       47.08         0.43        20.28        59.11 

$`3P LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       14.01         9.96        20.05         9.01        26.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       28.41        35.28        11.64        26.30        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-7661 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN 
       42.08        23.93        18.31        17.16        11.64        37.32 
TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 TCGA-55-8091 
       23.05         5.79         7.79         7.99        14.53        19.73 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       17.98        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-64-1677 TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 
       22.65        20.65        52.60         8.48        50.24        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-A4VK 
       13.71        16.18         6.12        17.29         2.86        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A443 
       18.18        17.92        20.52        17.75        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-05-4250 TCGA-05-4395 
       10.09        21.83        27.19        31.23         3.98         0.00 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       47.05        19.00        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 
       21.99        26.01        25.02        24.00         4.96        22.03 
TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        9.04         0.46         5.98         8.68        97.74       120.79 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
       44.61         4.37        44.94        42.77         3.19        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 
       28.01        23.15        23.18        32.45        22.72         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       36.07        18.87        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4507 TCGA-49-4512 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR4 
        8.81        29.75        53.29        22.26        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 
       20.52        71.47        15.72        60.16        47.41         9.27 
TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
       78.67        60.72        57.53        53.16        42.35        25.55 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ 
       10.13        36.99        36.79        27.25        13.94        35.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       30.58        14.30        80.52         5.62        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 TCGA-55-6986 
       46.03        53.65        69.34        45.34        24.99       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       70.26        28.67        32.71        23.15        25.41        18.64 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        5.06        23.64        15.65        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-A48Y 
       15.72        14.47        17.72        19.96        26.01        20.71 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8402 
        3.25         0.92        15.81        17.95        39.98        49.25 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 
       54.35        67.96        72.30        29.92        81.80        37.02 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       38.37         2.04        42.90        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 TCGA-69-7978 
        5.72         4.64         6.64         6.12         6.05         4.41 
TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4668 
       13.51        13.45         4.24        26.73        19.43        15.35 
TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 
        9.24         1.25        66.64        85.15        49.84       108.66 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10        27.16        19.27       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 
      119.51        19.50        38.50        32.09         5.88         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 
      104.19       238.29        53.33        39.35        39.75        77.59 
TCGA-78-8662 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 
      110.50        34.39        20.55        32.78        35.24         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8359 
        4.57         0.79        22.82        32.65        31.20        14.60 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
       13.64        26.47        10.62        12.23         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO 
       16.60        14.27        19.82        22.45        23.61         1.08 
TCGA-93-A4JP TCGA-95-7944 TCGA-95-8494 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       19.00        12.39         2.76        64.60        63.52        61.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
        0.59        15.91        18.67        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       21.60        20.58        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A5IP 
       21.57        21.63        18.08        35.47        14.30         1.91 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       15.65        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH 
       37.35        86.04         5.49        41.59        29.46        24.36 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       19.13        73.91        74.33         0.13         1.64         0.49 
TCGA-NJ-A55R TCGA-S2-AA1A 
       19.82        16.87 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.36              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           232.18            238.29 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           21.120            22.095 
[1] "0.4 - 232.2 (21.1)" "0.0 - 238.3 (22.1)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         2       51       55        1        27        28
  3P LOSS WILD-TYPE       3       82       84        0        23        44
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3P LOSS MUTATED           31          3       11
  3P LOSS WILD-TYPE         41          8       14
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                51                82
  STAGE IB                55                84
  STAGE II                 1                 0
  STAGE IIA               27                23
  STAGE IIB               28                44
  STAGE IIIA              31                41
  STAGE IIIB               3                 8
  STAGE IV                11                14
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED    72 124  10   5
  3P LOSS WILD-TYPE  99 154  36  14
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              72                99
  T2             124               154
  T3              10                36
  T4               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  3P LOSS MUTATED   129  45    33
  3P LOSS WILD-TYPE 204  51    43
D46V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                129               204
  N1                 45                51
  N2+N3              33                43
[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"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   147  11
  3P LOSS WILD-TYPE 202  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    147   11
  3P LOSS WILD-TYPE  202   14
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             147               202
  1              11                14
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   113  98
  3P LOSS WILD-TYPE 163 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    113   98
  3P LOSS WILD-TYPE  163  142
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             113               163
  MALE                98               142
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   174  24
  3P LOSS WILD-TYPE 236  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    174   24
  3P LOSS WILD-TYPE  236   36
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO              174               236
  YES              24                36
[1] 2 2
[1] FALSE
D46V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3P LOSS MUTATED                            8
  3P LOSS WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3P LOSS MUTATED                                  50
  3P LOSS WILD-TYPE                                57
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                  132
  3P LOSS WILD-TYPE                                                189
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3P LOSS MUTATED                                            0
  3P LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  3P LOSS MUTATED                                               6
  3P LOSS WILD-TYPE                                            13
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  3P LOSS MUTATED                                1
  3P LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  3P LOSS MUTATED                                    1
  3P LOSS WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  3P LOSS MUTATED                              0                             6
  3P LOSS WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  3P LOSS MUTATED                                 1
  3P LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  3P LOSS MUTATED                                               1
  3P LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3P LOSS MUTATED                              5
  3P LOSS WILD-TYPE                            5
D46V10, multiclass
                                                    clus
vv                                                   3P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             132
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    6
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    6
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     5
                                                    clus
vv                                                   3P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 57
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               189
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     13
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
D46V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED   140   2   1   6
  3P LOSS WILD-TYPE 204  11   3  20
D46V13, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0             140               204
  R1               2                11
  R2               1                 3
  RX               6                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     3
  3P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          23   162
  3P LOSS WILD-TYPE                        29   228
D46V14, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                     23                29
  WHITE                                        162               228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2 165
  3P LOSS WILD-TYPE   5 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2  165
  3P LOSS WILD-TYPE    5  219
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             165               219
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    91  51
  3Q LOSS WILD-TYPE 232 130
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              142               362 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               51               130 
$`3Q LOSS MUTATED`
TCGA-05-5420 TCGA-44-6776 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 
       15.02        86.01        29.23         9.37        11.08        16.04 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-7573 TCGA-55-8090 
       40.60        21.47        41.69        48.62        16.01        19.66 
TCGA-55-8203 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 
       17.98        19.59        20.19        13.87        82.68        39.09 
TCGA-78-8660 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-J2-8192 TCGA-J2-8194 
       10.55        15.65        21.40        17.92        24.30        23.80 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4390 TCGA-05-4397 
        5.29         2.43        10.09        50.07        37.02        24.03 
TCGA-05-4415 TCGA-05-4432 TCGA-05-5715 TCGA-35-4122 TCGA-38-4628 TCGA-44-2656 
        2.99        25.02         2.04         7.40        49.05        46.98 
TCGA-44-3917 TCGA-44-6144 TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 TCGA-44-7672 
       38.89        23.77        21.63        61.28        16.44        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-49-4506 TCGA-49-4510 TCGA-49-AAQV 
       12.66         8.55        15.98        32.84        29.46        22.26 
TCGA-50-5068 TCGA-50-5936 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       49.28         8.45         3.91        11.05        12.16         6.21 
TCGA-50-6673 TCGA-55-1596 TCGA-55-5899 TCGA-55-6712 TCGA-55-6975 TCGA-55-6982 
        0.72        67.89        30.58         5.62         3.88        32.71 
TCGA-55-6983 TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 
       92.81        20.02        22.03         3.91        11.28        34.19 
TCGA-55-8094 TCGA-55-8206 TCGA-55-8508 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
       17.79        29.19        20.28        17.10        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
       12.33        21.40        19.99         4.57        42.38        14.60 
TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46Y TCGA-62-A470 TCGA-64-1676 
       88.64        19.53        56.71        13.61        39.25        56.81 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 
       39.09        87.98        28.41        51.25        20.05        20.05 
TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-8253 
       18.84        22.68        13.61         5.42         6.05        14.01 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-A9RS TCGA-75-5146 
        8.42        23.38        26.30        30.31        11.18        77.85 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7148 TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 
       36.66       100.57        20.58        22.92        88.14        26.53 
TCGA-78-7535 TCGA-78-7539 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       31.20        26.01        93.11        27.09        12.36         5.88 
TCGA-86-7713 TCGA-86-7954 TCGA-86-8054 TCGA-86-8280 TCGA-86-8585 TCGA-86-A4D0 
       38.04        19.89        37.74        23.05        11.61         3.81 
TCGA-91-6847 TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-A4VP TCGA-97-7546 
       27.68        17.46        41.82        18.67        19.89        42.25 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M0 TCGA-97-A4M1 
       25.48        18.54         5.39        16.41        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A50W TCGA-MP-A4T6 
       20.84        18.67        32.48        19.00        14.53        58.85 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A55O TCGA-NJ-A7XG 
       14.10        11.15         0.43        20.28 

$`3Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       26.01        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 
       26.30        43.53        38.10        42.08        23.93        27.78 
TCGA-44-7661 TCGA-44-7670 TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       18.31        29.00        46.72        17.16        11.64       156.66 
TCGA-49-AARN TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 
       37.32        23.05         5.79         7.79         7.99        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 
       14.53        21.44         6.15        19.73        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-64-1677 TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 
       20.65        52.60         8.48        50.24        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       15.68        18.18        20.19        20.52        17.75        20.68 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-05-4250 
        6.35        10.09        21.83        27.19        31.23         3.98 
TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 
       45.01         0.00        47.05        19.00        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 
       12.00        30.02        21.99        26.01        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 
        4.96        29.00        22.03         9.04         0.46         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F 
        8.68        97.74       120.79        37.71        44.61         4.37 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 
       28.01        19.56        23.15        23.18        32.45        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B 
       19.46         7.17        36.07        18.87        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
       12.66        35.54        14.07         8.81        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       53.29        55.33        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 
        8.22         9.27        14.27        78.67        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-7109 
       60.72        57.53        53.16        42.35        25.55        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 
       35.21        38.73        14.30        80.52        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 
       15.25        46.03        53.65        69.34        45.34        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 
       40.54       107.21        70.26        28.67        27.09        32.71 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       23.15        25.41        18.64        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 
       29.23        29.72        15.19        23.08         5.06        23.64 
TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       15.65        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
        0.36        13.74        17.72        19.96        26.01        17.62 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 
       20.71         3.25         0.92        15.81        17.95        39.98 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
       49.25        47.80        54.35        67.96        72.30        40.96 
TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       29.92        81.80        37.02        38.37         2.04        42.90 
TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        6.64         6.12         7.56         4.41        13.41        13.51 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4668 TCGA-73-4670 
       13.45         4.24        26.73        19.43        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 
        9.24         1.25        50.33        66.64        43.82        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       49.84       108.66       163.10        27.16         5.69        19.27 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       32.09         5.88        64.90         9.57       104.19       238.29 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
        8.02        53.33        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
       77.59       110.50        31.13        34.39        20.55        32.78 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       35.24         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       32.65        31.04        31.20        21.47        14.60        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        12.23         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO 
       14.27         1.18        19.82        22.45        23.61         1.08 
TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7547 TCGA-97-7552 
       19.00        12.39        27.29         2.76        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 
       61.48         0.59        15.91        18.67        18.12        15.39 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       14.30        21.60        20.58        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 
        1.45        21.57        21.63        18.08        35.47        14.30 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        1.91        18.58        15.65        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
       58.45        49.35        37.35        86.04         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        11.05        24.36        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R 
       74.33         0.13         1.64        47.08         0.49        19.82 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.43              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           100.57            238.29 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           20.235            22.550 
[1] "0.4 - 100.6 (20.2)" "0.0 - 238.3 (22.5)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2       30       33        1        18        22
  3Q LOSS WILD-TYPE       3      103      106        0        32        50
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3Q LOSS MUTATED           26          3        6
  3Q LOSS WILD-TYPE         46          8       19
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                30               103
  STAGE IB                33               106
  STAGE II                 1                 0
  STAGE IIA               18                32
  STAGE IIB               22                50
  STAGE IIIA              26                46
  STAGE IIIB               3                 8
  STAGE IV                 6                19
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED    46  84   9   5
  3Q LOSS WILD-TYPE 125 194  37  14
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              46               125
  T2              84               194
  T3               9                37
  T4               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  3Q LOSS MUTATED    82  34    28
  3Q LOSS WILD-TYPE 251  62    48
D47V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0                 82               251
  N1                 34                62
  N2+N3              28                48
[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"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED   107   6
  3Q LOSS WILD-TYPE 242  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED    107    6
  3Q LOSS WILD-TYPE  242   19
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0             107               242
  1               6                19
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    78  66
  3Q LOSS WILD-TYPE 198 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     78   66
  3Q LOSS WILD-TYPE  198  174
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              78               198
  MALE                66               174
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED   114  21
  3Q LOSS WILD-TYPE 296  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED    114   21
  3Q LOSS WILD-TYPE  296   39
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO              114               296
  YES              21                39
[1] 2 2
[1] FALSE
D47V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3Q LOSS MUTATED                            6
  3Q LOSS WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3Q LOSS MUTATED                                  37
  3Q LOSS WILD-TYPE                                70
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                   83
  3Q LOSS WILD-TYPE                                                238
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3Q LOSS MUTATED                                            0
  3Q LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  3Q LOSS MUTATED                                               4
  3Q LOSS WILD-TYPE                                            15
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  3Q LOSS MUTATED                                1
  3Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  3Q LOSS MUTATED                                    1
  3Q LOSS WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  3Q LOSS MUTATED                              0                             5
  3Q LOSS WILD-TYPE                            2                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  3Q LOSS MUTATED                                 1
  3Q LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  3Q LOSS MUTATED                                               1
  3Q LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3Q LOSS MUTATED                              5
  3Q LOSS WILD-TYPE                            5
D47V10, multiclass
                                                    clus
vv                                                   3Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              83
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    4
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    5
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     5
                                                    clus
vv                                                   3Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               238
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     15
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
D47V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    91   2   0   5
  3Q LOSS WILD-TYPE 253  11   4  21
D47V13, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              91               253
  R1               2                11
  R2               0                 4
  RX               5                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     3
  3Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          17   108
  3Q LOSS WILD-TYPE                        35   282
D47V14, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                     17                35
  WHITE                                        108               282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V15, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0 114
  3Q LOSS WILD-TYPE   7 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0  114
  3Q LOSS WILD-TYPE    7  270
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO             114               270
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    79  37
  4P LOSS WILD-TYPE 244 144
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              116               388 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               37               144 
$`4P LOSS MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-5420 TCGA-44-6146 TCGA-44-6147 TCGA-49-4501 
        8.02        20.05        15.02        23.93        27.78        46.72 
TCGA-49-6742 TCGA-49-AAR0 TCGA-55-7724 TCGA-55-7726 TCGA-55-8203 TCGA-55-8204 
       16.04       156.66        23.18        21.44        17.98        16.93 
TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-95-7043 TCGA-95-A4VN TCGA-MP-A4TD 
       20.58        20.19        20.65        16.54        18.18        10.09 
TCGA-05-4249 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 
       50.07         0.00        24.03        47.05         2.99        29.98 
TCGA-05-4424 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-44-2659 TCGA-44-5643 
       30.02         5.98         8.68        97.74        44.94        33.30 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 
       28.37        23.77        19.56        61.28        19.46        36.07 
TCGA-44-8117 TCGA-44-A479 TCGA-49-4487 TCGA-49-4506 TCGA-49-4507 TCGA-49-6743 
       12.66        15.98        28.11        32.84         8.81        53.29 
TCGA-49-AARE TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5936 TCGA-50-5946 
       40.41       101.72        15.72        47.41         8.45        53.16 
TCGA-50-6590 TCGA-50-6673 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6968 
       42.35         0.72        30.54        35.21        67.89        42.51 
TCGA-55-6971 TCGA-55-6985 TCGA-55-7574 TCGA-55-7576 TCGA-55-7815 TCGA-55-7910 
       46.03        40.54        32.71        22.03        25.41        34.19 
TCGA-55-7913 TCGA-55-8505 TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       18.44        14.47        13.74        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8394 TCGA-62-8398 TCGA-62-A46U 
        1.58        21.40        19.99         4.57        14.60        67.96 
TCGA-62-A472 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-69-7763 
       29.92        42.90        28.41        28.47        20.05        22.68 
TCGA-69-7973 TCGA-69-7979 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
        7.56        13.41        26.73        19.43         8.42        23.38 
TCGA-73-4670 TCGA-73-4675 TCGA-78-7159 TCGA-78-7536 TCGA-78-8640 TCGA-86-7713 
        4.31        30.31        64.90         8.02       232.18        38.04 
TCGA-86-7954 TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 TCGA-86-8669 TCGA-86-A4JF 
       19.89         4.08        22.82        21.47        30.84        24.23 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JO 
       41.36         1.97        10.19        12.23        27.68         1.08 
TCGA-95-7567 TCGA-95-7944 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8033 
       18.67        12.39        21.44        19.76        34.85        21.57 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4TJ 
       18.08        19.00        18.58        15.65        38.63        11.15 
TCGA-NJ-A4YI TCGA-O1-A52J 
        0.13        59.11 

$`4P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         9.01        26.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       28.41        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 
       38.10        42.08        86.01        18.31        29.00        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 
        9.37        11.08        17.16        11.64        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       21.47        41.69        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
        7.99        16.01        14.53         6.15        19.66        19.73 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A492 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       19.59        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
        6.12        17.29         2.86        15.68        15.65        21.40 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       23.80         6.35        10.09        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4403 
       31.23         2.43         3.98        45.01        37.02        19.00 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       14.96        12.00        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        0.46         7.40       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        4.37        46.98        44.42        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06        33.73        26.56 
TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       28.01        23.15        21.63        23.18        32.45        16.44 
TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A47A 
       22.72         7.17        18.87        23.64         8.55        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 
        9.44        11.54        13.64        13.45        76.21        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       12.66        35.54        14.07        29.46        29.75        55.89 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.33        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
        8.55       123.58       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       71.47        60.16        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 
       78.67        15.12        48.46        60.72        57.53         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 
       25.55        11.05        12.16         6.21        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-5899 
       36.79        27.25        34.29        13.94        38.73        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       14.30        80.52         5.62        40.73        15.25        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7727 
      107.21        70.26        28.67        20.02        27.09         3.91 
TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
       23.15        18.64        11.28        17.65        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8620 
        0.36        20.28        17.72        19.96        26.01        12.33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 
       20.71         3.25         0.92        15.81        17.95        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 
       54.35        72.30        13.61        39.25        40.96        56.81 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       39.09        81.80        37.02        38.37        87.98         2.04 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       51.25        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        5.72         4.64         6.64         6.12        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        13.51        14.01        13.45         4.24 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS 
       26.30        15.35         9.24         1.25        50.33        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
      238.29        88.14        26.53        31.20        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       39.35        10.55        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
       27.09        12.36         5.88        31.13        34.39        20.55 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       32.78        35.24        37.74         4.57        24.33         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        31.20        23.05        14.60        11.61 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 TCGA-91-6848 
        3.81        13.64        26.47        10.62         2.60         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 
       17.46        23.61        19.00        41.82        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M5 
       15.39        16.41        14.30        21.60        20.58        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE 
       18.67        24.56        36.76         1.45        21.63        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        14.30        14.53         1.91         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        74.33         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.43        19.82        20.28        16.87 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.00              0.36 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           232.18            238.29 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           21.440            21.865 
[1] "0.0 - 232.2 (21.4)" "0.4 - 238.3 (21.9)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         2       30       35        0        10        14
  4P LOSS WILD-TYPE       3      103      104        1        40        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4P LOSS MUTATED           18          5        5
  4P LOSS WILD-TYPE         54          6       20
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                30               103
  STAGE IB                35               104
  STAGE II                 0                 1
  STAGE IIA               10                40
  STAGE IIB               14                58
  STAGE IIIA              18                54
  STAGE IIIB               5                 6
  STAGE IV                 5                20
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P LOSS MUTATED    39  64  11   4
  4P LOSS WILD-TYPE 132 214  35  15
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              39               132
  T2              64               214
  T3              11                35
  T4               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  4P LOSS MUTATED    76  17    22
  4P LOSS WILD-TYPE 257  79    54
D48V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                 76               257
  N1                 17                79
  N2+N3              22                54
[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"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    77   5
  4P LOSS WILD-TYPE 272  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     77    5
  4P LOSS WILD-TYPE  272   20
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              77               272
  1               5                20
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    62  57
  4P LOSS WILD-TYPE 214 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     62   57
  4P LOSS WILD-TYPE  214  183
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              62               214
  MALE                57               183
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    93  17
  4P LOSS WILD-TYPE 317  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     93   17
  4P LOSS WILD-TYPE  317   43
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               93               317
  YES              17                43
[1] 2 2
[1] FALSE
D48V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4P LOSS MUTATED                            3
  4P LOSS WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4P LOSS MUTATED                                  25
  4P LOSS WILD-TYPE                                82
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                   79
  4P LOSS WILD-TYPE                                                242
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4P LOSS MUTATED                                            0
  4P LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  4P LOSS MUTATED                                               3
  4P LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  4P LOSS MUTATED                                1
  4P LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  4P LOSS MUTATED                                    0
  4P LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  4P LOSS MUTATED                              1                             2
  4P LOSS WILD-TYPE                            1                            21
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  4P LOSS MUTATED                                 1
  4P LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  4P LOSS MUTATED                                               1
  4P LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  4P LOSS MUTATED                              3
  4P LOSS WILD-TYPE                            7
D48V10, multiclass
                                                    clus
vv                                                   4P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     3
                                                    clus
vv                                                   4P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               242
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
D48V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    77   3   1   9
  4P LOSS WILD-TYPE 267  10   3  17
D48V13, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              77               267
  R1               3                10
  R2               1                 3
  RX               9                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          15    86
  4P LOSS WILD-TYPE                        37   304
D48V14, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                     15                37
  WHITE                                         86               304
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  92
  4P LOSS WILD-TYPE   6 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   92
  4P LOSS WILD-TYPE    6  292
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              92               292
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    86  47
  4Q LOSS WILD-TYPE 237 134
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              133               371 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               47               134 
$`4Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-05-4434 TCGA-05-5420 TCGA-38-6178 
       19.96         8.02        20.05        15.02        15.02        14.73 
TCGA-44-6147 TCGA-49-4501 TCGA-49-AAR0 TCGA-55-1592 TCGA-55-7573 TCGA-55-7724 
       27.78        46.72       156.66        23.05        16.01        23.18 
TCGA-55-7726 TCGA-55-8203 TCGA-55-8204 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       21.44        17.98        16.93        20.58        19.59        20.19 
TCGA-64-1677 TCGA-73-4662 TCGA-95-7043 TCGA-95-A4VN TCGA-MP-A4TA TCGA-MP-A4TD 
       20.65        82.68        16.54        18.18        31.23        10.09 
TCGA-05-4249 TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 
       50.07         0.00        47.05         2.99        29.98        30.02 
TCGA-35-4123 TCGA-35-5375 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
        5.98         8.68        33.30        28.37        23.77        19.56 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-A479 TCGA-49-4487 TCGA-49-4506 
       61.28        19.46        36.07        15.98        28.11        32.84 
TCGA-49-4507 TCGA-49-6743 TCGA-49-AARE TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
        8.81        53.29        40.41       101.72        15.72        47.41 
TCGA-50-5936 TCGA-50-5946 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
        8.45        53.16        42.35         6.21         0.72        10.13 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-6968 TCGA-55-6971 TCGA-55-7574 
       35.21        38.73        67.89        42.51        46.03        32.71 
TCGA-55-7576 TCGA-55-7815 TCGA-55-7910 TCGA-55-7913 TCGA-55-8092 TCGA-55-8094 
       22.03        25.41        34.19        18.44         5.06        17.79 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8616 TCGA-55-A48Y 
       14.47        13.74        20.28        17.10         1.58        20.71 
TCGA-55-A48Z TCGA-62-8394 TCGA-62-8398 TCGA-62-A46O TCGA-62-A46U TCGA-62-A472 
       21.40         4.57        14.60        47.80        67.96        29.92 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-67-3771 TCGA-69-7763 
       81.80        38.37        42.90        28.41        20.05        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7979 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 
       13.61         7.56        13.41         4.24        26.73         8.42 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-75-6214 TCGA-78-7159 TCGA-78-7167 
       23.38         4.31        30.31        36.66        64.90        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 
       31.20         8.02       232.18        38.04        19.89        35.24 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 TCGA-86-A4JF 
        4.08        22.82        31.20        30.84         0.62        24.23 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JO 
       41.36         1.97        10.19        12.23        27.68         1.08 
TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VP TCGA-97-7937 TCGA-97-A4M0 TCGA-97-A4M1 
       18.67        12.39        19.89        18.54        21.44        19.76 
TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV 
       34.85         1.45        21.57        18.08        19.00        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YI 
       15.65        38.63        11.05        11.15        71.05         0.13 
TCGA-O1-A52J 
       59.11 

$`4Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 TCGA-38-4630 
       14.01         9.96         9.01        26.01        28.41        35.28 
TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       11.64        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       86.01        18.31        29.00        29.23         9.37        11.08 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       16.04        17.16        11.64        37.32        40.60        21.47 
TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 
       41.69        48.62         5.79         7.79         7.99        14.53 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
        6.15        19.66        19.73        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 
       13.68        16.93        22.65        13.87        52.60        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
        8.48        50.24        10.55        85.32        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        1.45         6.12        17.29         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       21.40        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       24.30        23.80         6.35        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 
        5.29         2.43         3.98        45.01        37.02        24.03 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       19.00        14.96        12.00        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         0.46         7.40        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       49.05        44.61         4.37        46.98        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 
       34.06        33.73        26.56        28.01        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 
       23.18        32.45        16.44        22.72         7.17        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       23.64        12.66         8.55        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 
       14.07        29.46        29.75        55.89        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO 
       22.26        73.12        62.24        28.90         8.55       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 
      221.33       164.12         9.86        20.52        71.47        60.16 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 
       49.28         8.22         9.27        14.27        78.67        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       48.46        60.72        57.53         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       12.16        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       13.94        30.58        14.30        80.52         5.62        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       15.25        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 
       20.02        27.09         3.91        23.15        18.64        11.28 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       15.72         0.36        17.72        19.96        26.01        17.62 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       14.66        12.33         3.25         0.92        15.81        19.99 
TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       17.95        39.98        42.38        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       56.71        54.35        72.30        13.61        39.25        40.96 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 
       56.81        39.09        37.02        87.98         2.04        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       28.47        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 
        5.72         4.64         6.64         6.12         5.42         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4666 
        4.41        13.51        14.01        13.45        19.43        26.30 
TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 
       15.35         9.24         1.25        50.33        11.18        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       77.85        43.82        85.15        49.84       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 
        5.88        22.92         9.57       104.19       238.29        26.53 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35        10.55        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       34.39        20.55        32.78        37.74         4.57        24.33 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
        0.79        32.65        31.04        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       11.61        13.91        27.58        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 TCGA-91-6848 
        3.81        13.64        26.47        10.62         2.60         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 
       17.46        23.61        19.00        41.82        27.29         2.76 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       42.25        64.60        63.52        61.48        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       14.30        21.60        20.58        20.84        18.67        24.56 
TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W 
       36.76        21.63        35.47        32.48        14.30        14.53 
TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
        1.91         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH 
       86.04        58.85         5.49        41.59        29.46        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       14.10        19.13        73.91        74.33         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.49         0.43        19.82        20.28        16.87 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.00              0.36 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           232.18            238.29 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            20.65             22.03 
[1] "0.0 - 232.2 (20.6)" "0.4 - 238.3 (22.0)"
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         2       40       35        0        12        11
  4Q LOSS WILD-TYPE       3       93      104        1        38        61
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4Q LOSS MUTATED           23          5        8
  4Q LOSS WILD-TYPE         49          6       17
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                40                93
  STAGE IB                35               104
  STAGE II                 0                 1
  STAGE IIA               12                38
  STAGE IIB               11                61
  STAGE IIIA              23                49
  STAGE IIIB               5                 6
  STAGE IV                 8                17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q LOSS MUTATED    47  73  10   5
  4Q LOSS WILD-TYPE 124 205  36  14
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              47               124
  T2              73               205
  T3              10                36
  T4               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  4Q LOSS MUTATED    90  15    27
  4Q LOSS WILD-TYPE 243  81    49
D49V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                 90               243
  N1                 15                81
  N2+N3              27                49
[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"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    89   8
  4Q LOSS WILD-TYPE 260  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     89    8
  4Q LOSS WILD-TYPE  260   17
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              89               260
  1               8                17
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    72  64
  4Q LOSS WILD-TYPE 204 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     72   64
  4Q LOSS WILD-TYPE  204  176
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              72               204
  MALE                64               176
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   105  22
  4Q LOSS WILD-TYPE 305  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    105   22
  4Q LOSS WILD-TYPE  305   38
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              105               305
  YES              22                38
[1] 2 2
[1] FALSE
D49V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4Q LOSS MUTATED                            4
  4Q LOSS WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4Q LOSS MUTATED                                  25
  4Q LOSS WILD-TYPE                                82
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                   93
  4Q LOSS WILD-TYPE                                                228
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4Q LOSS MUTATED                                            0
  4Q LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  4Q LOSS MUTATED                                               3
  4Q LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  4Q LOSS MUTATED                                1
  4Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  4Q LOSS MUTATED                                    1
  4Q LOSS WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  4Q LOSS MUTATED                              0                             3
  4Q LOSS WILD-TYPE                            2                            20
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  4Q LOSS MUTATED                                 1
  4Q LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  4Q LOSS MUTATED                                               2
  4Q LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  4Q LOSS MUTATED                              3
  4Q LOSS WILD-TYPE                            7
D49V10, multiclass
                                                    clus
vv                                                   4Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              93
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     3
                                                    clus
vv                                                   4Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               228
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
D49V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED    87   4   2   9
  4Q LOSS WILD-TYPE 257   9   2  17
D49V13, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              87               257
  R1               4                 9
  R2               2                 2
  RX               9                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          16   100
  4Q LOSS WILD-TYPE                        36   290
D49V14, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                     16                36
  WHITE                                        100               290
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2 104
  4Q LOSS WILD-TYPE   5 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2  104
  4Q LOSS WILD-TYPE    5  280
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             104               280
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    31  14
  5P LOSS WILD-TYPE 292 167
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               45               459 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14               167 
$`5P LOSS MUTATED`
TCGA-05-4382 TCGA-49-6742 TCGA-55-7914 TCGA-55-8203 TCGA-55-A492 TCGA-95-7043 
       19.96        16.04         6.15        17.98        19.59        16.54 
TCGA-MN-A4N1 TCGA-05-4249 TCGA-05-4420 TCGA-05-4432 TCGA-35-4122 TCGA-35-4123 
       27.19        50.07        29.98        25.02         7.40         5.98 
TCGA-44-3917 TCGA-44-6144 TCGA-44-6145 TCGA-44-8120 TCGA-49-6767 TCGA-49-AAR2 
       38.89        23.77        19.56         8.55        22.26        73.12 
TCGA-49-AARE TCGA-49-AARO TCGA-50-6590 TCGA-55-1596 TCGA-55-6968 TCGA-55-6975 
       40.41       123.58        42.35        67.89        42.51         3.88 
TCGA-55-7281 TCGA-55-7913 TCGA-55-8505 TCGA-55-A57B TCGA-62-8398 TCGA-64-5779 
       28.67        18.44        14.47        17.95        14.60        28.41 
TCGA-67-3771 TCGA-67-3772 TCGA-69-7979 TCGA-69-8255 TCGA-73-A9RS TCGA-75-5125 
       20.05        18.84        13.41         4.24        11.18        66.64 
TCGA-75-7027 TCGA-78-7160 TCGA-78-7161 TCGA-86-7713 TCGA-86-7955 TCGA-86-8074 
      100.57        22.92         9.57        38.04        35.24         0.79 
TCGA-91-6829 TCGA-97-8175 TCGA-MN-A4N4 
       41.36        18.12        38.63 

$`5P LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 
       26.30        43.53        38.10        42.08        23.93        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       86.01        18.31        29.00        29.23         9.37        11.08 
TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       46.72        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       21.47        41.69        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 
        7.99        16.01        23.18        14.53        21.44        19.66 
TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       19.73        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       16.93        22.65        20.58        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        21.83         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       10.09         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
       47.05        19.00         2.99        14.96        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       21.99        26.01        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 
       22.03         9.04         2.04         0.46         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       28.01        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       23.64        12.66        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 
       55.89        53.29        55.33        22.26        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
        8.55       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       60.72        57.53        53.16         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94        35.21        38.73 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       30.58        14.30        80.52         5.62        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       46.03        53.65        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 
       24.99        40.54       107.21        70.26        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       32.71        22.03         3.91        23.15        25.41        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       11.28        34.19        17.65        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
       29.19        22.16        15.42        17.56        15.72         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       29.92        56.81        39.09        81.80        37.02        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       87.98         2.04        42.90        51.25        28.47        20.05 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K 
        4.41        13.51        14.01        13.45        26.73        19.43 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        8.42        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        9.24         1.25        50.33        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       49.84        36.66       108.66       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
       19.50        38.50        32.09         5.88        64.90       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       34.39        20.55        32.78        19.89        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57        24.33        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       27.58         0.62        28.34        26.50        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
       24.23        13.64        26.47        10.62         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        21.57        21.63        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       19.00        14.30        14.53         1.91        18.58        15.65 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.10        11.15        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.79              0.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           123.58            238.29 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            20.05             21.63 
[1] "0.8 - 123.6 (20.1)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.2"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         0       15       13        0         5         7
  5P LOSS WILD-TYPE       5      118      126        1        45        65
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5P LOSS MUTATED            3          0        2
  5P LOSS WILD-TYPE         69         11       23
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                15               118
  STAGE IB                13               126
  STAGE II                 0                 1
  STAGE IIA                5                45
  STAGE IIB                7                65
  STAGE IIIA               3                69
  STAGE IIIB               0                11
  STAGE IV                 2                23
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED    19  22   3   1
  5P LOSS WILD-TYPE 152 256  43  18
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              19               152
  T2              22               256
  T3               3                43
  T4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  5P LOSS MUTATED    33   8     4
  5P LOSS WILD-TYPE 300  88    72
D50V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                 33               300
  N1                  8                88
  N2+N3               4                72
[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"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    32   2
  5P LOSS WILD-TYPE 317  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     32    2
  5P LOSS WILD-TYPE  317   23
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              32               317
  1               2                23
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    19  26
  5P LOSS WILD-TYPE 257 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     19   26
  5P LOSS WILD-TYPE  257  214
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              19               257
  MALE                26               214
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    33   6
  5P LOSS WILD-TYPE 377  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     33    6
  5P LOSS WILD-TYPE  377   54
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               33               377
  YES               6                54
[1] 2 2
[1] FALSE
D50V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5P LOSS MUTATED                            3
  5P LOSS WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5P LOSS MUTATED                                   9
  5P LOSS WILD-TYPE                                98
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                   28
  5P LOSS WILD-TYPE                                                293
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5P LOSS MUTATED                                            0
  5P LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  5P LOSS MUTATED                                               1
  5P LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  5P LOSS MUTATED                                0
  5P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  5P LOSS MUTATED                                    0
  5P LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  5P LOSS MUTATED                              0                             1
  5P LOSS WILD-TYPE                            2                            22
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  5P LOSS MUTATED                                 0
  5P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  5P LOSS MUTATED                                               2
  5P LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5P LOSS MUTATED                              1
  5P LOSS WILD-TYPE                            9
D50V10, multiclass
                                                    clus
vv                                                   5P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              28
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   5P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               293
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
D50V12, continuous
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    32   1   0   2
  5P LOSS WILD-TYPE 312  12   4  24
D50V13, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              32               312
  R1               1                12
  R2               0                 4
  RX               2                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     1
  5P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           9    29
  5P LOSS WILD-TYPE                        43   361
D50V14, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      9                43
  WHITE                                         29               361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V15, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1  34
  5P LOSS WILD-TYPE   6 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   34
  5P LOSS WILD-TYPE    6  350
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              34               350
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   101  40
  5Q LOSS WILD-TYPE 222 141
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              141               363 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               40               141 
$`5Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-38-4630 TCGA-38-4631 
       19.96         9.96        20.05        26.01        35.28        11.64 
TCGA-44-6146 TCGA-44-7670 TCGA-49-6742 TCGA-55-1592 TCGA-55-6979 TCGA-55-7726 
       23.93        29.00        16.04        23.05         7.79        21.44 
TCGA-55-7914 TCGA-55-8203 TCGA-55-8511 TCGA-55-A491 TCGA-55-A492 TCGA-93-8067 
        6.15        17.98        18.15        20.58        19.59         6.12 
TCGA-95-7043 TCGA-95-7948 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-05-4249 
       16.54        15.65        10.09        27.19         2.43        50.07 
TCGA-05-4389 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 
       45.01        14.96        29.98        30.02        25.02        29.00 
TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 
       22.03         2.04         7.40         5.98        97.74        49.05 
TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6778 
       38.89        33.30        28.37        23.77        19.56        61.28 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4505 
       19.46         7.17        36.07         8.55        13.64        14.07 
TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-50-5045 
       22.26        73.12        28.90        40.41       123.58        71.47 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 
      101.72        47.41        49.28        48.46        53.16        42.35 
TCGA-50-6593 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       11.05        34.29        35.21        38.73        67.89        30.58 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6975 TCGA-55-6985 TCGA-55-7281 TCGA-55-7570 
       42.51        40.73         3.88        40.54        28.67        27.09 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7913 TCGA-55-8094 TCGA-55-8302 TCGA-55-8505 
        3.91        11.28        18.44        17.79        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y 
        0.36        13.74        17.72        14.66         1.58        20.71 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       17.95         4.57        39.98        14.60        88.64        49.25 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 
       39.25        40.96        56.81        81.80        38.37        42.90 
TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 
       28.41        20.05        18.84        13.61         5.42        13.41 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4668 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 
        4.24         8.42        15.35        11.18        66.64        77.85 
TCGA-75-7027 TCGA-78-7149 TCGA-78-7150 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
      100.57       129.53        21.90        64.90        22.92         9.57 
TCGA-78-7167 TCGA-86-6562 TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 
       88.14        12.36         5.88        38.04        32.78        35.24 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8279 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 
       24.33         0.79        31.20        11.61         0.62        41.36 
TCGA-91-6840 TCGA-91-8499 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-97-7937 
       12.23         1.18         1.08        41.82        18.67        18.54 
TCGA-97-8175 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4T6 
       18.12        34.85        18.08        18.58        38.63        58.85 
TCGA-MP-A4TE TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        73.91        71.05 

$`5Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4402 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 
       14.01         8.02         9.01        15.02        15.02        28.41 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 
       14.73        26.30        43.53        38.10        42.08        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       86.01        18.31        29.23         9.37        11.08        46.72 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       17.16        11.64       156.66        37.32        40.60        21.47 
TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       41.69        48.62         5.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       14.53        19.66        19.73        16.93        19.69        32.12 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       13.68        16.93        22.65        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7562 
       85.32        13.71        16.18         1.45        17.29         2.86 
TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.68        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 
       17.75        20.68        24.30        23.80         6.35        21.83 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 
        5.29        31.23        10.09         3.98        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 
       24.03        47.05        19.00         2.99        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 TCGA-35-3615 
       26.01        25.02        24.00         4.96         9.04         0.46 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
        8.68       120.79        37.71        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 
       38.24        34.06        33.73        26.56        28.01        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7669 
       21.63        23.18        32.45        16.44        22.72        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       23.64        12.66        15.98        15.32         9.44        11.54 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR 
       55.33        22.26        62.24         8.55       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 
        9.86        20.52        15.72        60.16         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       14.27        78.67         8.45        15.12        60.72        57.53 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
        3.91        25.55        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-6543 
       36.99        36.79        27.25        30.54        13.94        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
       80.52         5.62        15.25        46.03        53.65        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
       45.34        32.71        92.81        24.99       107.21        70.26 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       20.02        32.71        22.03        23.15        25.41        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       23.08         5.06        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       15.42        17.56        20.28        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       17.62        12.33        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       19.99        42.38        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1678 TCGA-64-1680 
       67.96        72.30        13.61        29.92        39.09        37.02 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 
       87.98         2.04        51.25        28.47        20.05        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
       22.68         7.56         6.05         4.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 
       13.45        26.73        19.43        23.38        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5147 TCGA-75-6206 
       30.31         9.24         1.25        50.33        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       49.84        36.66       108.66       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       19.27        20.58        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 
       32.09         5.88       104.19       238.29        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
       39.75        77.59       110.50        93.11        27.09        31.13 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       34.39        20.55        19.89        37.74         4.08         4.57 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       22.82        32.65        31.04        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
        3.81        24.23        13.64        26.47        10.62         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP 
       14.27        19.82        22.45        17.46        23.61        19.00 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        61.48        25.48         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        5.39        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       21.44        19.76        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        21.63        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30        14.53         1.91        15.65         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
       58.45        49.35        37.35        86.04         5.49        41.59 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YG 
       11.05        24.36        14.10        11.15        19.13        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.36              0.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           129.53            238.29 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            22.92             21.47 
[1] "0.4 - 129.5 (22.9)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.5"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         0       36       41        0        15        24
  5Q LOSS WILD-TYPE       5       97       98        1        35        48
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5Q LOSS MUTATED           16          3        5
  5Q LOSS WILD-TYPE         56          8       20
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                36                97
  STAGE IB                41                98
  STAGE II                 0                 1
  STAGE IIA               15                35
  STAGE IIB               24                48
  STAGE IIIA              16                56
  STAGE IIIB               3                 8
  STAGE IV                 5                20
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED    47  79  12   5
  5Q LOSS WILD-TYPE 124 199  34  14
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              47               124
  T2              79               199
  T3              12                34
  T4               5                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  5Q LOSS MUTATED    95  29    18
  5Q LOSS WILD-TYPE 238  67    58
D51V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                 95               238
  N1                 29                67
  N2+N3              18                58
[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"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    96   5
  5Q LOSS WILD-TYPE 253  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     96    5
  5Q LOSS WILD-TYPE  253   20
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              96               253
  1               5                20
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    65  78
  5Q LOSS WILD-TYPE 211 162
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     65   78
  5Q LOSS WILD-TYPE  211  162
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              65               211
  MALE                78               162
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   113  17
  5Q LOSS WILD-TYPE 297  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    113   17
  5Q LOSS WILD-TYPE  297   43
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO              113               297
  YES              17                43
[1] 2 2
[1] FALSE
D51V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5Q LOSS MUTATED                            5
  5Q LOSS WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5Q LOSS MUTATED                                  34
  5Q LOSS WILD-TYPE                                73
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                   89
  5Q LOSS WILD-TYPE                                                232
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5Q LOSS MUTATED                                            0
  5Q LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  5Q LOSS MUTATED                                               3
  5Q LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  5Q LOSS MUTATED                                0
  5Q LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  5Q LOSS MUTATED                                    2
  5Q LOSS WILD-TYPE                                  1
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  5Q LOSS MUTATED                              1                             5
  5Q LOSS WILD-TYPE                            1                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  5Q LOSS MUTATED                                 0
  5Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  5Q LOSS MUTATED                                               3
  5Q LOSS WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5Q LOSS MUTATED                              1
  5Q LOSS WILD-TYPE                            9
D51V10, multiclass
                                                    clus
vv                                                   5Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              89
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    5
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   5Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               232
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
D51V12, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    96   3   0  10
  5Q LOSS WILD-TYPE 248  10   4  16
D51V13, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              96               248
  R1               3                10
  R2               0                 4
  RX              10                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     3
  5Q LOSS WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          19   102
  5Q LOSS WILD-TYPE                        33   288
D51V14, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                     19                33
  WHITE                                        102               288
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     4 106
  5Q LOSS WILD-TYPE   3 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4  106
  5Q LOSS WILD-TYPE    3  278
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             106               278
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    57  42
  6P LOSS WILD-TYPE 266 139
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               99               405 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               42               139 
$`6P LOSS MUTATED`
TCGA-38-4631 TCGA-44-2662 TCGA-44-A47F TCGA-49-6745 TCGA-50-5932 TCGA-50-5935 
       11.64        42.08        11.08        17.16        40.60        21.47 
TCGA-50-6597 TCGA-55-7724 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 TCGA-80-5611 
       41.69        23.18        19.66        19.73        32.12        85.32 
TCGA-95-7043 TCGA-95-7948 TCGA-J2-8192 TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-05-4250 
       16.54        15.65        24.30        27.19         2.43         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 TCGA-35-4123 TCGA-38-4632 
       45.01        37.02         0.00         2.99         5.98        44.61 
TCGA-44-2656 TCGA-44-3917 TCGA-44-6775 TCGA-49-4486 TCGA-49-4488 TCGA-49-4512 
       46.98        38.89        23.18        76.21        28.57        29.75 
TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 TCGA-50-5068 TCGA-53-7626 TCGA-55-6968 
       40.41       123.58        15.72        49.28        30.54        42.51 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 
       46.03        53.65        45.34        92.81        40.54        20.02 
TCGA-55-7576 TCGA-55-7815 TCGA-55-8089 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 
       22.03        25.41        23.08        15.72         0.36        20.28 
TCGA-55-8616 TCGA-55-A494 TCGA-62-8402 TCGA-62-A46R TCGA-62-A46S TCGA-62-A472 
        1.58        15.81        49.25        56.71        54.35        29.92 
TCGA-64-1676 TCGA-64-5781 TCGA-69-7760 TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 
       56.81        51.25         6.64         6.05        14.01        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 
       26.73        19.43         8.42        23.38        26.30        30.31 
TCGA-73-A9RS TCGA-75-7025 TCGA-78-7146 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       11.18       108.66         5.69        39.95       119.51        19.50 
TCGA-78-7158 TCGA-78-7535 TCGA-78-7536 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 
        5.88        31.20         8.02        27.09        31.13        38.04 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8359 TCGA-86-8672 TCGA-91-6831 
       32.78        35.24        37.74        14.60         0.62        10.19 
TCGA-93-7347 TCGA-93-7348 TCGA-95-8494 TCGA-97-7547 TCGA-97-8174 TCGA-97-8547 
       22.45        17.46         2.76        64.60         5.39        21.60 
TCGA-97-A4M0 TCGA-99-7458 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4TF TCGA-MP-A4TK 
       21.44        24.56        49.35        37.35        11.05        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI 
       73.91        71.05         0.13 

$`6P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 
       26.01        15.02        15.02        28.41        35.28        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       26.30        43.53        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 
       18.31        29.00        29.23         9.37        46.72        16.04 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
       11.64       156.66        37.32        23.05        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.79         7.99        16.01        14.53        21.44         6.15 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        19.69        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 
       13.71        16.18         1.45         6.12        17.29         2.86 
TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.68        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       17.75        20.68        23.80         6.35        10.09        21.83 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4397 TCGA-05-4398 
        5.29        31.23        10.09        50.07        24.03        47.05 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       19.00        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-5375 
       22.03         9.04         2.04         0.46         7.40         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F TCGA-44-2657 
       97.74       120.79        37.71        49.05         4.37        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.94        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       34.06        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 
       23.77        19.56        23.15        21.63        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 
       11.54        13.64        13.45        28.11        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 
       14.07        32.84         8.81        29.46        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.33        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
        8.55       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
      101.72        60.16        47.41         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       34.29        13.94        35.21        38.73        67.89        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6975 
       14.30        80.52         5.62        40.73        15.25         3.88 
TCGA-55-6980 TCGA-55-6982 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       69.34        32.71        24.99       107.21        70.26        28.67 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 
       27.09        32.71         3.91        23.15        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 
       22.16        15.42        17.56        14.47        13.74        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 
       19.96        26.01        17.10        17.62        14.66        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B 
       20.71        21.40         3.25         0.92        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O 
        4.57        39.98        42.38        14.60        88.64        47.80 
TCGA-62-A46P TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       19.53        67.96        72.30        13.61        39.25        40.96 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       39.09        81.80        37.02        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        28.47        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
       14.04        12.66        14.73         5.72         4.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         5.42         7.56         4.41        13.41 
TCGA-69-7980 TCGA-69-8255 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
       13.51         4.24        15.35         4.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
       36.66       100.57       163.10        27.16        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 
      129.53        21.90        38.50        32.09        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 
        9.57       104.19       238.29        88.14        26.53        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 
      110.50        93.11        12.36         5.88        34.39        20.55 
TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       19.89         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 
       32.65        31.04        31.20        23.05        21.47        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        1.97         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-A4JN TCGA-93-A4JO 
       16.60        14.27         1.18        19.82        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP 
       19.00        41.82        18.67        12.39        27.29        19.89 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       42.25        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       15.91        18.67        18.12        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 
       20.58        19.76        20.84        18.67        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        21.57        21.63        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       19.00        14.30        14.53         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T6 
       38.63         2.76        86.14        58.45        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
        5.49        41.59        29.46        24.36        14.10        11.15 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       74.33         1.64        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.00              0.43 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           123.58            238.29 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            24.56             20.68 
[1] "0.0 - 123.6 (24.6)" "0.4 - 238.3 (20.7)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         0       17       34        0         9        14
  6P LOSS WILD-TYPE       5      116      105        1        41        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6P LOSS MUTATED           19          3        4
  6P LOSS WILD-TYPE         53          8       21
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                17               116
  STAGE IB                34               105
  STAGE II                 0                 1
  STAGE IIA                9                41
  STAGE IIB               14                58
  STAGE IIIA              19                53
  STAGE IIIB               3                 8
  STAGE IV                 4                21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED    23  62  12   4
  6P LOSS WILD-TYPE 148 216  34  15
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              23               148
  T2              62               216
  T3              12                34
  T4               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  6P LOSS MUTATED    65  16    19
  6P LOSS WILD-TYPE 268  80    57
D52V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                 65               268
  N1                 16                80
  N2+N3              19                57
[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"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    68   4
  6P LOSS WILD-TYPE 281  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     68    4
  6P LOSS WILD-TYPE  281   21
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              68               281
  1               4                21
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    51  50
  6P LOSS WILD-TYPE 225 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     51   50
  6P LOSS WILD-TYPE  225  190
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              51               225
  MALE                50               190
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    84  10
  6P LOSS WILD-TYPE 326  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     84   10
  6P LOSS WILD-TYPE  326   50
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               84               326
  YES              10                50
[1] 2 2
[1] FALSE
D52V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6P LOSS MUTATED                            2
  6P LOSS WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6P LOSS MUTATED                                  22
  6P LOSS WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                   64
  6P LOSS WILD-TYPE                                                257
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6P LOSS MUTATED                                            0
  6P LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  6P LOSS MUTATED                                               2
  6P LOSS WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  6P LOSS MUTATED                                0
  6P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  6P LOSS MUTATED                                    0
  6P LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  6P LOSS MUTATED                              0                             7
  6P LOSS WILD-TYPE                            2                            16
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  6P LOSS MUTATED                                 0
  6P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  6P LOSS MUTATED                                               1
  6P LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  6P LOSS MUTATED                              3
  6P LOSS WILD-TYPE                            7
D52V10, multiclass
                                                    clus
vv                                                   6P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              64
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    7
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     3
                                                    clus
vv                                                   6P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               257
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     16
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
D52V12, continuous
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    69   2   1   5
  6P LOSS WILD-TYPE 275  11   3  21
D52V13, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              69               275
  R1               2                11
  R2               1                 3
  RX               5                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     1
  6P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                          10    78
  6P LOSS WILD-TYPE                        42   312
D52V14, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                     10                42
  WHITE                                         78               312
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  76
  6P LOSS WILD-TYPE   6 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   76
  6P LOSS WILD-TYPE    6  308
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              76               308
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   132  80
  6Q LOSS WILD-TYPE 191 101
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              212               292 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               80               101 
$`6Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4405 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 
       19.96        20.05        11.64        14.73        42.08        27.78 
TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       11.08        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-55-1595 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 
       21.47        48.62        23.18        14.53         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8207 TCGA-55-A48X TCGA-64-1677 TCGA-73-4658 
       19.73        17.98        32.12        22.65        20.65        52.60 
TCGA-73-7498 TCGA-78-7633 TCGA-80-5611 TCGA-91-7771 TCGA-95-7043 TCGA-95-7948 
       39.09        50.24        85.32        16.18        16.54        15.65 
TCGA-95-A4VN TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       18.18        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 
        6.35        10.09        27.19         2.43         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 TCGA-05-4425 TCGA-05-4430 TCGA-05-5425 
       37.02         0.00         2.99        21.99        25.02        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-38-4632 TCGA-44-2656 
       22.03         9.04         0.46         5.98        44.61        46.98 
TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-5644 
       44.94         3.19        25.02        38.89        34.06        28.37 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-8117 
       21.63        23.18        32.45        16.44        22.72        12.66 
TCGA-44-8120 TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 
        8.55        13.45        76.21        28.57        35.54        14.07 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-AAR9 
        8.81        29.46        29.75        55.89        55.33         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 TCGA-50-5068 TCGA-50-5933 TCGA-50-5941 
       40.41       123.58        15.72        49.28        78.67        48.46 
TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6594 TCGA-53-7624 TCGA-53-7626 
       60.72        53.16        42.35        12.16        34.29        30.54 
TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 
       13.94        14.30        80.52        42.51        46.03        53.65 
TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7576 TCGA-55-7815 
       45.34        92.81        40.54        20.02        22.03        25.41 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 
       18.64        17.65        18.44        19.82        29.72        23.08 
TCGA-55-8094 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8615 
       17.79        15.72         0.36        20.28        19.96        14.66 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A494 TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 
        1.58        20.71        15.81        39.98        14.60        49.25 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 
       56.71        54.35        72.30        39.25        29.92        56.81 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       39.09        87.98        28.41        51.25        28.47        20.05 
TCGA-67-4679 TCGA-67-6216 TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       14.73         4.64         6.64         7.56         6.05         4.41 
TCGA-69-8253 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
       14.01        26.73        19.43         8.42        23.38        26.30 
TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 
       30.31        50.33        11.18        85.15        36.66       108.66 
TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
      100.57         5.69       129.53        39.95       119.51        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7535 TCGA-78-7536 
       32.09         5.88        64.90       104.19        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 
       53.33        39.35        10.55        77.59        27.09        12.36 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
       31.13        38.04        20.55        32.78        35.24        37.74 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 TCGA-86-8674 
       31.20        23.05        21.47        14.60         0.62        26.50 
TCGA-86-A456 TCGA-91-6831 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7567 
       29.46        10.19        19.82        22.45        17.46        18.67 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
        2.76        19.89        64.60        25.48        18.54         0.59 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-7458 
        5.39        15.39        21.60        21.44        20.84        24.56 
TCGA-L4-A4E5 TCGA-L9-A50W TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
       19.00        14.53         2.76        49.35        37.35        58.85 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI 
       29.46        11.05        19.13        73.91        71.05         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ 
        1.64        47.08 

$`6Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       14.01         9.96         8.02         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       15.02        28.41        35.28        26.30        43.53        38.10 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 
       23.93        86.01        18.31        29.00        29.23         9.37 
TCGA-49-4501 TCGA-49-6742 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 
       46.72        16.04        41.69        23.05         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7726 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 
        7.99        16.01        21.44        16.93        19.69        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 
       13.68        16.93        20.58        19.59        20.19        13.87 
TCGA-73-4662 TCGA-78-7166 TCGA-78-8660 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 
       82.68         8.48        10.55        13.71         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX 
       17.29         2.86        15.68        21.40        17.92        20.19 
TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4397 
       21.83         5.29        31.23        10.09        50.07        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       47.05        19.00        14.96        29.98        12.00        30.02 
TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5715 TCGA-35-4122 
       26.01        25.02        24.00         4.96         2.04         7.40 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F 
        8.68        97.74       120.79        37.71        49.05         4.37 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       44.42        42.77        37.15        38.24        33.73        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6778 
       33.30        28.01        23.77        19.56        23.15        61.28 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 
       19.46         7.17        36.07        18.87        23.64        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4487 TCGA-49-4490 
       15.32         9.44        11.54        13.64        28.11        12.66 
TCGA-49-4506 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       32.84        53.29        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
       28.90       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
      101.72        60.16        47.41         8.22         9.27        14.27 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
        8.45        15.12        57.53         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6712 TCGA-55-6969 
       35.21        38.73        67.89        30.58         5.62        40.73 
TCGA-55-6970 TCGA-55-6975 TCGA-55-6980 TCGA-55-6982 TCGA-55-6984 TCGA-55-6986 
       15.25         3.88        69.34        32.71        24.99       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 
       70.26        28.67        27.09        32.71         3.91        23.15 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 
       11.28        34.19        29.23        15.19         5.06        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
       15.65        29.19        22.16        15.42        17.56        14.47 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8620 
       13.74        17.72        26.01        17.10        17.62        12.33 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       21.40         3.25         0.92        19.99        17.95         4.57 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U TCGA-62-A46Y 
       42.38        88.64        47.80        19.53        67.96        13.61 
TCGA-62-A471 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       40.96        81.80        37.02        38.37         2.04        42.90 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-69-7761 
       20.05        18.84        14.04        12.66         5.72         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
       22.68        13.61         5.42        13.41        13.51        13.45 
TCGA-69-8255 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 
        4.24        15.35         4.31         9.24         1.25        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       77.85        43.82        49.84       163.10        27.16        19.27 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 
       20.58        21.90        38.50        22.92         9.57       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 
       88.14        26.53        26.01       232.18        39.75       110.50 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 
       93.11         5.88        34.39        19.89         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 
       24.33         0.79        22.82        32.65        31.04        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4JF 
       13.91        30.84        27.58        28.34         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
       13.64        26.47        10.62        41.36         1.97         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 
        1.18        23.61         1.08        19.00        41.82        12.39 
TCGA-95-8039 TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
       27.29        42.25        63.52        61.48        15.91        18.67 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 
       18.12        16.41        14.30        20.58        19.76        18.67 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       34.85        36.76         1.45        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       35.47        32.48        14.30         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
       38.63        86.14        58.45        86.04         5.49        41.59 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A55A TCGA-NJ-A55O 
       24.36        14.10        11.15        74.33         0.49         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.00              0.43 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           156.66            238.29 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           23.065            20.400 
[1] "0.0 - 156.7 (23.1)" "0.4 - 238.3 (20.4)"
[1] "hr=" "1"  
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         1       51       60        0        22        28
  6Q LOSS WILD-TYPE       4       82       79        1        28        44
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6Q LOSS MUTATED           37          6       10
  6Q LOSS WILD-TYPE         35          5       15
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                51                82
  STAGE IB                60                79
  STAGE II                 0                 1
  STAGE IIA               22                28
  STAGE IIB               28                44
  STAGE IIIA              37                35
  STAGE IIIB               6                 5
  STAGE IV                10                15
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED    69 116  24   8
  6Q LOSS WILD-TYPE 102 162  22  11
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              69               102
  T2             116               162
  T3              24                22
  T4               8                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  6Q LOSS MUTATED   137  39    37
  6Q LOSS WILD-TYPE 196  57    39
D53V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                137               196
  N1                 39                57
  N2+N3              37                39
[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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   147  10
  6Q LOSS WILD-TYPE 202  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    147   10
  6Q LOSS WILD-TYPE  202   15
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             147               202
  1              10                15
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   113 104
  6Q LOSS WILD-TYPE 163 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    113  104
  6Q LOSS WILD-TYPE  163  136
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE             113               163
  MALE               104               136
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   175  24
  6Q LOSS WILD-TYPE 235  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    175   24
  6Q LOSS WILD-TYPE  235   36
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO              175               235
  YES              24                36
[1] 2 2
[1] FALSE
D53V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6Q LOSS MUTATED                            6
  6Q LOSS WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6Q LOSS MUTATED                                  51
  6Q LOSS WILD-TYPE                                56
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                  131
  6Q LOSS WILD-TYPE                                                190
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6Q LOSS MUTATED                                            2
  6Q LOSS WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  6Q LOSS MUTATED                                               7
  6Q LOSS WILD-TYPE                                            12
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  6Q LOSS MUTATED                                1
  6Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  6Q LOSS MUTATED                                    1
  6Q LOSS WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  6Q LOSS MUTATED                              0                            13
  6Q LOSS WILD-TYPE                            2                            10
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  6Q LOSS MUTATED                                 0
  6Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  6Q LOSS MUTATED                                               2
  6Q LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  6Q LOSS MUTATED                              3
  6Q LOSS WILD-TYPE                            7
D53V10, multiclass
                                                    clus
vv                                                   6Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             131
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    7
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                   13
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     3
                                                    clus
vv                                                   6Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               190
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     12
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     10
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
D53V12, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED   153   4   1   9
  6Q LOSS WILD-TYPE 191   9   3  17
D53V13, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0             153               191
  R1               4                 9
  R2               1                 3
  RX               9                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     3
  6Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          20   168
  6Q LOSS WILD-TYPE                        32   222
D53V14, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                     20                32
  WHITE                                        168               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3 160
  6Q LOSS WILD-TYPE   4 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  160
  6Q LOSS WILD-TYPE    4  224
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             160               224
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    24  10
  7P LOSS WILD-TYPE 299 171
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               34               470 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               10               171 
$`7P LOSS MUTATED`
TCGA-05-4427 TCGA-38-4630 TCGA-44-7670 TCGA-44-8119 TCGA-49-6742 TCGA-91-7771 
       26.01        35.28        29.00         9.37        16.04        16.18 
TCGA-93-8067 TCGA-05-4249 TCGA-44-5643 TCGA-44-6145 TCGA-44-A47B TCGA-49-AAR9 
        6.12        50.07        33.30        19.56         9.44         8.55 
TCGA-50-5931 TCGA-53-7813 TCGA-55-1594 TCGA-55-8507 TCGA-62-A46O TCGA-62-A471 
       14.27        13.94        38.73        13.74        47.80        40.96 
TCGA-67-3774 TCGA-69-7763 TCGA-73-4659 TCGA-75-5146 TCGA-78-7167 TCGA-78-7220 
       12.66        22.68        23.38        77.85        88.14        26.53 
TCGA-86-8278 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6840 TCGA-91-8499 TCGA-95-7039 
       31.04         3.81        10.62        12.23         1.18        41.82 
TCGA-95-A4VP TCGA-97-8174 TCGA-97-A4M1 TCGA-97-A4M5 
       19.89         5.39        19.76        20.84 

$`7P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       43.53        38.10        42.08        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 
       18.31        29.23        11.08        46.72        17.16        11.64 
TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
      156.66        37.32        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       85.32        13.71         1.45        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       10.09        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       10.09         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
        4.96        29.00        22.03         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       49.05        44.61         4.37        46.98        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       34.06        33.73        26.56        28.37        28.01        23.77 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS 
       12.66         8.55        15.98        15.32        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       53.29        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       28.90        40.41       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
       49.28         8.22         9.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       36.99        36.79        27.25        34.29        30.54        35.21 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       67.89        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        3.91        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        19.99        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 
       54.35        67.96        72.30        13.61        39.25        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       56.81        39.09        81.80        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.64         6.12        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       26.73        19.43         8.42        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 
       30.31         9.24         1.25        50.33        11.18        66.64 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        22.82        32.65        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 
       26.47        41.36         1.97        10.19         2.60        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
        7.36         1.15        16.60        14.27        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 
       17.46        23.61         1.08        19.00        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       27.29         2.76        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       25.48        18.54         0.59        15.91        18.67        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        18.58        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       11.15        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        47.08         0.49         0.43        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1.18              0.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            88.14            238.29 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           19.825            21.730 
[1] "1.2 - 88.1 (19.8)"  "0.0 - 238.3 (21.7)"
[1] "hr=" "1"  
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        8        8        0         4         7
  7P LOSS WILD-TYPE       5      125      131        1        46        65
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7P LOSS MUTATED            5          1        1
  7P LOSS WILD-TYPE         67         10       24
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 8               125
  STAGE IB                 8               131
  STAGE II                 0                 1
  STAGE IIA                4                46
  STAGE IIB                7                65
  STAGE IIIA               5                67
  STAGE IIIB               1                10
  STAGE IV                 1                24
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED     9  20   4   1
  7P LOSS WILD-TYPE 162 258  42  18
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               9               162
  T2              20               258
  T3               4                42
  T4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  7P LOSS MUTATED    24   5     5
  7P LOSS WILD-TYPE 309  91    71
D54V5, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0                 24               309
  N1                  5                91
  N2+N3               5                71
[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"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    27   1
  7P LOSS WILD-TYPE 322  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     27    1
  7P LOSS WILD-TYPE  322   24
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              27               322
  1               1                24
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    15  19
  7P LOSS WILD-TYPE 261 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     15   19
  7P LOSS WILD-TYPE  261  221
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE              15               261
  MALE                19               221
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    30   2
  7P LOSS WILD-TYPE 380  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     30    2
  7P LOSS WILD-TYPE  380   58
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               30               380
  YES               2                58
[1] 2 2
[1] FALSE
D54V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7P LOSS MUTATED                            1
  7P LOSS WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7P LOSS MUTATED                                   5
  7P LOSS WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                   23
  7P LOSS WILD-TYPE                                                298
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7P LOSS MUTATED                                            0
  7P LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  7P LOSS MUTATED                                               1
  7P LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  7P LOSS MUTATED                                0
  7P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  7P LOSS MUTATED                                    0
  7P LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  7P LOSS MUTATED                              0                             3
  7P LOSS WILD-TYPE                            2                            20
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  7P LOSS MUTATED                                 0
  7P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  7P LOSS MUTATED                                               0
  7P LOSS WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7P LOSS MUTATED                              1
  7P LOSS WILD-TYPE                            9
D54V10, multiclass
                                                    clus
vv                                                   7P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              23
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   7P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               298
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
D54V12, continuous
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    18   1   0   2
  7P LOSS WILD-TYPE 326  12   4  24
D54V13, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              18               326
  R1               1                12
  R2               0                 4
  RX               2                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     1
  7P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           2    28
  7P LOSS WILD-TYPE                        50   362
D54V14, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      2                50
  WHITE                                         28               362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  27
  7P LOSS WILD-TYPE   6 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   27
  7P LOSS WILD-TYPE    6  357
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              27               357
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    31  10
  7Q LOSS WILD-TYPE 292 171
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               41               463 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10               171 
$`7Q LOSS MUTATED`
TCGA-05-4427 TCGA-38-4630 TCGA-44-7670 TCGA-44-8119 TCGA-49-6742 TCGA-55-1595 
       26.01        35.28        29.00         9.37        16.04        48.62 
TCGA-55-A491 TCGA-91-7771 TCGA-93-8067 TCGA-97-A4M7 TCGA-05-4249 TCGA-05-4417 
       20.58        16.18         6.12        20.68        50.07        14.96 
TCGA-44-5643 TCGA-44-A47B TCGA-49-AAR9 TCGA-50-5931 TCGA-50-6673 TCGA-53-7813 
       33.30         9.44         8.55        14.27         0.72        13.94 
TCGA-55-1594 TCGA-55-6982 TCGA-55-7727 TCGA-55-A4DG TCGA-62-8402 TCGA-62-A46O 
       38.73        32.71         3.91        19.99        49.25        47.80 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3774 TCGA-75-5146 TCGA-75-6214 TCGA-75-7025 
       20.05        20.05        12.66        77.85        36.66       108.66 
TCGA-86-8278 TCGA-91-6828 TCGA-91-6840 TCGA-95-7039 TCGA-95-A4VP TCGA-97-8174 
       31.04        10.62        12.23        41.82        19.89         5.39 
TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8032 
       16.41        19.76        20.84        18.67         1.45 

$`7Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       43.53        38.10        42.08        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 
       18.31        29.23        11.08        46.72        17.16        11.64 
TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
      156.66        37.32        40.60        21.47        41.69        23.05 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        1.45        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       24.30        23.80         6.35        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 
        5.29        31.23         2.43        10.09         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        2.04         0.46         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       38.24        38.89        34.06        33.73        26.56        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       15.32        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO 
       22.26        73.12        62.24        28.90        40.41       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      221.33       164.12         9.86        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        6.21        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        35.21        67.89        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        3.88        69.34        45.34        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
       22.03        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       42.38        14.60        88.64        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       56.81        39.09        81.80        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        2.04        42.90        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
       13.41        13.51        14.01        13.45         4.24        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       19.43         8.42        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 
       30.31         9.24         1.25        50.33        11.18        66.64 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       43.82        85.15        49.84       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        22.82        32.65        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
        0.62        28.34        26.50        29.46         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        41.36         1.97        10.19         2.60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 
       18.67        12.39        27.29         2.76        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.67        18.12        15.39        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R 
       21.44        24.56        34.85        36.76        21.57        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
       18.08        35.47        32.48        19.00        14.30        14.53 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        1.91        18.58        15.65        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.72              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           108.66            238.29 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            19.99             22.03 
[1] "0.7 - 108.7 (20.0)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1.3"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         1       12       11        0         3         7
  7Q LOSS WILD-TYPE       4      121      128        1        47        65
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7Q LOSS MUTATED            6          1        0
  7Q LOSS WILD-TYPE         66         10       25
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                12               121
  STAGE IB                11               128
  STAGE II                 0                 1
  STAGE IIA                3                47
  STAGE IIB                7                65
  STAGE IIIA               6                66
  STAGE IIIB               1                10
  STAGE IV                 0                25
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED    15  21   4   1
  7Q LOSS WILD-TYPE 156 257  42  18
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              15               156
  T2              21               257
  T3               4                42
  T4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  7Q LOSS MUTATED    30   5     6
  7Q LOSS WILD-TYPE 303  91    70
D55V5, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0                 30               303
  N1                  5                91
  N2+N3               6                70
[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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    34   0
  7Q LOSS WILD-TYPE 315  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     34    0
  7Q LOSS WILD-TYPE  315   25
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              34               315
  1               0                25
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    23  18
  7Q LOSS WILD-TYPE 253 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     23   18
  7Q LOSS WILD-TYPE  253  222
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              23               253
  MALE                18               222
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    35   2
  7Q LOSS WILD-TYPE 375  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     35    2
  7Q LOSS WILD-TYPE  375   58
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               35               375
  YES               2                58
[1] 2 2
[1] FALSE
D55V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7Q LOSS MUTATED                            1
  7Q LOSS WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7Q LOSS MUTATED                                   8
  7Q LOSS WILD-TYPE                                99
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                   27
  7Q LOSS WILD-TYPE                                                294
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7Q LOSS MUTATED                                            0
  7Q LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  7Q LOSS MUTATED                                               1
  7Q LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  7Q LOSS MUTATED                                1
  7Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  7Q LOSS MUTATED                                    0
  7Q LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  7Q LOSS MUTATED                              0                             2
  7Q LOSS WILD-TYPE                            2                            21
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  7Q LOSS MUTATED                                 0
  7Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  7Q LOSS MUTATED                                               0
  7Q LOSS WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7Q LOSS MUTATED                              1
  7Q LOSS WILD-TYPE                            9
D55V10, multiclass
                                                    clus
vv                                                   7Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              27
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   7Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               294
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
D55V12, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    24   1   0   2
  7Q LOSS WILD-TYPE 320  12   4  24
D55V13, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              24               320
  R1               1                12
  R2               0                 4
  RX               2                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     2
  7Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           3    30
  7Q LOSS WILD-TYPE                        49   360
D55V14, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                      3                49
  WHITE                                         30               360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V15, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  31
  7Q LOSS WILD-TYPE   6 353
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   31
  7Q LOSS WILD-TYPE    6  353
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              31               353
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   127  69
  8P LOSS WILD-TYPE 196 112
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              196               308 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               69               112 
$`8P LOSS MUTATED`
TCGA-05-4402 TCGA-05-4427 TCGA-38-4631 TCGA-44-2662 TCGA-44-6147 TCGA-44-7670 
        8.02        26.01        11.64        42.08        27.78        29.00 
TCGA-49-4501 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-50-6597 TCGA-55-1595 
       46.72        11.64        37.32        40.60        41.69        48.62 
TCGA-55-6979 TCGA-55-7573 TCGA-55-7726 TCGA-55-7914 TCGA-55-8205 TCGA-55-8207 
        7.79        16.01        21.44         6.15        19.69        32.12 
TCGA-55-A491 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-8660 TCGA-80-5611 
       20.58        13.87        82.68        39.09        10.55        85.32 
TCGA-91-6836 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
       13.71         6.12        17.29        16.54         2.86        15.68 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       21.40        18.18        17.75        20.68        24.30        23.80 
TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4420 
        2.43        50.07        45.01        37.02         0.00        29.98 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4433 TCGA-05-5425 TCGA-35-4122 TCGA-35-4123 
       12.00        21.99        24.00        29.00         7.40         5.98 
TCGA-38-4628 TCGA-44-2657 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       49.05        44.42        25.02        38.89        34.06        33.73 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 TCGA-44-6774 TCGA-44-6777 TCGA-44-7660 
       33.30        28.37        19.56        21.63        32.45        19.46 
TCGA-44-7662 TCGA-44-8117 TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
        7.17        12.66        13.45        28.11        28.57        12.66 
TCGA-49-4505 TCGA-49-4510 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV 
       14.07        29.46        53.29        55.33        22.26        22.26 
TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 
       28.90       123.58       221.33       101.72        47.41        49.28 
TCGA-50-5931 TCGA-50-5939 TCGA-50-5941 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 
       14.27        15.12        48.46         3.91        11.05        12.16 
TCGA-50-6673 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 
        0.72        34.29        30.54        35.21        38.73        30.58 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-7283 TCGA-55-7570 
       69.34        45.34        32.71        40.54        20.02        27.09 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       22.03         3.91        18.64        18.44        19.82        29.23 
TCGA-55-8092 TCGA-55-8097 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-A493 
        5.06        15.65        15.72         0.36        17.72         0.92 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8402 TCGA-62-A46O 
       19.99        17.95         4.57        39.98        49.25        47.80 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
       67.96        29.92        56.81        39.09        81.80        38.37 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.47        20.05        20.05        18.84 
TCGA-69-7760 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 
        6.64         4.41        13.41        13.51         4.24        26.73 
TCGA-73-4668 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 
       15.35        50.33        11.18        43.82        49.84        36.66 
TCGA-75-7025 TCGA-78-7150 TCGA-78-7152 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 
      108.66        21.90        39.95         8.02        26.01        10.55 
TCGA-78-8640 TCGA-78-8662 TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
      232.18       110.50         5.88        38.04        32.78        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8359 
       37.74         4.08         0.79        22.82        31.20        14.60 
TCGA-86-8668 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6847 
       13.91        29.46         3.81        24.23        13.64        27.68 
TCGA-91-8499 TCGA-91-A4BD TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.18        19.82        41.82        12.39        27.29         2.76 
TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 TCGA-97-8547 
       42.25        25.48        18.54         0.59        18.67        21.60 
TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8032 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W 
       21.44        24.56         1.45        35.47        19.00        14.53 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        1.91        18.58        15.65        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TJ TCGA-MP-A4TK 
       58.45        86.04         5.49        41.59        11.15        19.13 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-O1-A52J 
       71.05         0.13        47.08        59.11 

$`8P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 
       19.96        14.01         9.96        20.05         9.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       15.02        28.41        35.28        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 
       38.10        23.93        86.01        18.31        29.23         9.37 
TCGA-44-A47F TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 TCGA-50-5935 TCGA-55-1592 
       11.08        16.04        17.16       156.66        21.47        23.05 
TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-8090 TCGA-55-8091 
        5.79         7.99        23.18        14.53        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.98        16.93        18.15        13.68        16.93        22.65 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 
       19.59        20.19        20.65        52.60         8.48        50.24 
TCGA-91-7771 TCGA-91-A4BC TCGA-95-7948 TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       16.18         1.45        15.65        17.92        20.19        20.52 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
        6.35        10.09        21.83        27.19         5.29        31.23 
TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       10.09         3.98        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 
       14.96        30.02        26.01        25.02        25.02         4.96 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 
       22.03         9.04         2.04         0.46         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2659 
      120.79        37.71        44.61         4.37        46.98        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5645 
       42.77         3.19        37.15        38.24        26.56        28.01 
TCGA-44-6144 TCGA-44-6148 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.77        23.15        23.18        61.28        16.44        22.72 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       36.07        18.87        23.64         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 
        9.44        11.54        13.64        76.21        35.54        32.84 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 
        8.81        29.75        55.89        73.12        62.24         8.55 
TCGA-49-AARE TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
       40.41       164.12         9.86        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5942 
       60.16         8.22         9.27        78.67         8.45        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 TCGA-50-7109 
       57.53        53.16        42.35        25.55         6.21        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-55-1596 TCGA-55-6543 
       36.99        36.79        27.25        13.94        67.89        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
       53.65         3.88        92.81        24.99       107.21        70.26 
TCGA-55-7281 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
       28.67        32.71        23.15        25.41        11.28        34.19 
TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 
       17.65        29.72        15.19        23.08        17.79        23.64 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 
       29.19        22.16        15.42        17.56        14.47        13.74 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       20.28        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A494 
        1.58        12.33        20.71        21.40         3.25        15.81 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       42.38        14.60        88.64        19.53        56.71        54.35 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5774 
       72.30        13.61        39.25        40.96        37.02        87.98 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       28.41        51.25        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        4.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
        6.05        14.01        13.45        19.43         8.42        23.38 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 
       26.30         4.31        30.31         9.24         1.25        66.64 
TCGA-75-5146 TCGA-75-6206 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       77.85        85.15       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       19.27        20.58       129.53       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 
      238.29        88.14        26.53        31.20        53.33        39.35 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       39.75        77.59        93.11        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
       34.39        20.55        35.24         4.57        24.33        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 
       31.04        23.05        21.47        11.61        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        0.62        28.34        26.50        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
        1.97        10.19         2.60        12.23         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
       16.60        14.27        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7567 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       19.00        18.67        19.89        64.60        63.52        61.48 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       15.91         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 
       20.58        19.76        20.84        18.67        34.85        36.76 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4SY 
       21.57        21.63        18.08        32.48        14.30        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       37.35        58.85        29.46        11.05        24.36        14.10 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       73.91        74.33         1.64         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-S2-AA1A 
       20.28        16.87 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.00              0.43 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           232.18            238.29 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           22.145            21.120 
[1] "0.0 - 232.2 (22.1)" "0.4 - 238.3 (21.1)"
[1] "hr=" "1"  
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         4       53       49        1        22        32
  8P LOSS WILD-TYPE       1       80       90        0        28        40
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8P LOSS MUTATED           27          2        8
  8P LOSS WILD-TYPE         45          9       17
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                53                80
  STAGE IB                49                90
  STAGE II                 1                 0
  STAGE IIA               22                28
  STAGE IIB               32                40
  STAGE IIIA              27                45
  STAGE IIIB               2                 9
  STAGE IV                 8                17
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P LOSS MUTATED    73 106  17   4
  8P LOSS WILD-TYPE  98 172  29  15
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              73                98
  T2             106               172
  T3              17                29
  T4               4                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  8P LOSS MUTATED   126  40    30
  8P LOSS WILD-TYPE 207  56    46
D56V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                126               207
  N1                 40                56
  N2+N3              30                46
[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"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   133   8
  8P LOSS WILD-TYPE 216  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    133    8
  8P LOSS WILD-TYPE  216   17
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             133               216
  1               8                17
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   120  80
  8P LOSS WILD-TYPE 156 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    120   80
  8P LOSS WILD-TYPE  156  160
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE             120               156
  MALE                80               160
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   158  24
  8P LOSS WILD-TYPE 252  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    158   24
  8P LOSS WILD-TYPE  252   36
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              158               252
  YES              24                36
[1] 2 2
[1] FALSE
D56V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8P LOSS MUTATED                            7
  8P LOSS WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8P LOSS MUTATED                                  38
  8P LOSS WILD-TYPE                                69
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                  132
  8P LOSS WILD-TYPE                                                189
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8P LOSS MUTATED                                            1
  8P LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  8P LOSS MUTATED                                               7
  8P LOSS WILD-TYPE                                            12
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  8P LOSS MUTATED                                2
  8P LOSS WILD-TYPE                              0
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  8P LOSS MUTATED                                    3
  8P LOSS WILD-TYPE                                  0
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  8P LOSS MUTATED                              0                             5
  8P LOSS WILD-TYPE                            2                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  8P LOSS MUTATED                                 1
  8P LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  8P LOSS MUTATED                                               3
  8P LOSS WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  8P LOSS MUTATED                              1
  8P LOSS WILD-TYPE                            9
D56V10, multiclass
                                                    clus
vv                                                   8P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             132
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    7
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    5
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   8P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               189
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     12
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
D56V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   137   2   1  12
  8P LOSS WILD-TYPE 207  11   3  14
D56V13, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             137               207
  R1               2                11
  R2               1                 3
  RX              12                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1     4
  8P LOSS WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          21   146
  8P LOSS WILD-TYPE                        31   244
D56V14, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 3
  BLACK OR AFRICAN AMERICAN                     21                31
  WHITE                                        146               244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4 149
  8P LOSS WILD-TYPE   3 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4  149
  8P LOSS WILD-TYPE    3  235
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             149               235
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    37  19
  8Q LOSS WILD-TYPE 286 162
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               56               448 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               19               162 
$`8Q LOSS MUTATED`
TCGA-49-4501 TCGA-50-6597 TCGA-55-7573 TCGA-67-6217 TCGA-73-7498 TCGA-80-5611 
       46.72        41.69        16.01        13.87        39.09        85.32 
TCGA-97-A4M7 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-44-2657 
       20.68         2.99        29.98        12.00        21.99        44.42 
TCGA-44-3919 TCGA-44-6145 TCGA-44-7660 TCGA-49-4487 TCGA-49-4490 TCGA-49-6743 
       33.73        19.56        19.46        28.11        12.66        53.29 
TCGA-49-6744 TCGA-49-AAR4 TCGA-50-5049 TCGA-50-5068 TCGA-53-7626 TCGA-55-7727 
       55.33        28.90       101.72        49.28        30.54         3.91 
TCGA-55-7903 TCGA-55-8506 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-64-1676 
       18.64         0.36        19.99        17.95         4.57        56.81 
TCGA-64-1679 TCGA-69-7980 TCGA-69-8453 TCGA-73-4668 TCGA-73-A9RS TCGA-75-6212 
       81.80        13.51        26.73        15.35        11.18        49.84 
TCGA-75-7025 TCGA-78-7150 TCGA-78-8640 TCGA-86-6851 TCGA-86-8055 TCGA-86-8074 
      108.66        21.90       232.18         5.88         4.08         0.79 
TCGA-86-8279 TCGA-86-A4JF TCGA-95-7039 TCGA-95-7944 TCGA-95-8494 TCGA-97-7546 
       31.20        24.23        41.82        12.39         2.76        42.25 
TCGA-97-7554 TCGA-97-8171 TCGA-97-8547 TCGA-MN-A4N4 TCGA-MP-A4T7 TCGA-MP-A4TK 
       25.48        18.67        21.60        38.63         5.49        19.13 
TCGA-NJ-A4YI TCGA-O1-A52J 
        0.13        59.11 

$`8Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 
       27.78        86.01        18.31        29.00        29.23         9.37 
TCGA-44-A47F TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
       11.08        16.04        17.16        11.64       156.66        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       40.60        21.47        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
        7.99        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
       19.73        17.98        16.93        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       13.68        16.93        22.65        20.58        19.59        20.19 
TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       20.65        52.60        82.68         8.48        50.24        10.55 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.19        20.52        17.75        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       10.09        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4424 TCGA-05-4426 
       24.03        47.05        19.00        14.96        30.02        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
        9.04         2.04         0.46         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       46.98        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        38.89        34.06        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       28.01        23.77        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       61.28        16.44        22.72         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4494 
       11.54        13.64        13.45        76.21        28.57        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        22.26        73.12        62.24         8.55        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       15.72        60.16        47.41         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       34.29        13.94        35.21        38.73        67.89        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 
       20.02        27.09        32.71        22.03        23.15        25.41 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       14.47        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 
       21.40         3.25         0.92        15.81        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        39.09        37.02        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       42.90        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        13.41        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
       19.43         8.42        23.38        26.30         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       85.15        36.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       19.27        20.58       129.53        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35        10.55        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
      110.50        93.11        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       38.04        20.55        32.78        19.89        35.24        37.74 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
        4.57        24.33        22.82        32.65        31.04        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
        0.62        28.34        26.50        29.46         3.81        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7567 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       19.00        18.67        27.29        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 
       61.48        18.54         0.59        15.91         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        16.41        14.30        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        21.63        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 
       14.30        14.53         1.91        18.58        15.65         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        74.33         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.43        19.82        20.28        16.87 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.13              0.00 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           232.18            238.29 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           21.945            21.520 
[1] "0.1 - 232.2 (21.9)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.2"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         1       15        8        0         9        10
  8Q LOSS WILD-TYPE       4      118      131        1        41        62
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8Q LOSS MUTATED            8          2        3
  8Q LOSS WILD-TYPE         64          9       22
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                15               118
  STAGE IB                 8               131
  STAGE II                 0                 1
  STAGE IIA                9                41
  STAGE IIB               10                62
  STAGE IIIA               8                64
  STAGE IIIB               2                 9
  STAGE IV                 3                22
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED    22  26   6   2
  8Q LOSS WILD-TYPE 149 252  40  17
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              22               149
  T2              26               252
  T3               6                40
  T4               2                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  8Q LOSS MUTATED    30  14    11
  8Q LOSS WILD-TYPE 303  82    65
D57V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0                 30               303
  N1                 14                82
  N2+N3              11                65
[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"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    37   3
  8Q LOSS WILD-TYPE 312  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     37    3
  8Q LOSS WILD-TYPE  312   22
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              37               312
  1               3                22
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    32  24
  8Q LOSS WILD-TYPE 244 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     32   24
  8Q LOSS WILD-TYPE  244  216
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              32               244
  MALE                24               216
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    45   7
  8Q LOSS WILD-TYPE 365  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     45    7
  8Q LOSS WILD-TYPE  365   53
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               45               365
  YES               7                53
[1] 2 2
[1] FALSE
D57V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8Q LOSS MUTATED                            1
  8Q LOSS WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8Q LOSS MUTATED                                  10
  8Q LOSS WILD-TYPE                                97
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                   36
  8Q LOSS WILD-TYPE                                                285
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8Q LOSS MUTATED                                            0
  8Q LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  8Q LOSS MUTATED                                               1
  8Q LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  8Q LOSS MUTATED                                1
  8Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  8Q LOSS MUTATED                                    2
  8Q LOSS WILD-TYPE                                  1
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  8Q LOSS MUTATED                              0                             3
  8Q LOSS WILD-TYPE                            2                            20
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  8Q LOSS MUTATED                                 0
  8Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  8Q LOSS MUTATED                                               1
  8Q LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  8Q LOSS MUTATED                              1
  8Q LOSS WILD-TYPE                            9
D57V10, multiclass
                                                    clus
vv                                                   8Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              36
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   8Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               285
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     20
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
D57V12, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    39   1   0   0
  8Q LOSS WILD-TYPE 305  12   4  26
D57V13, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              39               305
  R1               1                12
  R2               0                 4
  RX               0                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  1     1
  8Q LOSS WILD-TYPE                                0     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           3    40
  8Q LOSS WILD-TYPE                        49   350
D57V14, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      3                49
  WHITE                                         40               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  41
  8Q LOSS WILD-TYPE   7 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   41
  8Q LOSS WILD-TYPE    7  343
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              41               343
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   161 104
  9P LOSS WILD-TYPE 162  77
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              265               239 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              104                77 
$`9P LOSS MUTATED`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-5420 
       14.01         9.96         8.02        20.05         9.01        15.02 
TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       35.28        11.64        14.73        38.10        42.08        23.93 
TCGA-44-7670 TCGA-44-7671 TCGA-49-4501 TCGA-49-6742 TCGA-49-AAR0 TCGA-50-5932 
       29.00        29.23        46.72        16.04       156.66        40.60 
TCGA-50-5935 TCGA-55-1592 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 
       21.47        23.05        16.01        23.18        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-A48X 
       19.66        19.73        17.98        16.93        32.12        22.65 
TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       19.59        13.87        82.68         8.48        50.24        10.55 
TCGA-80-5611 TCGA-95-7948 TCGA-95-A4VK TCGA-97-A4M7 TCGA-J2-8192 TCGA-MN-A4N1 
       85.32        15.65        21.40        20.68        24.30        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
        5.29        31.23        10.09        50.07         3.98        45.01 
TCGA-05-4395 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4433 TCGA-05-5423 
        0.00         2.99        29.98        30.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-38-4627 
       29.00        22.03         9.04         2.04         7.40        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-3917 
       49.05        44.61         4.37        44.42        44.94        38.89 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       33.30        28.37        23.77        32.45        61.28        16.44 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 
       19.46         7.17        36.07        18.87        12.66         8.55 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.64        13.45        28.11        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV 
       32.84        29.46        55.89        53.29        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO TCGA-50-5055 TCGA-50-5068 
       73.12        62.24         8.55       123.58        60.16        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 
       57.53        53.16        25.55        11.05        12.16         0.72 
TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       10.13        36.79        27.25        34.29        30.54        13.94 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 
       38.73        67.89        30.58        80.52         5.62        46.03 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 
        3.88        69.34        45.34        32.71        40.54       107.21 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 TCGA-55-7907 TCGA-55-7994 
       28.67        20.02        27.09        22.03        11.28        19.82 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8505 
       23.08         5.06        17.79        15.65        29.19        14.47 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8614 TCGA-55-8615 TCGA-55-A490 
       13.74        17.72        19.96        17.62        14.66         3.25 
TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
        0.92        19.99        17.95        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       88.64        49.25        47.80        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
       40.96        29.92        56.81        39.09        81.80        37.02 
TCGA-64-1681 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
       38.37        28.47        20.05        20.05        18.84        12.66 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7974 
        4.64         6.64         6.12        22.68        13.61         6.05 
TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       13.51         4.24        26.73        15.35         4.31        30.31 
TCGA-73-A9RS TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       11.18        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 
       32.09        22.92         9.57        88.14        26.53        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 
       10.55       232.18        77.59        34.39        38.04        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
       35.24        37.74         4.08         4.57         0.79        22.82 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 
       31.20        23.05        21.47        11.61        13.91         0.62 
TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       29.46        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JN 
       27.68         7.36         1.15         1.18        17.46        23.61 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7937 
       18.67        27.29         2.76        19.89        64.60        18.54 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        5.39        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       21.44        19.76        18.67         1.45        21.57        18.08 
TCGA-J2-A4AG TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       32.48        14.53        18.58        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       86.14        58.45        49.35        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG 
       29.46        11.05        73.91         0.13        47.08        20.28 
TCGA-O1-A52J 
       59.11 

$`9P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4427 TCGA-05-4434 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 
       19.96        26.01        15.02        28.41        26.30        43.53 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-8119 TCGA-44-A47F TCGA-49-6745 
       27.78        86.01        18.31         9.37        11.08        17.16 
TCGA-49-6761 TCGA-49-AARN TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       11.64        37.32        41.69        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7725 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
        7.99        14.53        19.69        18.15        13.68        16.93 
TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-7498 TCGA-91-6836 
       20.58        20.19        20.65        52.60        39.09        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       15.68        18.18        17.92        20.19        20.52        17.75 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TC TCGA-05-4390 
       23.80         6.35        10.09        21.83         2.43        37.02 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
       24.03        47.05        19.00        14.96        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 
       26.01        25.02        25.02         0.46         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-44-2656 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       97.74       120.79        46.98        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        34.06        33.73        26.56        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-7659 TCGA-44-7672 
       19.56        23.15        21.63        23.18        22.72        23.64 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4488 
       15.98        15.32         9.44        11.54        76.21        28.57 
TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARQ 
        8.81        29.75        55.33        28.90        40.41       221.33 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47       101.72        15.72 
TCGA-50-5066 TCGA-50-5941 TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 TCGA-50-6595 
       47.41        48.46        60.72        42.35         3.91         6.21 
TCGA-50-8457 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       36.99        35.21        14.30        42.51        40.73        15.25 
TCGA-55-6972 TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 TCGA-55-7574 TCGA-55-7727 
       53.65        92.81        24.99        70.26        32.71         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       23.15        25.41        18.64        34.19        17.65        18.44 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8208 TCGA-55-8299 
       29.23        29.72        15.19        23.64        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8513 TCGA-55-8514 
       17.56        15.72         0.36        20.28        26.01        17.10 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A494 TCGA-62-8394 
        1.58        12.33        20.71        21.40        15.81         4.57 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-64-5774 TCGA-64-5775 
       19.53        56.71        54.35        67.96        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       42.90        28.41        51.25        14.04        14.73         5.72 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        5.42         7.56         4.41        13.41        14.01        13.45 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 
       19.43         8.42        23.38        26.30         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-78-7152 
       50.33        66.64        77.85        43.82        85.15        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
      119.51        19.50        38.50         5.88        64.90       104.19 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-8648 
      238.29        31.20         8.02        53.33        26.01        39.75 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7714 TCGA-86-7953 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 
       20.55        32.78        24.33        32.65        31.04        14.60 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF 
       30.84        27.58        28.34        26.50         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       13.64        26.47        10.62        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-97-7546 
       22.45         1.08        19.00        41.82        12.39        42.25 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        61.48        25.48         0.59        15.91        18.67 
TCGA-97-8175 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R 
       18.12        20.84        24.56        34.85        36.76        21.63 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-MP-A4T2 TCGA-MP-A4T4 
       35.47        19.00        14.30         1.91        37.35        86.04 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        11.15        19.13        71.05        74.33 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        1.64         0.49         0.43        19.82        16.87 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.00              0.36 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           232.18            238.29 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            21.57             21.63 
[1] "0.0 - 232.2 (21.6)" "0.4 - 238.3 (21.6)"
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         3       60       68        1        29        43
  9P LOSS WILD-TYPE       2       73       71        0        21        29
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9P LOSS MUTATED           43          6       14
  9P LOSS WILD-TYPE         29          5       11
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                60                73
  STAGE IB                68                71
  STAGE II                 1                 0
  STAGE IIA               29                21
  STAGE IIB               43                29
  STAGE IIIA              43                29
  STAGE IIIB               6                 5
  STAGE IV                14                11
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED    84 147  26  11
  9P LOSS WILD-TYPE  87 131  20   8
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              84                87
  T2             147               131
  T3              26                20
  T4              11                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  9P LOSS MUTATED   161  61    43
  9P LOSS WILD-TYPE 172  35    33
D58V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                161               172
  N1                 61                35
  N2+N3              43                33
[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"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   185  14
  9P LOSS WILD-TYPE 164  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    185   14
  9P LOSS WILD-TYPE  164   11
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             185               164
  1              14                11
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   133 136
  9P LOSS WILD-TYPE 143 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    133  136
  9P LOSS WILD-TYPE  143  104
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE             133               143
  MALE               136               104
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   210  36
  9P LOSS WILD-TYPE 200  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    210   36
  9P LOSS WILD-TYPE  200   24
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              210               200
  YES              36                24
[1] 2 2
[1] FALSE
D58V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9P LOSS MUTATED                           11
  9P LOSS WILD-TYPE                          7
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9P LOSS MUTATED                                  57
  9P LOSS WILD-TYPE                                50
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                  167
  9P LOSS WILD-TYPE                                                154
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9P LOSS MUTATED                                            2
  9P LOSS WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  9P LOSS MUTATED                                              10
  9P LOSS WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  9P LOSS MUTATED                                1
  9P LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  9P LOSS MUTATED                                    3
  9P LOSS WILD-TYPE                                  0
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  9P LOSS MUTATED                              1                            10
  9P LOSS WILD-TYPE                            1                            13
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  9P LOSS MUTATED                                 0
  9P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  9P LOSS MUTATED                                               3
  9P LOSS WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9P LOSS MUTATED                              4
  9P LOSS WILD-TYPE                            6
D58V10, multiclass
                                                    clus
vv                                                   9P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               57
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             167
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                   10
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     4
                                                    clus
vv                                                   9P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               154
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     13
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
D58V12, continuous
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED   179   7   2  13
  9P LOSS WILD-TYPE 165   6   2  13
D58V13, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             179               165
  R1               7                 6
  R2               2                 2
  RX              13                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  1     2
  9P LOSS WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          25   206
  9P LOSS WILD-TYPE                        27   184
D58V14, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                     25                27
  WHITE                                        206               184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4 193
  9P LOSS WILD-TYPE   3 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  193
  9P LOSS WILD-TYPE    3  191
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             193               191
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   154  92
  9Q LOSS WILD-TYPE 169  89
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              246               258 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               92                89 
$`9Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4418 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 
       19.96         8.02         9.01        15.02        35.28        11.64 
TCGA-38-6178 TCGA-44-2661 TCGA-44-2662 TCGA-44-7670 TCGA-44-7671 TCGA-49-4501 
       14.73        38.10        42.08        29.00        29.23        46.72 
TCGA-49-6742 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-7573 
       16.04       156.66        40.60        21.47        23.05        16.01 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 
       23.18        21.44         6.15        19.66        17.98        16.93 
TCGA-55-8207 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 
       32.12        22.65        20.58        19.59        20.19        13.87 
TCGA-73-4662 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-95-7948 TCGA-95-A4VK 
       82.68        50.24        10.55        85.32        15.65        21.40 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 
       20.68        24.30        27.19        31.23        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 
        3.98        45.01         2.99        29.98        30.02        25.02 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 
       24.00        29.00        22.03         2.04         7.40         8.68 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 
       97.74        37.71        49.05        44.61         4.37        44.42 
TCGA-44-2659 TCGA-44-3917 TCGA-44-5644 TCGA-44-6144 TCGA-44-6774 TCGA-44-6777 
       44.94        38.89        28.37        23.77        21.63        32.45 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 
       19.46         7.17        36.07        18.87        12.66         8.55 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.64        13.45        28.11        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV 
       32.84        29.46        55.89        53.29        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO TCGA-50-5055 TCGA-50-5068 
       73.12        62.24         8.55       123.58        60.16        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5944 TCGA-50-6593 
        8.22        14.27        78.67         8.45        57.53        11.05 
TCGA-50-6594 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       12.16         0.72        10.13        36.79        27.25        34.29 
TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
       13.94        38.73        67.89        30.58        80.52         5.62 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 
       46.03         3.88        69.34        45.34        32.71        40.54 
TCGA-55-6986 TCGA-55-7283 TCGA-55-7570 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 
      107.21        20.02        27.09        11.28        17.65        19.82 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8505 TCGA-55-8507 
       23.08        17.79        15.65        29.19        14.47        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       20.28        17.72        19.96        17.10        17.62        14.66 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 
        0.92        15.81        19.99        17.95        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y 
       88.64        49.25        47.80        56.71        72.30        13.61 
TCGA-62-A470 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       39.25        56.81        81.80        37.02        38.37        87.98 
TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-69-7760 
       28.41        20.05        20.05        18.84        12.66         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 
        6.12        22.68         7.56         6.05        13.51         4.24 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-A9RS 
       19.43        23.38        15.35         4.31        30.31        11.18 
TCGA-75-5146 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       77.85        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-8640 TCGA-80-5608 
       64.90         9.57        88.14        26.53       232.18        93.11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 
       34.39        38.04        19.89        35.24         4.08         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
       22.82        31.20        23.05        21.47        11.61        13.91 
TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
        0.62        29.46        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-93-7348 TCGA-95-7039 
       12.23        27.68         7.36         1.18        17.46        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7937 
       18.67        27.29         2.76        19.89        64.60        18.54 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
        5.39        15.39        16.41        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG 
       19.76        18.67         1.45        21.57        18.08        32.48 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
       14.53        18.58        15.65        38.63        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       49.35        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
       11.15        73.91         0.13        47.08        20.28        59.11 

$`9Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 TCGA-38-4629 
       14.01         9.96        20.05        26.01        15.02        28.41 
TCGA-38-7271 TCGA-44-2655 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        43.53        23.93        27.78        86.01        18.31 
TCGA-44-8119 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-6597 
        9.37        11.08        17.16        11.64        37.32        41.69 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 TCGA-55-8091 
       48.62         5.79         7.79         7.99        14.53        19.73 
TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-64-1677 TCGA-73-4658 
       19.69        18.15        13.68        16.93        20.65        52.60 
TCGA-73-7498 TCGA-78-7166 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       39.09         8.48        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN TCGA-97-8172 
       17.29        16.54         2.86        15.68        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       20.19        20.52        17.75        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       21.83         5.29         2.43        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       47.05        19.00        14.96        12.00        21.99        26.01 
TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 
       25.02         4.96         9.04         0.46         5.98       120.79 
TCGA-44-2656 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       46.98        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 
       34.06        33.73        26.56        33.30        28.01        19.56 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7672 
       23.15        23.18        61.28        16.44        22.72        23.64 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4488 
       15.98        15.32         9.44        11.54        76.21        28.57 
TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARQ 
        8.81        29.75        55.33        28.90        40.41       221.33 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47       101.72        15.72 
TCGA-50-5066 TCGA-50-5930 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
       47.41         9.27        15.12        48.46        60.72        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-8457 TCGA-53-7626 
       42.35         3.91        25.55         6.21        36.99        30.54 
TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       35.21        14.30        42.51        40.73        15.25        53.65 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 TCGA-55-7574 TCGA-55-7576 
       92.81        24.99        70.26        28.67        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7913 
        3.91        23.15        25.41        18.64        34.19        18.44 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8208 
       29.23        29.72        15.19         5.06        23.64        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8513 TCGA-55-8616 
       15.42        17.56        15.72         0.36        26.01         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-62-8394 TCGA-62-8395 
       12.33        20.71        21.40         3.25         4.57        39.98 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 
       19.53        54.35        67.96        40.96        29.92        39.09 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-4679 
        2.04        42.90        51.25        28.47        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 
        5.72         4.64        13.61         5.42         4.41        13.41 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4666 TCGA-73-4676 
       14.01        13.45        26.73         8.42        26.30         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 TCGA-78-7152 
        1.25        50.33        66.64        43.82        85.15        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
      119.51        19.50        38.50        32.09         5.88        22.92 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      104.19       238.29        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
       39.35        10.55        39.75        77.59       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 
       12.36         5.88        31.13        20.55        32.78        37.74 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8669 
        4.57        24.33        32.65        31.04        14.60        30.84 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       27.58        28.34        26.50         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       26.47        10.62         1.15        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-97-7546 
       22.45        23.61         1.08        19.00        12.39        42.25 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        61.48        25.48         0.59        15.91        18.67 
TCGA-97-8175 TCGA-97-8179 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       18.12        14.30        20.84        24.56        34.85        36.76 
TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-MN-A4N5 
       21.63        35.47        19.00        14.30         1.91         2.76 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF 
       37.35        86.04        24.36        14.10        19.13        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
       74.33         1.64         0.49         0.43        19.82        16.87 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           232.18            238.29 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           21.585            21.730 
[1] "0.1 - 232.2 (21.6)" "0.0 - 238.3 (21.7)"
[1] "hr=" "1"  
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         3       58       67        1        28        35
  9Q LOSS WILD-TYPE       2       75       72        0        22        37
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9Q LOSS MUTATED           40          4       12
  9Q LOSS WILD-TYPE         32          7       13
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                58                75
  STAGE IB                67                72
  STAGE II                 1                 0
  STAGE IIA               28                22
  STAGE IIB               35                37
  STAGE IIIA              40                32
  STAGE IIIB               4                 7
  STAGE IV                12                13
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED    82 138  22   6
  9Q LOSS WILD-TYPE  89 140  24  13
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              82                89
  T2             138               140
  T3              22                24
  T4               6                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  9Q LOSS MUTATED   150  54    40
  9Q LOSS WILD-TYPE 183  42    36
D59V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                150               183
  N1                 54                42
  N2+N3              40                36
[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"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   168  12
  9Q LOSS WILD-TYPE 181  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    168   12
  9Q LOSS WILD-TYPE  181   13
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             168               181
  1              12                13
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   133 116
  9Q LOSS WILD-TYPE 143 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    133  116
  9Q LOSS WILD-TYPE  143  124
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE             133               143
  MALE               116               124
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   197  34
  9Q LOSS WILD-TYPE 213  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    197   34
  9Q LOSS WILD-TYPE  213   26
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              197               213
  YES              34                26
[1] 2 2
[1] FALSE
D59V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9Q LOSS MUTATED                            9
  9Q LOSS WILD-TYPE                          9
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9Q LOSS MUTATED                                  48
  9Q LOSS WILD-TYPE                                59
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                  159
  9Q LOSS WILD-TYPE                                                162
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9Q LOSS MUTATED                                            1
  9Q LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  9Q LOSS MUTATED                                              10
  9Q LOSS WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  9Q LOSS MUTATED                                1
  9Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  9Q LOSS MUTATED                                    3
  9Q LOSS WILD-TYPE                                  0
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  9Q LOSS MUTATED                              0                            10
  9Q LOSS WILD-TYPE                            2                            13
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  9Q LOSS MUTATED                                 1
  9Q LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  9Q LOSS MUTATED                                               3
  9Q LOSS WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9Q LOSS MUTATED                              4
  9Q LOSS WILD-TYPE                            6
D59V10, multiclass
                                                    clus
vv                                                   9Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             159
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                   10
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     4
                                                    clus
vv                                                   9Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               162
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     13
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
D59V12, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED   168   7   2  12
  9Q LOSS WILD-TYPE 176   6   2  14
D59V13, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0             168               176
  R1               7                 6
  R2               2                 2
  RX              12                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  1     2
  9Q LOSS WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          24   191
  9Q LOSS WILD-TYPE                        28   199
D59V14, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                     24                28
  WHITE                                        191               199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V15, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     4 185
  9Q LOSS WILD-TYPE   3 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4  185
  9Q LOSS WILD-TYPE    3  199
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             185               199
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    61  47
  10P LOSS WILD-TYPE 262 134
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               108                396 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                47                134 
$`10P LOSS MUTATED`
TCGA-05-4402 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 TCGA-44-7670 TCGA-49-4501 
        8.02        11.64        14.73        42.08        29.00        46.72 
TCGA-49-6742 TCGA-49-AAR0 TCGA-50-6597 TCGA-55-8091 TCGA-55-A48X TCGA-55-A4DF 
       16.04       156.66        41.69        19.73        22.65        20.19 
TCGA-78-8660 TCGA-80-5611 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
       10.55        85.32        17.29        16.54         2.86        15.68 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-05-5429 TCGA-05-5715 TCGA-38-4627 TCGA-38-4628 
       20.68        24.30         9.04         2.04        37.71        49.05 
TCGA-44-2657 TCGA-44-3398 TCGA-44-3919 TCGA-44-6775 TCGA-44-6779 TCGA-44-7660 
       44.42        38.24        33.73        23.18        16.44        19.46 
TCGA-44-7662 TCGA-44-7669 TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
        7.17        18.87        13.45        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-6767 TCGA-49-AARQ TCGA-50-5931 TCGA-50-5944 TCGA-50-6591 
       14.07        22.26       221.33        14.27        57.53         3.91 
TCGA-50-6593 TCGA-55-1596 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6986 
       11.05        67.89        69.34        45.34        32.71       107.21 
TCGA-55-7281 TCGA-55-7994 TCGA-55-8094 TCGA-55-8514 TCGA-55-8614 TCGA-55-A4DG 
       28.67        19.82        17.79        17.10        17.62        19.99 
TCGA-62-8394 TCGA-62-8402 TCGA-62-A46Y TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
        4.57        49.25        13.61        56.81        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-69-7973 
       87.98         2.04        28.41        20.05        18.84         7.56 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-75-5147 TCGA-75-6212 
       19.43        23.38        26.30        15.35        43.82        49.84 
TCGA-78-7147 TCGA-78-7540 TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 TCGA-86-6851 
       19.27        39.35       232.18        77.59        27.09         5.88 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 
       19.89        37.74         4.08         0.79        22.82        31.04 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8669 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6835 
       23.05        14.60        30.84        24.23        10.62         2.60 
TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 TCGA-95-8494 TCGA-97-7546 TCGA-97-8547 
       12.23         1.18        17.46         2.76        42.25        21.60 
TCGA-97-A4M1 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       19.76        18.08        32.48        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TJ TCGA-NJ-A4YI TCGA-NJ-A55A TCGA-O1-A52J 
       58.85        41.59        11.15         0.13         0.49        59.11 

$`10P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 
       15.02        15.02        28.41        35.28        26.30        43.53 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 
       38.10        23.93        27.78        86.01        18.31        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 
        9.37        11.08        17.16        11.64        37.32        40.60 
TCGA-50-5935 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       21.47        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       16.93        20.58        19.59        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-91-6836 TCGA-91-7771 
       82.68        39.09         8.48        50.24        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        1.45         6.12        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       20.19        20.52        17.75        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       21.83        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
        4.96        29.00        22.03         0.46         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
        8.68        97.74       120.79        44.61         4.37        46.98 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 
       44.94        42.77         3.19        25.02        37.15        38.89 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       34.06        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       19.56        23.15        21.63        32.45        61.28        22.72 
TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       36.07        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4506 
        9.44        11.54        13.64        76.21        28.11        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      123.58       164.12         9.86        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
       78.67         8.45        15.12        48.46        60.72        53.16 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       42.35        25.55        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       35.21        38.73        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 
       92.81        24.99        40.54        70.26        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       32.71        22.03         3.91        23.15        25.41        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 
       11.28        34.19        17.65        18.44        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19        23.08         5.06        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
       13.74        20.28        17.72        19.96        26.01        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       15.81        17.95        39.98        42.38        14.60        88.64 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1680 TCGA-64-5778 
       39.25        40.96        29.92        39.09        37.02        42.90 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       51.25        28.47        20.05        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4670 TCGA-73-4675 
       13.45         4.24        26.73         8.42         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 
        9.24         1.25        50.33        11.18        66.64        77.85 
TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       85.15        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-8648 TCGA-78-8662 
        8.02        53.33        26.01        10.55        39.75       110.50 
TCGA-80-5608 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       93.11        12.36        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 
       32.78        35.24         4.57        24.33        32.65        31.20 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       21.47        11.61        13.91        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       26.50        29.46         3.81        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        1.97        10.19        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       14.27        19.82        22.45        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7547 
       41.82        18.67        12.39        27.29        19.89        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       20.58        21.44        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E5 
       36.76         1.45        21.57        21.63        35.47        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.30        14.53         1.91        18.58        15.65        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
        2.76        86.14        58.45         5.49        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        1.64        47.08         0.43        19.82        20.28        16.87 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.13               0.00 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            232.18             238.29 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             21.14              21.63 
[1] "0.1 - 232.2 (21.1)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         1       32       24        0        13        17
  10P LOSS WILD-TYPE       4      101      115        1        37        55
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10P LOSS MUTATED           17          1        5
  10P LOSS WILD-TYPE         55         10       20
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 32                101
  STAGE IB                 24                115
  STAGE II                  0                  1
  STAGE IIA                13                 37
  STAGE IIB                17                 55
  STAGE IIIA               17                 55
  STAGE IIIB                1                 10
  STAGE IV                  5                 20
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED    44  56   8   2
  10P LOSS WILD-TYPE 127 222  38  17
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               44                127
  T2               56                222
  T3                8                 38
  T4                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  10P LOSS MUTATED    65  25    18
  10P LOSS WILD-TYPE 268  71    58
D60V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  65                268
  N1                  25                 71
  N2+N3               18                 58
[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"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    76   5
  10P LOSS WILD-TYPE 273  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     76    5
  10P LOSS WILD-TYPE  273   20
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               76                273
  1                5                 20
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    71  39
  10P LOSS WILD-TYPE 205 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     71   39
  10P LOSS WILD-TYPE  205  201
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               71                205
  MALE                 39                201
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    91  10
  10P LOSS WILD-TYPE 319  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     91   10
  10P LOSS WILD-TYPE  319   50
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                91                319
  YES               10                 50
[1] 2 2
[1] FALSE
D60V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10P LOSS MUTATED                            5
  10P LOSS WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10P LOSS MUTATED                                  15
  10P LOSS WILD-TYPE                                92
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                   79
  10P LOSS WILD-TYPE                                                242
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10P LOSS MUTATED                                            1
  10P LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  10P LOSS MUTATED                                               4
  10P LOSS WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  10P LOSS MUTATED                                0
  10P LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  10P LOSS MUTATED                                    2
  10P LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  10P LOSS MUTATED                              0                             1
  10P LOSS WILD-TYPE                            2                            22
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  10P LOSS MUTATED                                 1
  10P LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  10P LOSS MUTATED                                               1
  10P LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  10P LOSS MUTATED                              1
  10P LOSS WILD-TYPE                            9
D60V10, multiclass
                                                    clus
vv                                                   10P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     1
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   10P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                242
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
D60V12, continuous
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    80   1   1   6
  10P LOSS WILD-TYPE 264  12   3  20
D60V13, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               80                264
  R1                1                 12
  R2                1                  3
  RX                6                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  1     1
  10P LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           6    89
  10P LOSS WILD-TYPE                        46   301
D60V14, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                       6                 46
  WHITE                                          89                301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  84
  10P LOSS WILD-TYPE   5 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   84
  10P LOSS WILD-TYPE    5  300
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               84                300
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    74  55
  10Q LOSS WILD-TYPE 249 126
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               129                375 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                55                126 
$`10Q LOSS MUTATED`
TCGA-05-4402 TCGA-38-4631 TCGA-44-2662 TCGA-44-7670 TCGA-49-6742 TCGA-49-AAR0 
        8.02        11.64        42.08        29.00        16.04       156.66 
TCGA-50-6597 TCGA-55-6979 TCGA-55-8091 TCGA-55-8207 TCGA-55-A48X TCGA-55-A4DF 
       41.69         7.79        19.73        32.12        22.65        20.19 
TCGA-78-8660 TCGA-80-5611 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
       10.55        85.32        17.29        16.54         2.86        15.68 
TCGA-95-7948 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-05-4397 TCGA-05-4420 
       15.65        20.68        24.30         6.35        24.03        29.98 
TCGA-05-4424 TCGA-05-5429 TCGA-05-5715 TCGA-38-4627 TCGA-38-4628 TCGA-44-2657 
       30.02         9.04         2.04        37.71        49.05        44.42 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-6775 TCGA-44-6779 TCGA-44-7660 
       37.15        38.24        33.73        23.18        16.44        19.46 
TCGA-44-7662 TCGA-44-7669 TCGA-44-A4SU TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
        7.17        18.87        13.45        12.66        35.54        14.07 
TCGA-49-AARE TCGA-49-AARQ TCGA-50-5931 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 
       40.41       221.33        14.27        57.53         3.91        25.55 
TCGA-50-6673 TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 
        0.72        67.89        30.58        46.03        69.34        45.34 
TCGA-55-6982 TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 TCGA-55-8206 TCGA-55-8505 
       32.71       107.21        28.67        19.82        29.19        14.47 
TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8402 
       20.28        17.10        17.62        19.99         4.57        49.25 
TCGA-62-A46Y TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       13.61        56.81        81.80        38.37        87.98         2.04 
TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
       28.41        20.05        18.84         7.56         4.41        13.41 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4668 TCGA-73-A9RS TCGA-75-5125 
        4.24        19.43        26.30        15.35        11.18        66.64 
TCGA-75-5147 TCGA-75-6212 TCGA-78-7147 TCGA-78-7535 TCGA-78-7540 TCGA-78-7542 
       43.82        49.84        19.27        31.20        39.35        10.55 
TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 
      232.18        77.59        27.09         5.88        19.89        35.24 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 
        4.08         0.79        22.82        31.04        23.05        14.60 
TCGA-86-8669 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6840 
       30.84        24.23        10.62        41.36         2.60        12.23 
TCGA-91-6847 TCGA-91-8499 TCGA-93-7348 TCGA-95-7944 TCGA-97-7546 TCGA-97-8175 
       27.68         1.18        17.46        12.39        42.25        18.12 
TCGA-97-8547 TCGA-97-A4M1 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-MP-A4SY TCGA-MP-A4T2 
       21.60        19.76        18.08        32.48        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YF 
       86.04        58.85        41.59        11.05        11.15        71.05 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-O1-A52J 
        0.13        47.08        59.11 

$`10Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        35.28        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       43.53        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 
       29.23         9.37        11.08        46.72        17.16        11.64 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
       37.32        40.60        21.47        23.05        48.62         5.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 
       19.66        17.98        16.93        19.69        18.15        13.68 
TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       16.93        20.58        19.59        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-91-6836 TCGA-91-7771 
       82.68        39.09         8.48        50.24        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        1.45         6.12        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       20.52        17.75        23.80        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       45.01        37.02         0.00        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       14.96        12.00        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 
       24.00         4.96        29.00        22.03         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F 
        5.98         8.68        97.74       120.79        44.61         4.37 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 
       46.98        44.94        42.77         3.19        25.02        38.89 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       34.06        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       19.56        23.15        21.63        32.45        61.28        22.72 
TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       36.07        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
        9.44        11.54        13.64        76.21        28.11        28.57 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.33        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
        8.55       123.58       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 
       53.16        42.35        11.05        12.16         6.21        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        38.73        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6983 TCGA-55-6984 
       40.73        15.25        53.65         3.88        92.81        24.99 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       40.54        70.26        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        3.91        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        18.44        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 
        5.06        17.79        23.64        15.65        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 
       17.56        15.72         0.36        13.74        17.72        19.96 
TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       26.01        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
        3.25         0.92        15.81        17.95        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 
       67.96        72.30        39.25        40.96        29.92        39.09 
TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 
       37.02        42.90        51.25        28.47        20.05        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 
       22.68        13.61         5.42         6.05        13.51        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 
       13.45        26.73         8.42        23.38         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5146 TCGA-75-6206 TCGA-75-6214 
        9.24         1.25        50.33        77.85        85.15        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
      108.66       100.57       163.10        27.16         5.69        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      238.29        88.14        26.53         8.02        53.33        26.01 
TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       39.75       110.50        93.11        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       38.04        20.55        32.78        37.74         4.57        24.33 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
       32.65        31.20        21.47        11.61        13.91        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
        0.62        28.34        26.50        29.46         3.81        13.64 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       26.47         1.97        10.19         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       14.27        19.82        22.45        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 
       41.82        18.67        27.29         2.76        19.89        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
       18.67         5.39        15.39        16.41        14.30        20.58 
TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       21.44        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
        1.45        21.57        21.63        35.47        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        18.58        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
       86.14        58.45         5.49        29.46        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       19.13        73.91        74.33         1.64         0.49         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       19.82        20.28        16.87 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.13               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            232.18             238.29 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             22.65              21.57 
[1] "0.1 - 232.2 (22.6)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         2       38       35        0        14        21
  10Q LOSS WILD-TYPE       3       95      104        1        36        51
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10Q LOSS MUTATED           16          1        4
  10Q LOSS WILD-TYPE         56         10       21
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 38                 95
  STAGE IB                 35                104
  STAGE II                  0                  1
  STAGE IIA                14                 36
  STAGE IIB                21                 51
  STAGE IIIA               16                 56
  STAGE IIIB                1                 10
  STAGE IV                  4                 21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED    52  69   9   2
  10Q LOSS WILD-TYPE 119 209  37  17
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               52                119
  T2               69                209
  T3                9                 37
  T4                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  10Q LOSS MUTATED    84  29    17
  10Q LOSS WILD-TYPE 249  67    59
D61V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  84                249
  N1                  29                 67
  N2+N3               17                 59
[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"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    92   4
  10Q LOSS WILD-TYPE 257  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     92    4
  10Q LOSS WILD-TYPE  257   21
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               92                257
  1                4                 21
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    80  52
  10Q LOSS WILD-TYPE 196 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     80   52
  10Q LOSS WILD-TYPE  196  188
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               80                196
  MALE                 52                188
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   107  14
  10Q LOSS WILD-TYPE 303  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    107   14
  10Q LOSS WILD-TYPE  303   46
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO               107                303
  YES               14                 46
[1] 2 2
[1] FALSE
D61V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10Q LOSS MUTATED                            6
  10Q LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10Q LOSS MUTATED                                  21
  10Q LOSS WILD-TYPE                                86
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                   90
  10Q LOSS WILD-TYPE                                                231
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10Q LOSS MUTATED                                            1
  10Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  10Q LOSS MUTATED                                               5
  10Q LOSS WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  10Q LOSS MUTATED                                0
  10Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  10Q LOSS MUTATED                                    2
  10Q LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  10Q LOSS MUTATED                              0                             1
  10Q LOSS WILD-TYPE                            2                            22
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  10Q LOSS MUTATED                                 1
  10Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  10Q LOSS MUTATED                                               3
  10Q LOSS WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  10Q LOSS MUTATED                              2
  10Q LOSS WILD-TYPE                            8
D61V10, multiclass
                                                    clus
vv                                                   10Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               90
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     1
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   10Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                231
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
D61V12, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    93   1   1   9
  10Q LOSS WILD-TYPE 251  12   3  17
D61V13, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               93                251
  R1                1                 12
  R2                1                  3
  RX                9                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  1     1
  10Q LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          10   102
  10Q LOSS WILD-TYPE                        42   288
D61V14, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                      10                 42
  WHITE                                         102                288
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3  96
  10Q LOSS WILD-TYPE   4 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   96
  10Q LOSS WILD-TYPE    4  288
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               96                288
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    68  42
  11P LOSS WILD-TYPE 255 139
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               110                394 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                42                139 
$`11P LOSS MUTATED`
TCGA-05-4382 TCGA-05-4427 TCGA-05-4434 TCGA-44-2662 TCGA-44-7671 TCGA-44-A47F 
       19.96        26.01        15.02        42.08        29.23        11.08 
TCGA-55-1595 TCGA-55-7573 TCGA-55-8511 TCGA-55-A492 TCGA-91-6836 TCGA-93-8067 
       48.62        16.01        18.15        19.59        13.71         6.12 
TCGA-95-7948 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-05-4389 TCGA-05-4390 TCGA-05-4433 
       15.65        27.19         5.29        45.01        37.02        24.00 
TCGA-05-5425 TCGA-05-5428 TCGA-35-5375 TCGA-38-4632 TCGA-44-3917 TCGA-44-3918 
       29.00        22.03         8.68        44.61        38.89        34.06 
TCGA-44-5643 TCGA-44-7662 TCGA-44-7667 TCGA-44-A4SS TCGA-49-4487 TCGA-49-4490 
       33.30         7.17        36.07        13.64        28.11        12.66 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-6767 TCGA-49-AAQV 
       14.07        32.84         8.81        29.46        22.26        22.26 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-6592 TCGA-50-6593 
        8.22        14.27         8.45        15.12        25.55        11.05 
TCGA-50-6594 TCGA-50-6673 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1596 
       12.16         0.72        34.29        30.54        35.21        67.89 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6972 TCGA-55-7570 TCGA-55-7727 TCGA-55-7815 
       30.58        80.52        53.65        27.09         3.91        25.41 
TCGA-55-7903 TCGA-55-7994 TCGA-55-8089 TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 
       18.64        19.82        23.08        15.72        13.74        17.72 
TCGA-55-A490 TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46S TCGA-62-A471 TCGA-62-A472 
        3.25        19.99        42.38        54.35        40.96        29.92 
TCGA-64-1676 TCGA-64-1679 TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 TCGA-69-7763 
       56.81        81.80        87.98        42.90        28.47        22.68 
TCGA-69-7764 TCGA-69-A59K TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 
       13.61        19.43        23.38         4.31        30.31        50.33 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-7025 TCGA-78-7145 TCGA-78-7148 TCGA-78-7154 
       11.18        66.64       108.66        27.16        20.58        19.50 
TCGA-78-7160 TCGA-78-7535 TCGA-78-8640 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       22.92        31.20       232.18        31.13        34.39        38.04 
TCGA-86-7953 TCGA-86-8074 TCGA-86-8358 TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4JF 
       32.78         0.79        21.47        30.84         3.81        24.23 
TCGA-91-6847 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 TCGA-97-8174 TCGA-97-A4M1 
       27.68        27.29         2.76        61.48         5.39        19.76 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4T2 TCGA-MP-A4TE 
       18.08        19.00        18.58        15.65        37.35        29.46 
TCGA-MP-A4TF TCGA-NJ-A4YQ 
       11.05        47.08 

$`11P LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-5420 
       14.01         9.96         8.02        20.05         9.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       28.41        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
        9.37        46.72        16.04        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 
       37.32        40.60        21.47        41.69        23.05         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.79         7.99        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       19.66        19.73        17.98        16.93        19.69        32.12 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 
       13.68        16.93        22.65        20.58        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 
       10.55        85.32        16.18         1.45        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        2.86        15.68        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       10.09        21.83        31.23         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
        3.98         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       25.02        25.02         4.96         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98        97.74       120.79        37.71        49.05 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 
        4.37        46.98        44.42        44.94        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       25.02        37.15        38.24        33.73        26.56        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7669 
       32.45        61.28        16.44        22.72        19.46        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4494 TCGA-49-4512 
       11.54        13.45        76.21        28.57        35.54        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.89        53.29        55.33        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       49.28         9.27        78.67        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 
       53.16        42.35         3.91         6.21        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 
       36.79        27.25        13.94        38.73        14.30         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 
       42.51        40.73        15.25        46.03         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 
       70.26        28.67        20.02        32.71        22.03        23.15 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 
       11.28        34.19        17.65        18.44        29.23        29.72 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       22.16        15.42        17.56        14.47         0.36        20.28 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B 
       12.33        20.71        21.40         0.92        15.81        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        67.96        72.30        13.61        39.25 
TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       39.09        37.02        38.37         2.04        28.41        51.25 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       20.05        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7973 
        5.72         4.64         6.64         6.12         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
        4.24        26.73         8.42        26.30        15.35         9.24 
TCGA-73-4677 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
        1.25        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
      100.57       163.10         5.69        19.27       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.95       119.51        38.50        32.09         5.88        64.90 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        9.57       104.19       238.29        88.14        26.53         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35        10.55        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7714 
      110.50        93.11        27.09        12.36         5.88        20.55 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       22.82        32.65        31.04        31.20        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       11.61        13.91        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       29.46        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        12.23         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VP 
        1.08        19.00        41.82        18.67        12.39        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       42.25        64.60        63.52        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       15.91        18.67        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       21.60        20.58        21.44        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        21.63        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MN-A4N5 
       32.48        14.30        14.53         1.91        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        49.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       41.59        24.36        14.10        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        74.33         0.13         1.64         0.49         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.72               0.00 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            232.18             238.29 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             23.69              21.12 
[1] "0.7 - 232.2 (23.7)" "0.0 - 238.3 (21.1)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         2       23       29        1        15        19
  11P LOSS WILD-TYPE       3      110      110        0        35        53
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11P LOSS MUTATED           14          0        7
  11P LOSS WILD-TYPE         58         11       18
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 23                110
  STAGE IB                 29                110
  STAGE II                  1                  0
  STAGE IIA                15                 35
  STAGE IIB                19                 53
  STAGE IIIA               14                 58
  STAGE IIIB                0                 11
  STAGE IV                  7                 18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED    34  61  13   3
  11P LOSS WILD-TYPE 137 217  33  16
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               34                137
  T2               61                217
  T3               13                 33
  T4                3                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  11P LOSS MUTATED    71  27    13
  11P LOSS WILD-TYPE 262  69    63
D62V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                  71                262
  N1                  27                 69
  N2+N3               13                 63
[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"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    77   7
  11P LOSS WILD-TYPE 272  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     77    7
  11P LOSS WILD-TYPE  272   18
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               77                272
  1                7                 18
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    44  67
  11P LOSS WILD-TYPE 232 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     44   67
  11P LOSS WILD-TYPE  232  173
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               44                232
  MALE                 67                173
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    87  17
  11P LOSS WILD-TYPE 323  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     87   17
  11P LOSS WILD-TYPE  323   43
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                87                323
  YES               17                 43
[1] 2 2
[1] FALSE
D62V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11P LOSS MUTATED                            2
  11P LOSS WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11P LOSS MUTATED                                  23
  11P LOSS WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                   79
  11P LOSS WILD-TYPE                                                242
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11P LOSS MUTATED                                            0
  11P LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  11P LOSS MUTATED                                               2
  11P LOSS WILD-TYPE                                            17
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  11P LOSS MUTATED                                1
  11P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  11P LOSS MUTATED                                    0
  11P LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  11P LOSS MUTATED                              0                             3
  11P LOSS WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  11P LOSS MUTATED                                 0
  11P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  11P LOSS MUTATED                                               0
  11P LOSS WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  11P LOSS MUTATED                              1
  11P LOSS WILD-TYPE                            9
D62V10, multiclass
                                                    clus
vv                                                   11P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   11P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                242
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
D62V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    76   2   1   9
  11P LOSS WILD-TYPE 268  11   3  17
D62V13, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               76                268
  R1                2                 11
  R2                1                  3
  RX                9                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     3
  11P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          12    82
  11P LOSS WILD-TYPE                        40   308
D62V14, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                      12                 40
  WHITE                                          82                308
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V15, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     3  85
  11P LOSS WILD-TYPE   4 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3   85
  11P LOSS WILD-TYPE    4  299
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               85                299
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    56  31
  11Q LOSS WILD-TYPE 267 150
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                87                417 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                31                150 
$`11Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4427 TCGA-05-5420 TCGA-38-4631 TCGA-44-7671 TCGA-44-A47F 
       19.96        26.01        15.02        11.64        29.23        11.08 
TCGA-55-1595 TCGA-55-8511 TCGA-73-4662 TCGA-93-8067 TCGA-95-A4VN TCGA-MN-A4N1 
       48.62        18.15        82.68         6.12        18.18        27.19 
TCGA-MP-A4T8 TCGA-05-4389 TCGA-05-4390 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 
        5.29        45.01        37.02        24.00        29.00        22.03 
TCGA-35-5375 TCGA-38-4625 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 
        8.68        97.74        38.89        34.06        26.56        33.30 
TCGA-44-7667 TCGA-44-A4SS TCGA-49-4487 TCGA-49-4506 TCGA-49-4510 TCGA-49-6767 
       36.07        13.64        28.11        32.84        29.46        22.26 
TCGA-49-AAQV TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 TCGA-50-6592 TCGA-50-6594 
       22.26         8.22        14.27         8.45        25.55        12.16 
TCGA-50-6673 TCGA-53-7626 TCGA-55-6972 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
        0.72        30.54        53.65         3.91        25.41        18.64 
TCGA-55-7995 TCGA-55-8094 TCGA-55-8302 TCGA-55-8615 TCGA-55-A490 TCGA-62-8397 
       29.23        17.79        15.72        14.66         3.25        42.38 
TCGA-62-A46S TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       54.35        39.25        29.92        56.81        39.09        81.80 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 TCGA-69-7763 TCGA-69-7764 TCGA-69-8453 
       87.98        42.90        28.47        22.68        13.61        26.73 
TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7148 
       30.31        50.33        36.66       108.66        27.16        20.58 
TCGA-78-7160 TCGA-78-8640 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 
       22.92       232.18        31.13        38.04        32.78        37.74 
TCGA-86-8074 TCGA-86-8358 TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6847 
        0.79        21.47        30.84         3.81        24.23        27.68 
TCGA-95-8039 TCGA-95-8494 TCGA-97-8174 TCGA-J2-A4AD TCGA-MN-A4N5 TCGA-MP-A4T2 
       27.29         2.76         5.39        18.08         2.76        37.35 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-NJ-A4YQ 
       29.46        11.05        47.08 

$`11Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 
       14.01         9.96         8.02        20.05         9.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       28.41        35.28        14.73        26.30        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       42.08        23.93        27.78        86.01        18.31        29.00 
TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
        9.37        46.72        16.04        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 
       37.32        40.60        21.47        41.69        23.05         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       32.12        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 
       20.19        20.65        13.87        52.60        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TA TCGA-MP-A4TC 
       23.80         6.35        10.09        21.83        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
       10.09        50.07         3.98         0.00        24.03        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5429 
       21.99        26.01        25.02        25.02         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 
        2.04         0.46         7.40         5.98       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       49.05        44.61         4.37        46.98        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
       42.77         3.19        25.02        37.15        38.24        33.73 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 
       15.32         9.44        11.54        13.45        76.21        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
       12.66        35.54        14.07         8.81        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       53.29        55.33        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       40.41       123.58       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        9.27        78.67        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6595 TCGA-50-7109 
       53.16        42.35         3.91        11.05         6.21        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
       36.99        36.79        27.25        34.29        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       38.73        67.89        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 
       42.51        40.73        15.25        46.03         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       23.15        11.28        34.19        17.65        18.44        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19        23.08         5.06        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
       29.19        22.16        15.42        17.56        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 
       17.62         1.58        12.33        20.71        21.40         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
       15.81        19.99        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U 
       88.64        49.25        47.80        19.53        56.71        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
       72.30        13.61        40.96        37.02        38.37         2.04 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        51.25        20.05        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       14.01        13.45         4.24        19.43         8.42        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS 
       26.30        15.35         4.31         9.24         1.25        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7027 
       66.64        77.85        43.82        85.15        49.84       100.57 
TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10         5.69        19.27       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
        8.02        53.33        26.01        39.35        10.55        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       34.39        20.55        19.89        35.24         4.08         4.57 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       24.33        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        11.61        13.91        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       26.50        29.46        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
        1.97        10.19         2.60        12.23         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 
       18.54         0.59        15.91        18.67        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        21.63        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
       14.53         1.91        18.58        15.65        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       58.45        49.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       24.36        14.10        11.15        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       74.33         0.13         1.64         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.72               0.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            232.18             238.29 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             27.16              20.58 
[1] "0.7 - 232.2 (27.2)" "0.0 - 238.3 (20.6)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         1       18       23        1        13        14
  11Q LOSS WILD-TYPE       4      115      116        0        37        58
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11Q LOSS MUTATED           12          0        4
  11Q LOSS WILD-TYPE         60         11       21
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 18                115
  STAGE IB                 23                116
  STAGE II                  1                  0
  STAGE IIA                13                 37
  STAGE IIB                14                 58
  STAGE IIIA               12                 60
  STAGE IIIB                0                 11
  STAGE IV                  4                 21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED    26  50   9   2
  11Q LOSS WILD-TYPE 145 228  37  17
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               26                145
  T2               50                228
  T3                9                 37
  T4                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  11Q LOSS MUTATED    57  18    12
  11Q LOSS WILD-TYPE 276  78    64
D63V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                  57                276
  N1                  18                 78
  N2+N3               12                 64
[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"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    67   4
  11Q LOSS WILD-TYPE 282  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     67    4
  11Q LOSS WILD-TYPE  282   21
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               67                282
  1                4                 21
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    35  52
  11Q LOSS WILD-TYPE 241 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     35   52
  11Q LOSS WILD-TYPE  241  188
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               35                241
  MALE                 52                188
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    70  12
  11Q LOSS WILD-TYPE 340  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     70   12
  11Q LOSS WILD-TYPE  340   48
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                70                340
  YES               12                 48
[1] 2 2
[1] FALSE
D63V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11Q LOSS MUTATED                            3
  11Q LOSS WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11Q LOSS MUTATED                                  16
  11Q LOSS WILD-TYPE                                91
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                   60
  11Q LOSS WILD-TYPE                                                261
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11Q LOSS MUTATED                                            0
  11Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  11Q LOSS MUTATED                                               1
  11Q LOSS WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  11Q LOSS MUTATED                                1
  11Q LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  11Q LOSS MUTATED                                    0
  11Q LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  11Q LOSS MUTATED                              0                             3
  11Q LOSS WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  11Q LOSS MUTATED                                 0
  11Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  11Q LOSS MUTATED                                               1
  11Q LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  11Q LOSS MUTATED                              2
  11Q LOSS WILD-TYPE                            8
D63V10, multiclass
                                                    clus
vv                                                   11Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               60
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   11Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  91
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                261
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
D63V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    62   2   0   7
  11Q LOSS WILD-TYPE 282  11   4  19
D63V13, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               62                282
  R1                2                 11
  R2                0                  4
  RX                7                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           6    66
  11Q LOSS WILD-TYPE                        46   324
D63V14, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  5
  BLACK OR AFRICAN AMERICAN                       6                 46
  WHITE                                          66                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V15, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  68
  11Q LOSS WILD-TYPE   7 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   68
  11Q LOSS WILD-TYPE    7  316
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               68                316
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    73  36
  12P LOSS WILD-TYPE 250 145
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               109                395 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                36                145 
$`12P LOSS MUTATED`
TCGA-05-4405 TCGA-05-4434 TCGA-38-6178 TCGA-44-2661 TCGA-44-7671 TCGA-44-A47F 
       20.05        15.02        14.73        38.10        29.23        11.08 
TCGA-49-4501 TCGA-49-AARN TCGA-50-5932 TCGA-55-1592 TCGA-55-6979 TCGA-55-7573 
       46.72        37.32        40.60        23.05         7.79        16.01 
TCGA-55-7914 TCGA-55-8204 TCGA-55-8511 TCGA-55-8619 TCGA-55-A48X TCGA-55-A491 
        6.15        16.93        18.15        13.68        22.65        20.58 
TCGA-67-6217 TCGA-73-7498 TCGA-80-5611 TCGA-91-7771 TCGA-95-7043 TCGA-95-7947 
       13.87        39.09        85.32        16.18        16.54        15.68 
TCGA-95-7948 TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4426 TCGA-44-2656 TCGA-44-2657 
       15.65         2.43        50.07        26.01        46.98        44.42 
TCGA-44-2666 TCGA-44-6775 TCGA-44-6779 TCGA-44-7662 TCGA-44-8117 TCGA-44-8120 
        3.19        23.18        16.44         7.17        12.66         8.55 
TCGA-44-A47B TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-6743 TCGA-49-6744 
        9.44        13.45        28.57        12.66        53.29        55.33 
TCGA-49-AARE TCGA-49-AARQ TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 TCGA-50-5939 
       40.41       221.33       101.72        15.72        49.28        15.12 
TCGA-50-5942 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 
       60.72        53.16         3.91        11.05        12.16        36.99 
TCGA-55-5899 TCGA-55-6982 TCGA-55-6984 TCGA-55-7727 TCGA-55-8087 TCGA-55-8510 
       30.58        32.71        24.99         3.91        15.19        17.72 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-A46R 
       17.10        17.62         1.58        21.40        19.99        56.71 
TCGA-62-A46S TCGA-64-1676 TCGA-64-5778 TCGA-67-3771 TCGA-69-7763 TCGA-69-7765 
       54.35        56.81        42.90        20.05        22.68         5.42 
TCGA-69-7974 TCGA-69-8253 TCGA-71-6725 TCGA-73-4677 TCGA-75-6214 TCGA-78-7147 
        6.05        14.01         8.42         1.25        36.66        19.27 
TCGA-78-7153 TCGA-78-7535 TCGA-86-7955 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
      119.51        31.20        35.24        24.33         0.79        22.82 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8672 TCGA-91-6847 TCGA-91-6849 TCGA-95-7039 
       31.20        21.47         0.62        27.68         1.15        41.82 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7938 TCGA-97-8177 TCGA-97-A4M1 
       42.25        64.60        25.48         0.59        16.41        19.76 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A7SV TCGA-L9-A8F4 
       18.67        24.56        34.85        18.08        18.58        15.65 
TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A7XG 
       19.13        71.05         0.13        47.08         0.43        20.28 
TCGA-O1-A52J 
       59.11 

$`12P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 
       15.02        28.41        35.28        11.64        26.30        43.53 
TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       42.08        23.93        27.78        86.01        18.31        29.00 
TCGA-44-8119 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-50-5935 
        9.37        16.04        17.16        11.64       156.66        21.47 
TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 
       41.69        48.62         5.79         7.99        23.18        14.53 
TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 
       21.44        19.66        19.73        17.98        19.69        32.12 
TCGA-55-8621 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 
       16.93        19.59        20.19        20.65        52.60        82.68 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 
        8.48        50.24        10.55        13.71         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       17.29         2.86        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD 
       10.09        21.83        27.19         5.29        31.23        10.09 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
        3.98        45.01        37.02         0.00        24.03        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       21.99        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
       22.03         9.04         2.04         0.46         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2659 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        4.37        44.94        42.77        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.89        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 
       28.01        23.77        19.56        23.15        21.63        32.45 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       61.28        22.72        19.46        36.07        18.87        23.64 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 
       15.98        15.32        11.54        13.64        76.21        28.11 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.89        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
        8.55       123.58       164.12         9.86        20.52        71.47 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        47.41         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 
        8.45        48.46        57.53        42.35        25.55         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        0.72        10.13        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
       13.94        35.21        38.73        67.89        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        3.88        69.34        45.34        92.81        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       23.15        25.41        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
       18.44        19.82        29.23        29.72        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 
       19.96        26.01        14.66        12.33        20.71         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        17.95         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U 
       14.60        88.64        49.25        47.80        19.53        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 
       72.30        13.61        39.25        40.96        29.92        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       81.80        37.02        38.37        87.98         2.04        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       51.25        28.47        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
       14.73         5.72         4.64         6.64         6.12        13.61 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 
        7.56         4.41        13.41        13.51        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       26.73        19.43        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 
       30.31         9.24        50.33        11.18        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       43.82        85.15        49.84       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        20.58       129.53        21.90        39.95 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        9.57       104.19       238.29        88.14        26.53         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
       37.74         4.08         4.57        32.65        31.04        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       14.60        11.61        13.91        30.84        27.58        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       26.50        29.46         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        7.36        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 
       17.46        23.61         1.08        19.00        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       27.29         2.76        19.89        63.52        61.48        18.54 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
       15.91        18.67         5.39        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-8028 TCGA-99-8032 
       21.60        20.58        21.44        20.84        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        21.63        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       14.53         1.91        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        11.15        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R TCGA-S2-AA1A 
       74.33         1.64         0.49        19.82        16.87 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.13               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            221.33             238.29 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             20.05              22.03 
[1] "0.1 - 221.3 (20.1)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         1       27       37        0         9        13
  12P LOSS WILD-TYPE       4      106      102        1        41        59
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12P LOSS MUTATED           16          1        2
  12P LOSS WILD-TYPE         56         10       23
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 27                106
  STAGE IB                 37                102
  STAGE II                  0                  1
  STAGE IIA                 9                 41
  STAGE IIB                13                 59
  STAGE IIIA               16                 56
  STAGE IIIB                1                 10
  STAGE IV                  2                 23
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED    36  62   7   4
  12P LOSS WILD-TYPE 135 216  39  15
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               36                135
  T2               62                216
  T3                7                 39
  T4                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  12P LOSS MUTATED    72  21    15
  12P LOSS WILD-TYPE 261  75    61
D64V5, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                  72                261
  N1                  21                 75
  N2+N3               15                 61
[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"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    66   2
  12P LOSS WILD-TYPE 283  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     66    2
  12P LOSS WILD-TYPE  283   23
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               66                283
  1                2                 23
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    73  36
  12P LOSS WILD-TYPE 203 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     73   36
  12P LOSS WILD-TYPE  203  204
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               73                203
  MALE                 36                204
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    91  12
  12P LOSS WILD-TYPE 319  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     91   12
  12P LOSS WILD-TYPE  319   48
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                91                319
  YES               12                 48
[1] 2 2
[1] FALSE
D64V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12P LOSS MUTATED                            1
  12P LOSS WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12P LOSS MUTATED                                  23
  12P LOSS WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                   71
  12P LOSS WILD-TYPE                                                250
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12P LOSS MUTATED                                            0
  12P LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12P LOSS MUTATED                                               5
  12P LOSS WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  12P LOSS MUTATED                                1
  12P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  12P LOSS MUTATED                                    0
  12P LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  12P LOSS MUTATED                              0                             5
  12P LOSS WILD-TYPE                            2                            18
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  12P LOSS MUTATED                                 0
  12P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  12P LOSS MUTATED                                               1
  12P LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12P LOSS MUTATED                              2
  12P LOSS WILD-TYPE                            8
D64V10, multiclass
                                                    clus
vv                                                   12P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               71
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     5
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   12P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                250
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      18
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
D64V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    63   1   1   5
  12P LOSS WILD-TYPE 281  12   3  21
D64V13, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               63                281
  R1                1                 12
  R2                1                  3
  RX                5                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                          17    84
  12P LOSS WILD-TYPE                        35   306
D64V14, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                      17                 35
  WHITE                                          84                306
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  90
  12P LOSS WILD-TYPE   5 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   90
  12P LOSS WILD-TYPE    5  294
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               90                294
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    60  34
  12Q LOSS WILD-TYPE 263 147
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                94                410 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                34                147 
$`12Q LOSS MUTATED`
TCGA-05-4434 TCGA-38-6178 TCGA-44-2661 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 
       15.02        14.73        38.10        29.23        11.08        46.72 
TCGA-49-AARN TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 TCGA-55-6979 TCGA-55-7914 
       37.32        40.60        41.69        23.05         7.79         6.15 
TCGA-55-8204 TCGA-55-8511 TCGA-55-8619 TCGA-55-A48X TCGA-67-6217 TCGA-73-4658 
       16.93        18.15        13.68        22.65        13.87        52.60 
TCGA-73-7498 TCGA-80-5611 TCGA-91-7771 TCGA-95-7043 TCGA-95-7948 TCGA-MN-A4N1 
       39.09        85.32        16.18        16.54        15.65        27.19 
TCGA-MP-A4TC TCGA-05-4426 TCGA-05-5428 TCGA-44-2657 TCGA-44-6775 TCGA-44-6779 
        2.43        26.01        22.03        44.42        23.18        16.44 
TCGA-44-7662 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-6743 
        7.17         8.55        13.45        28.57        12.66        53.29 
TCGA-49-6744 TCGA-49-AARE TCGA-49-AARQ TCGA-50-5049 TCGA-50-5068 TCGA-50-5939 
       55.33        40.41       221.33       101.72        49.28        15.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-8457 TCGA-55-6980 TCGA-55-6982 
       53.16         3.91        11.05        36.99        69.34        32.71 
TCGA-55-6984 TCGA-55-7283 TCGA-55-7727 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 
       24.99        20.02         3.91        17.72        17.10        17.62 
TCGA-55-8616 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
        1.58        21.40        19.99        56.71        54.35        67.96 
TCGA-62-A46Y TCGA-64-5778 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-8253 
       13.61        42.90        22.68         5.42         6.05        14.01 
TCGA-71-6725 TCGA-73-4677 TCGA-75-6214 TCGA-78-7147 TCGA-78-7153 TCGA-78-7535 
        8.42         1.25        36.66        19.27       119.51        31.20 
TCGA-86-7955 TCGA-86-8074 TCGA-86-8075 TCGA-91-6829 TCGA-91-6847 TCGA-95-7039 
       35.24         0.79        22.82        41.36        27.68        41.82 
TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8177 TCGA-97-A4M1 
       27.29        42.25        64.60        25.48        16.41        19.76 
TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4TK 
       24.56        34.85        18.08        15.65         2.76        19.13 
TCGA-NJ-A4YF TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       71.05         0.43        20.28        59.11 

$`12Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
       26.01        15.02        28.41        35.28        11.64        26.30 
TCGA-44-2655 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       43.53        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-8119 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       29.00         9.37        16.04        17.16        11.64       156.66 
TCGA-50-5935 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       21.47        48.62         5.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 
       14.53        21.44        19.66        19.73        17.98        19.69 
TCGA-55-8207 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       32.12        16.93        20.58        19.59        20.19        20.65 
TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 TCGA-91-A4BC 
       82.68         8.48        50.24        10.55        13.71         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN 
        6.12        17.29         2.86        15.68        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        21.83         5.29        31.23 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       12.00        30.02        21.99        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
        4.96        29.00         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 
       44.61         4.37        46.98        44.94        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       25.02        37.15        38.24        38.89        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       23.15        21.63        32.45        61.28        22.72        19.46 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A 
       36.07        18.87        23.64        12.66        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 
        9.44        11.54        13.64        76.21        28.11        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26        73.12        62.24        28.90         8.55 
TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
      123.58       164.12         9.86        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        47.41         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 
        8.45        48.46        60.72        57.53        42.35        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21         0.72        10.13        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 
       34.29        30.54        13.94        35.21        38.73        67.89 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6981 TCGA-55-6983 
       15.25        46.03        53.65         3.88        45.34        92.81 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 
       40.54       107.21        70.26        28.67        27.09        32.71 
TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
       22.03        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 
       13.74        20.28        19.96        26.01        14.66        12.33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 
       20.71         3.25         0.92        15.81        17.95         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       19.53        72.30        39.25        40.96        29.92        56.81 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       39.09        81.80        37.02        38.37        87.98         2.04 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       28.41        51.25        28.47        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        6.12        13.61         7.56         4.41        13.41        13.51 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 
       13.45         4.24        26.73        19.43        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS 
       15.35         4.31        30.31         9.24        50.33        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 
       66.64        77.85        43.82        85.15        49.84       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
      100.57       163.10        27.16         5.69        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       32.78        19.89        37.74         4.08         4.57        24.33 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       11.61        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       26.50        29.46         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 
       10.62         1.97        10.19         2.60        12.23         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 
       17.46        23.61         1.08        19.00        18.67        12.39 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
        2.76        19.89        63.52        61.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
       15.91        18.67         5.39        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8028 
       21.60        20.58        21.44        20.84        18.67        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        21.63        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV 
       14.30        14.53         1.91        18.58        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55R TCGA-S2-AA1A 
       19.82        16.87 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.43               0.00 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            221.33             238.29 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            22.665             21.520 
[1] "0.4 - 221.3 (22.7)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         1       21       31        0         9        13
  12Q LOSS WILD-TYPE       4      112      108        1        41        59
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12Q LOSS MUTATED           14          1        2
  12Q LOSS WILD-TYPE         58         10       23
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 21                112
  STAGE IB                 31                108
  STAGE II                  0                  1
  STAGE IIA                 9                 41
  STAGE IIB                13                 59
  STAGE IIIA               14                 58
  STAGE IIIB                1                 10
  STAGE IV                  2                 23
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED    30  54   6   4
  12Q LOSS WILD-TYPE 141 224  40  15
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               30                141
  T2               54                224
  T3                6                 40
  T4                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  12Q LOSS MUTATED    59  21    13
  12Q LOSS WILD-TYPE 274  75    63
D65V5, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                  59                274
  N1                  21                 75
  N2+N3               13                 63
[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"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    53   2
  12Q LOSS WILD-TYPE 296  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     53    2
  12Q LOSS WILD-TYPE  296   23
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               53                296
  1                2                 23
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    64  30
  12Q LOSS WILD-TYPE 212 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     64   30
  12Q LOSS WILD-TYPE  212  210
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               64                212
  MALE                 30                210
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    79  11
  12Q LOSS WILD-TYPE 331  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     79   11
  12Q LOSS WILD-TYPE  331   49
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                79                331
  YES               11                 49
[1] 2 2
[1] FALSE
D65V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12Q LOSS MUTATED                            2
  12Q LOSS WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12Q LOSS MUTATED                                  23
  12Q LOSS WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                   55
  12Q LOSS WILD-TYPE                                                266
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12Q LOSS MUTATED                                            0
  12Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12Q LOSS MUTATED                                               6
  12Q LOSS WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  12Q LOSS MUTATED                                1
  12Q LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  12Q LOSS MUTATED                                    0
  12Q LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  12Q LOSS MUTATED                              0                             4
  12Q LOSS WILD-TYPE                            2                            19
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  12Q LOSS MUTATED                                 0
  12Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  12Q LOSS MUTATED                                               1
  12Q LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12Q LOSS MUTATED                              2
  12Q LOSS WILD-TYPE                            8
D65V10, multiclass
                                                    clus
vv                                                   12Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               55
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   12Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                266
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      19
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
D65V12, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    54   1   1   5
  12Q LOSS WILD-TYPE 290  12   3  21
D65V13, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               54                290
  R1                1                 12
  R2                1                  3
  RX                5                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     1
  12Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                          14    73
  12Q LOSS WILD-TYPE                        38   317
D65V14, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                      14                 38
  WHITE                                          73                317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V15, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  77
  12Q LOSS WILD-TYPE   6 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   77
  12Q LOSS WILD-TYPE    6  307
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               77                307
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   162  85
  13Q LOSS WILD-TYPE 161  96
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               247                257 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                85                 96 
$`13Q LOSS MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-38-4629 TCGA-38-6178 TCGA-44-6147 TCGA-44-7670 
        8.02        20.05        28.41        14.73        27.78        29.00 
TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
        9.37        11.08        46.72        11.64       156.66        37.32 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-7573 TCGA-55-7724 
       21.47        41.69        48.62         5.79        16.01        23.18 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 
       19.66        19.73        17.98        16.93        32.12        18.15 
TCGA-55-A491 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-78-8660 
       20.58        20.65        13.87        52.60        82.68        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7948 
       85.32        13.71         6.12        17.29         2.86        15.65 
TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 
       18.18        20.19        20.52        17.75        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 
        6.35        21.83         2.43        10.09         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 
       37.02         0.00        24.03        47.05        14.96        29.98 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 
       30.02        21.99        25.02        25.02         4.96        29.00 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 
        7.40         5.98         8.68        97.74        49.05        44.61 
TCGA-44-2656 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6777 TCGA-44-6778 
       46.98        38.89        33.30        28.37        32.45        61.28 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8120 TCGA-44-A479 
       16.44         7.17        36.07        18.87         8.55        15.98 
TCGA-44-A47B TCGA-44-A4SU TCGA-49-4487 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        9.44        13.45        28.11        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR9 
       29.46        29.75        53.29        22.26        62.24         8.55 
TCGA-49-AARO TCGA-4B-A93V TCGA-50-5045 TCGA-50-5051 TCGA-50-5068 TCGA-50-5930 
      123.58         9.86        71.47        15.72        49.28         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
       14.27        78.67         8.45        48.46        57.53        53.16 
TCGA-50-6593 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 
       11.05        10.13        27.25        13.94        35.21        67.89 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       30.58        80.52         5.62        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       69.34        45.34        32.71        40.54       107.21        70.26 
TCGA-55-7570 TCGA-55-7576 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 
       27.09        22.03        25.41        18.64        17.65        18.44 
TCGA-55-7994 TCGA-55-8094 TCGA-55-8301 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 
       19.82        17.79        17.56        15.72        13.74        20.28 
TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Z 
       17.72        17.10        17.62        14.66         1.58        21.40 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
        0.92        19.99         4.57        39.98        42.38        88.64 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       47.80        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5779 
       40.96        29.92        56.81        81.80        38.37        28.41 
TCGA-64-5781 TCGA-67-3770 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
       51.25        20.05         6.64         6.12        13.61         5.42 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
        4.41        13.41         4.24        19.43         8.42        23.38 
TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 
       15.35        30.31        50.33        66.64        43.82        85.15 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 
       27.16         5.69        19.50        38.50        22.92         9.57 
TCGA-78-7539 TCGA-78-8640 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       26.01       232.18        27.09        31.13        34.39        38.04 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 
       32.78        19.89        37.74         4.08        22.82        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-A456 
       23.05        21.47        14.60        13.91        30.84        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
        3.81        24.23        10.62        41.36        10.19         2.60 
TCGA-91-6840 TCGA-91-8499 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 
       12.23         1.18         1.08        41.82        18.67        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 
        2.76        19.89        42.25        25.48         5.39        16.41 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 
       21.60        20.58        21.44        19.76        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 
       19.00        18.58        15.65        86.14        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF 
       58.85        41.59        11.05        14.10        19.13        71.05 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.13        47.08         0.49         0.43        19.82        20.28 
TCGA-O1-A52J 
       59.11 

$`13Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       15.02        35.28        11.64        26.30        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-49-6742 
       42.08        23.93        86.01        18.31        29.23        16.04 
TCGA-49-6745 TCGA-50-5932 TCGA-55-1592 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 
       17.16        40.60        23.05         7.79         7.99        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       21.44         6.15        19.69        13.68        16.93        22.65 
TCGA-55-A492 TCGA-55-A4DF TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-91-7771 
       19.59        20.19        39.09         8.48        50.24        16.18 
TCGA-91-A4BC TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4M7 
        1.45        16.54        15.68        21.40        17.92        20.68 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4249 TCGA-05-4403 
       10.09        27.19         5.29        31.23        50.07        19.00 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4426 TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 
        2.99        12.00        26.01        24.00        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2657 
        2.04         0.46       120.79        37.71         4.37        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.94        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       34.06        33.73        26.56        28.01        23.77        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-7659 TCGA-44-7660 TCGA-44-7672 
       23.15        21.63        23.18        22.72        19.46        23.64 
TCGA-44-8117 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 
       12.66        15.32        11.54        13.64        76.21        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR2 
       12.66        35.54        55.89        55.33        22.26        73.12 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5049 
       28.90        40.41       221.33       164.12        20.52       101.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 
       60.16        47.41         8.22        15.12        60.72        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
        3.91        25.55        12.16         6.21         0.72        36.99 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 TCGA-55-6968 
       36.79        34.29        30.54        38.73        14.30        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6983 TCGA-55-6984 TCGA-55-7281 TCGA-55-7283 
       40.73        15.25        92.81        24.99        28.67        20.02 
TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 
       32.71         3.91        23.15        11.28        34.19        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19        23.08         5.06        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 TCGA-55-8512 
       29.19        22.16        15.42        14.47         0.36        19.96 
TCGA-55-8513 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 TCGA-55-A57B 
       26.01        12.33        20.71         3.25        15.81        17.95 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P TCGA-62-A470 TCGA-64-1678 TCGA-64-1680 
       14.60        49.25        19.53        39.25        39.09        37.02 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       87.98         2.04        42.90        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 
       14.04        12.66        14.73         5.72         4.64        22.68 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        7.56         6.05        13.51        14.01        13.45        26.73 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5146 
       26.30         4.31         9.24         1.25        11.18        77.85 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7147 
       49.84        36.66       108.66       100.57       163.10        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
       20.58       129.53        21.90        39.95       119.51        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
        5.88        64.90       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
       31.20         8.02        53.33        39.35        10.55        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 TCGA-86-6851 TCGA-86-7714 
       77.59       110.50        93.11        12.36         5.88        20.55 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
       35.24         4.57        24.33         0.79        32.65        31.04 
TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 
       11.61        27.58         0.62        28.34        26.50        13.64 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       26.47         1.97        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP 
       14.27        19.82        22.45        17.46        23.61        19.00 
TCGA-95-7944 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       12.39        64.60        63.52        61.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M5 
       15.91        18.67        18.12        15.39        14.30        20.84 
TCGA-97-A4M6 TCGA-99-AA5R TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N4 
       18.67        21.63        14.30        14.53         1.91        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TH 
        2.76        58.45        49.35         5.49        29.46        24.36 
TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-S2-AA1A 
       11.15        73.91        74.33         1.64        16.87 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.00               0.36 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            232.18             238.29 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             21.57              21.63 
[1] "0.0 - 232.2 (21.6)" "0.4 - 238.3 (21.6)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         2       62       67        1        25        40
  13Q LOSS WILD-TYPE       3       71       72        0        25        32
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  13Q LOSS MUTATED           36          6        9
  13Q LOSS WILD-TYPE         36          5       16
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 62                 71
  STAGE IB                 67                 72
  STAGE II                  1                  0
  STAGE IIA                25                 25
  STAGE IIB                40                 32
  STAGE IIIA               36                 36
  STAGE IIIB                6                  5
  STAGE IV                  9                 16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED    78 140  22  10
  13Q LOSS WILD-TYPE  93 138  24   9
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               78                 93
  T2              140                138
  T3               22                 24
  T4               10                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  13Q LOSS MUTATED   157  52    38
  13Q LOSS WILD-TYPE 176  44    38
D66V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                 157                176
  N1                  52                 44
  N2+N3               38                 38
[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"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   164   9
  13Q LOSS WILD-TYPE 185  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    164    9
  13Q LOSS WILD-TYPE  185   16
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0              164                185
  1                9                 16
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   138 113
  13Q LOSS WILD-TYPE 138 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    138  113
  13Q LOSS WILD-TYPE  138  127
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE              138                138
  MALE                113                127
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   204  30
  13Q LOSS WILD-TYPE 206  30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    204   30
  13Q LOSS WILD-TYPE  206   30
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               204                206
  YES               30                 30
[1] 2 2
[1] FALSE
D66V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  13Q LOSS MUTATED                           11
  13Q LOSS WILD-TYPE                          7
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  13Q LOSS MUTATED                                  52
  13Q LOSS WILD-TYPE                                55
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                  160
  13Q LOSS WILD-TYPE                                                161
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  13Q LOSS MUTATED                                            1
  13Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  13Q LOSS MUTATED                                               8
  13Q LOSS WILD-TYPE                                            11
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  13Q LOSS MUTATED                                2
  13Q LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  13Q LOSS MUTATED                                    1
  13Q LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  13Q LOSS MUTATED                              0                            10
  13Q LOSS WILD-TYPE                            2                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  13Q LOSS MUTATED                                 0
  13Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  13Q LOSS MUTATED                                               3
  13Q LOSS WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  13Q LOSS MUTATED                              3
  13Q LOSS WILD-TYPE                            7
D66V10, multiclass
                                                    clus
vv                                                   13Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              160
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     8
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                    10
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   13Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                161
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      11
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
D66V12, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED   163   8   2  14
  13Q LOSS WILD-TYPE 181   5   2  12
D66V13, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0              163                181
  R1                8                  5
  R2                2                  2
  RX               14                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     5
  13Q LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          30   185
  13Q LOSS WILD-TYPE                        22   205
D66V14, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           5                  2
  BLACK OR AFRICAN AMERICAN                      30                 22
  WHITE                                         185                205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4 191
  13Q LOSS WILD-TYPE   3 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4  191
  13Q LOSS WILD-TYPE    3  193
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              191                193
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    75  39
  14Q LOSS WILD-TYPE 248 142
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               114                390 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                39                142 
$`14Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-44-2662 TCGA-44-6146 
        9.96        20.05         9.01        26.01        42.08        23.93 
TCGA-44-7671 TCGA-44-A47F TCGA-49-6742 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       29.23        11.08        16.04        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-95-7948 
       48.62        20.58        19.59        13.87        82.68        15.65 
TCGA-95-A4VN TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4398 
       18.18        21.83        27.19         5.29         2.43        47.05 
TCGA-05-4420 TCGA-05-5425 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-44-3398 
       29.98        29.00        97.74        49.05        44.61        38.24 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 TCGA-44-6775 TCGA-44-7669 TCGA-44-8120 
       33.30        28.37        19.56        23.18        18.87         8.55 
TCGA-44-A4SS TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-AARE TCGA-50-5068 
       13.64         8.81        29.46        55.89        40.41        49.28 
TCGA-50-5931 TCGA-50-5936 TCGA-50-6593 TCGA-50-8457 TCGA-55-1596 TCGA-55-7281 
       14.27         8.45        11.05        36.99        67.89        28.67 
TCGA-55-7283 TCGA-55-7727 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8505 
       20.02         3.91         5.06        17.79        15.65        14.47 
TCGA-55-8508 TCGA-55-8514 TCGA-62-8398 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U 
       20.28        17.10        14.60        47.80        54.35        67.96 
TCGA-62-A471 TCGA-64-1680 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3774 
       40.96        37.02        42.90        28.41        51.25        12.66 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7980 TCGA-69-A59K TCGA-73-4675 TCGA-73-A9RS 
        6.12         5.42        13.51        19.43        30.31        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 
       66.64        77.85        43.82        85.15        36.66       100.57 
TCGA-78-7146 TCGA-78-7150 TCGA-78-7535 TCGA-78-8640 TCGA-86-7711 TCGA-86-7713 
        5.69        21.90        31.20       232.18        34.39        38.04 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8279 TCGA-86-8359 
       32.78        19.89        37.74         4.57        31.20        14.60 
TCGA-86-8669 TCGA-86-8672 TCGA-91-6830 TCGA-91-6848 TCGA-93-7347 TCGA-93-A4JO 
       30.84         0.62         1.97         7.36        22.45         1.08 
TCGA-95-7039 TCGA-95-7944 TCGA-95-8494 TCGA-97-7547 TCGA-97-8174 TCGA-97-8176 
       41.82        12.39         2.76        64.60         5.39        15.39 
TCGA-97-8177 TCGA-97-A4M0 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       16.41        21.44        34.85         1.45        21.57        18.08 
TCGA-J2-A4AG TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A7XG 
       32.48        58.45         5.49        71.05        47.08        20.28 

$`14Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 
       19.96        14.01         8.02        15.02        15.02        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       35.28        11.64        14.73        26.30        43.53        38.10 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 
       27.78        86.01        18.31        29.00         9.37        46.72 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-55-6978 
       17.16        11.64       156.66        37.32        40.60         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF 
       32.12        18.15        13.68        16.93        22.65        20.19 
TCGA-64-1677 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       20.65        52.60        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX 
       16.54         2.86        15.68        21.40        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       10.09        31.23        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
       37.02         0.00        24.03        19.00         2.99        14.96 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       24.00         4.96        22.03         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F 
        7.40         5.98         8.68       120.79        37.71         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        44.42        44.94        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.89        34.06        33.73        26.56        28.01 
TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.77        23.15        21.63        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 
       22.72        19.46         7.17        36.07        23.64        12.66 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
       15.98        15.32         9.44        11.54        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       29.75        53.29        55.33        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90         8.55       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        9.86        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 
       47.41         8.22         9.27        78.67        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21         0.72        10.13        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 
       34.29        30.54        13.94        35.21        38.73        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 
       92.81        24.99        40.54       107.21        70.26        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       32.71        22.03        23.15        25.41        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       15.19        23.08        23.64        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 
       17.56        15.72         0.36        13.74        17.72        19.96 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       26.01        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       21.40         3.25         0.92        15.81        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
        4.57        39.98        42.38        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 
       56.71        72.30        13.61        39.25        29.92        56.81 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5815 
       39.09        81.80        38.37        87.98         2.04        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       20.05        20.05        18.84        14.04        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
        4.64         6.64        22.68        13.61         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        4.41        13.41        14.01        13.45         4.24        26.73 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
        8.42        23.38        26.30        15.35         4.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 
        1.25        50.33        49.84       108.66       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       19.27        20.58       129.53        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
      104.19       238.29        88.14        26.53         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       26.01        39.35        10.55        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 
       93.11        27.09        12.36         5.88        31.13        20.55 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       35.24         4.08        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
       31.04        23.05        21.47        11.61        13.91        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       28.34        26.50        29.46         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       26.47        10.62        41.36        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
       27.68         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7567 TCGA-95-8039 TCGA-95-A4VP 
       17.46        23.61        19.00        18.67        27.29        19.89 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       42.25        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       15.91        18.67        18.12        14.30        21.60        20.58 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R 
       19.76        20.84        18.67        24.56        36.76        21.63 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV 
       35.47        19.00        14.30        14.53         1.91        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 
       15.65        38.63         2.76        86.14        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       86.04        58.85        41.59        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        11.15        19.13        73.91        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        1.64         0.49         0.43        19.82        59.11        16.87 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.62               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            232.18             238.29 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            22.175             21.455 
[1] "0.6 - 232.2 (22.2)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         1       24       27        0        14        19
  14Q LOSS WILD-TYPE       4      109      112        1        36        53
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  14Q LOSS MUTATED           21          2        5
  14Q LOSS WILD-TYPE         51          9       20
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 24                109
  STAGE IB                 27                112
  STAGE II                  0                  1
  STAGE IIA                14                 36
  STAGE IIB                19                 53
  STAGE IIIA               21                 51
  STAGE IIIB                2                  9
  STAGE IV                  5                 20
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED    31  64  13   5
  14Q LOSS WILD-TYPE 140 214  33  14
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               31                140
  T2               64                214
  T3               13                 33
  T4                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  14Q LOSS MUTATED    64  31    18
  14Q LOSS WILD-TYPE 269  65    58
D67V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                  64                269
  N1                  31                 65
  N2+N3               18                 58
[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"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    85   5
  14Q LOSS WILD-TYPE 264  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     85    5
  14Q LOSS WILD-TYPE  264   20
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               85                264
  1                5                 20
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    56  58
  14Q LOSS WILD-TYPE 220 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     56   58
  14Q LOSS WILD-TYPE  220  182
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               56                220
  MALE                 58                182
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    96  13
  14Q LOSS WILD-TYPE 314  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     96   13
  14Q LOSS WILD-TYPE  314   47
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                96                314
  YES               13                 47
[1] 2 2
[1] FALSE
D67V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  14Q LOSS MUTATED                            4
  14Q LOSS WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  14Q LOSS MUTATED                                  24
  14Q LOSS WILD-TYPE                                83
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                   73
  14Q LOSS WILD-TYPE                                                248
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  14Q LOSS MUTATED                                            0
  14Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  14Q LOSS MUTATED                                               3
  14Q LOSS WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  14Q LOSS MUTATED                                1
  14Q LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  14Q LOSS MUTATED                                    0
  14Q LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  14Q LOSS MUTATED                              1                             4
  14Q LOSS WILD-TYPE                            1                            19
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  14Q LOSS MUTATED                                 0
  14Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  14Q LOSS MUTATED                                               1
  14Q LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  14Q LOSS MUTATED                              3
  14Q LOSS WILD-TYPE                            7
D67V10, multiclass
                                                    clus
vv                                                   14Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               73
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   14Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                248
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      19
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
D67V12, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    78   0   0   7
  14Q LOSS WILD-TYPE 266  13   4  19
D67V13, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               78                266
  R1                0                 13
  R2                0                  4
  RX                7                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     2
  14Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          18    78
  14Q LOSS WILD-TYPE                        34   312
D67V14, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  5
  BLACK OR AFRICAN AMERICAN                      18                 34
  WHITE                                          78                312
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V15, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2  90
  14Q LOSS WILD-TYPE   5 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   90
  14Q LOSS WILD-TYPE    5  294
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               90                294
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   155  82
  15Q LOSS WILD-TYPE 168  99
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               237                267 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                82                 99 
$`15Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 
       19.96         8.02        35.28        11.64        14.73        42.08 
TCGA-44-6147 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       27.78        18.31        29.00         9.37        11.08        46.72 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       11.64       156.66        37.32        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 TCGA-55-8511 
       48.62         6.15        19.73        17.98        19.69        18.15 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-73-4662 TCGA-80-5611 TCGA-91-6836 
       22.65        20.58        20.19        82.68        85.32        13.71 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-A4VN TCGA-97-8172 
        1.45         6.12        17.29         2.86        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M3 TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       20.19        17.75        24.30         6.35        10.09        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4398 TCGA-05-4417 
        5.29         2.43        10.09        50.07        47.05        14.96 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 
       29.98        30.02        25.02        25.02        29.00        22.03 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68        97.74        37.71        49.05 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       46.98        44.42        44.94        38.89        34.06        33.73 
TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 
       23.77        21.63        23.18        32.45        61.28        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-49-4487 
        7.17        36.07        23.64        12.66         8.55        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 
       28.57        12.66         8.81        29.46        55.89        55.33 
TCGA-49-6767 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 
       22.26        40.41       123.58       221.33        71.47       101.72 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6591 
       15.72        47.41        78.67        48.46        53.16         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 
       27.25        30.54        13.94        35.21        67.89        30.58 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       80.52        40.73        46.03        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       92.81        28.67        20.02        32.71        22.03         3.91 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7994 TCGA-55-8089 TCGA-55-8094 TCGA-55-8301 
       25.41        18.64        19.82        23.08        17.79        17.56 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       13.74        20.28        17.72        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 
       12.33        21.40         3.25         0.92        19.99         4.57 
TCGA-62-8397 TCGA-62-A46R TCGA-62-A46S TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 
       42.38        56.71        54.35        13.61        29.92        56.81 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 
       81.80        38.37        87.98        42.90        28.41        20.05 
TCGA-67-3772 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       18.84         5.42         7.56         6.05         4.41        13.41 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 
       19.43        23.38        26.30        15.35        30.31        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 
       66.64        77.85        49.84        36.66       108.66       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 
       27.16         5.69        19.27       119.51         5.88        64.90 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-80-5608 
       88.14        31.20         8.02        10.55       232.18        93.11 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7954 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       12.36        31.13        19.89        24.33         0.79        22.82 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 TCGA-86-A456 TCGA-86-A4D0 
       31.20        21.47        14.60        30.84        29.46         3.81 
TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       24.23        10.62        41.36        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       27.68         7.36         1.18        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
        1.08        41.82        18.67         2.76        19.89        42.25 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8177 TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 
       25.48        18.54        16.41        19.76        24.56        34.85 
TCGA-99-8028 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 
       36.76        18.08        32.48        19.00        18.58        15.65 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TE 
       38.63        86.14        58.45        37.35        86.04        29.46 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YI TCGA-NJ-A55O 
       11.05        14.10        11.15        19.13         0.13         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       19.82        20.28        59.11 

$`15Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       14.01         9.96        20.05         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 
       15.02        28.41        26.30        43.53        38.10        23.93 
TCGA-44-6776 TCGA-44-7671 TCGA-49-6742 TCGA-49-6745 TCGA-50-5932 TCGA-55-6978 
       86.01        29.23        16.04        17.16        40.60         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-8090 TCGA-55-8204 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 
       19.66        16.93        32.12        13.68        16.93        19.59 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       20.65        13.87        52.60        39.09         8.48        50.24 
TCGA-78-8660 TCGA-91-7771 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       10.55        16.18        16.54        15.68        15.65        21.40 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A743 TCGA-MP-A4TA TCGA-05-4250 
       20.52        20.68        23.80        21.83        31.23         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 
       45.01        37.02         0.00        24.03        19.00         2.99 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 
       12.00        21.99        26.01        24.00         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F TCGA-44-2665 
        2.04         0.46       120.79        44.61         4.37        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 
        3.19        25.02        37.15        38.24        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6779 TCGA-44-7659 
       28.37        28.01        19.56        23.15        16.44        22.72 
TCGA-44-7669 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       18.87        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 
       13.45        76.21        35.54        14.07        32.84        29.75 
TCGA-49-6743 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       53.29        22.26        73.12        62.24        28.90         8.55 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 
      164.12         9.86        20.52        60.16        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
        9.27        14.27         8.45        15.12        60.72        57.53 
TCGA-50-6590 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-55-1594 TCGA-55-6543 
       42.35        36.99        36.79        34.29        38.73        14.30 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6984 
        5.62        42.51        15.25        53.65         3.88        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7728 TCGA-55-7907 
       40.54       107.21        70.26        27.09        23.15        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        18.44        29.23        29.72        15.19 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
        5.06        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       15.72        14.47         0.36        19.96        26.01        17.10 
TCGA-55-A48Y TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
       20.71        15.81        17.95        39.98        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 
       49.25        47.80        19.53        67.96        72.30        39.25 
TCGA-62-A471 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
       40.96        39.09        37.02         2.04        51.25        28.47 
TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7980 TCGA-69-8253 
        6.64         6.12        22.68        13.61        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4670 TCGA-73-4676 
       13.45         4.24        26.73         8.42         4.31         9.24 
TCGA-73-4677 TCGA-73-A9RS TCGA-75-5147 TCGA-75-6206 TCGA-75-7027 TCGA-78-7148 
        1.25        11.18        43.82        85.15       100.57        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
      129.53        21.90        39.95        19.50        38.50        32.09 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7537 
       22.92         9.57       104.19       238.29        26.53        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
       26.01        39.35        39.75        77.59       110.50        27.09 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
        5.88        34.39        38.04        20.55        32.78        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
       37.74         4.08         4.57        32.65        31.04        23.05 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       11.61        13.91        27.58         0.62        28.34        26.50 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       13.64        26.47         1.97         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 TCGA-97-7547 TCGA-97-7552 
       19.82        19.00        12.39        27.29        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       61.48         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 
       15.39        14.30        21.60        20.58        21.44        20.84 
TCGA-97-A4M6 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E6 
       18.67         1.45        21.57        21.63        35.47        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 
       14.53         1.91         2.76        49.35        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP 
       41.59        24.36        73.91        71.05        74.33         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-S2-AA1A 
       47.08         0.49        16.87 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.13               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            232.18             238.29 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             22.65              20.84 
[1] "0.1 - 232.2 (22.6)" "0.0 - 238.3 (20.8)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         3       60       70        0        27        28
  15Q LOSS WILD-TYPE       2       73       69        1        23        44
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  15Q LOSS MUTATED           37          6       10
  15Q LOSS WILD-TYPE         35          5       15
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 60                 73
  STAGE IB                 70                 69
  STAGE II                  0                  1
  STAGE IIA                27                 23
  STAGE IIB                28                 44
  STAGE IIIA               37                 35
  STAGE IIIB                6                  5
  STAGE IV                 10                 15
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED    81 135  19   9
  15Q LOSS WILD-TYPE  90 143  27  10
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               81                 90
  T2              135                143
  T3               19                 27
  T4                9                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  15Q LOSS MUTATED   154  46    39
  15Q LOSS WILD-TYPE 179  50    37
D68V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                 154                179
  N1                  46                 50
  N2+N3               39                 37
[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"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   166  10
  15Q LOSS WILD-TYPE 183  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    166   10
  15Q LOSS WILD-TYPE  183   15
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              166                183
  1               10                 15
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   135 109
  15Q LOSS WILD-TYPE 141 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    135  109
  15Q LOSS WILD-TYPE  141  131
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              135                141
  MALE                109                131
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   191  36
  15Q LOSS WILD-TYPE 219  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    191   36
  15Q LOSS WILD-TYPE  219   24
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               191                219
  YES               36                 24
[1] 2 2
[1] FALSE
D68V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  15Q LOSS MUTATED                            8
  15Q LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  15Q LOSS MUTATED                                  37
  15Q LOSS WILD-TYPE                                70
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                  170
  15Q LOSS WILD-TYPE                                                151
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  15Q LOSS MUTATED                                            0
  15Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  15Q LOSS MUTATED                                               9
  15Q LOSS WILD-TYPE                                            10
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  15Q LOSS MUTATED                                1
  15Q LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  15Q LOSS MUTATED                                    3
  15Q LOSS WILD-TYPE                                  0
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  15Q LOSS MUTATED                              0                            10
  15Q LOSS WILD-TYPE                            2                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  15Q LOSS MUTATED                                 1
  15Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  15Q LOSS MUTATED                                               2
  15Q LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  15Q LOSS MUTATED                              3
  15Q LOSS WILD-TYPE                            7
D68V10, multiclass
                                                    clus
vv                                                   15Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              170
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     9
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                    10
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   15Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                151
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      10
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  0
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
D68V12, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED   161   6   2  14
  15Q LOSS WILD-TYPE 183   7   2  12
D68V13, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              161                183
  R1                6                  7
  R2                2                  2
  RX               14                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  1     4
  15Q LOSS WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                          22   186
  15Q LOSS WILD-TYPE                        30   204
D68V14, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  3
  BLACK OR AFRICAN AMERICAN                      22                 30
  WHITE                                         186                204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V15, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3 180
  15Q LOSS WILD-TYPE   4 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3  180
  15Q LOSS WILD-TYPE    4  204
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              180                204
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    68  37
  16P LOSS WILD-TYPE 255 144
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               105                399 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                37                144 
$`16P LOSS MUTATED`
TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-44-7661 TCGA-44-8119 
        9.96         8.02         9.01        26.01        18.31         9.37 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-55-6978 TCGA-55-6979 TCGA-55-7914 
       16.04        17.16        11.64         5.79         7.79         6.15 
TCGA-55-8204 TCGA-55-8205 TCGA-55-A491 TCGA-64-1677 TCGA-73-4662 TCGA-91-7771 
       16.93        19.69        20.58        20.65        82.68        16.18 
TCGA-95-7562 TCGA-95-A4VN TCGA-97-A4M3 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
        2.86        18.18        17.75        10.09        27.19         5.29 
TCGA-05-4389 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-35-4122 
       45.01        47.05         2.99        29.98        30.02         7.40 
TCGA-44-3918 TCGA-44-5643 TCGA-44-6777 TCGA-44-7660 TCGA-44-8117 TCGA-49-4488 
       34.06        33.30        32.45        19.46        12.66        28.57 
TCGA-49-4494 TCGA-49-4510 TCGA-49-6743 TCGA-49-6767 TCGA-50-5066 TCGA-50-5068 
       35.54        29.46        53.29        22.26        47.41        49.28 
TCGA-50-5936 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-53-7624 TCGA-53-7813 
        8.45        53.16         3.91        11.05        34.29        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-6986 TCGA-55-7576 
       35.21        30.58        42.51        46.03       107.21        22.03 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7913 TCGA-55-8094 TCGA-55-8505 TCGA-55-8506 
        3.91        18.64        18.44        17.79        14.47         0.36 
TCGA-55-8507 TCGA-55-8616 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
       13.74         1.58        42.38        49.25        67.96        72.30 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 
       39.25        40.96        29.92        28.41        20.05        20.05 
TCGA-69-7763 TCGA-69-7974 TCGA-69-8255 TCGA-69-A59K TCGA-73-A9RS TCGA-75-5146 
       22.68         6.05         4.24        19.43        11.18        77.85 
TCGA-75-6214 TCGA-78-7143 TCGA-78-7146 TCGA-78-7149 TCGA-78-7167 TCGA-78-7535 
       36.66       163.10         5.69       129.53        88.14        31.20 
TCGA-78-7536 TCGA-83-5908 TCGA-86-6851 TCGA-86-7953 TCGA-86-8054 TCGA-86-8073 
        8.02        27.09         5.88        32.78        37.74        24.33 
TCGA-86-8672 TCGA-91-6829 TCGA-91-6831 TCGA-91-6847 TCGA-91-8499 TCGA-93-A4JO 
        0.62        41.36        10.19        27.68         1.18         1.08 
TCGA-95-7567 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-L4-A4E5 
       18.67         2.76        25.48        18.54        18.67        19.00 
TCGA-L9-A7SV TCGA-MP-A4TF TCGA-MP-A4TI 
       18.58        11.05        14.10 

$`16P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4405 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 
       19.96        14.01        20.05        15.02        15.02        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       35.28        11.64        14.73        26.30        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 
       42.08        23.93        27.78        86.01        29.00        29.23 
TCGA-44-A47F TCGA-49-4501 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       11.08        46.72       156.66        37.32        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       41.69        23.05        48.62         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8207 
       14.53        21.44        19.66        19.73        17.98        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF 
       18.15        13.68        16.93        22.65        19.59        20.19 
TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       13.87        52.60        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       85.32        13.71         1.45         6.12        17.29        16.54 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.68        15.65        21.40        17.92        20.19        20.52 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 TCGA-MP-A4TA 
       20.68        24.30        23.80         6.35        21.83        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 
        2.43        10.09        50.07         3.98        37.02         0.00 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       24.03        19.00        14.96        12.00        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         2.04         0.46         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 
       38.24        38.89        33.73        26.56        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 
       23.77        19.56        23.15        21.63        23.18        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       16.44        22.72         7.17        36.07        18.87        23.64 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 
       13.45        76.21        28.11        12.66        14.07        32.84 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 
        8.81        29.75        55.89        55.33        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ 
       62.24        28.90         8.55        40.41       123.58       221.33 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 
       60.16         8.22         9.27        14.27        78.67        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 
       48.46        60.72        57.53        42.35        25.55        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       30.54        38.73        67.89        14.30        80.52         5.62 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
       32.71        92.81        24.99        40.54        70.26        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
       20.02        27.09        32.71        23.15        25.41        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       23.08         5.06        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       15.42        17.56        15.72        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y 
       26.01        17.10        17.62        14.66        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       21.40         3.25         0.92        15.81        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
        4.57        39.98        14.60        88.64        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46Y TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       56.71        54.35        13.61        56.81        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
       37.02        38.37        87.98         2.04        42.90        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       28.47        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        4.64         6.64         6.12        13.61         5.42         7.56 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        4.41        13.41        13.51        14.01        13.45        26.73 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        8.42        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 
        9.24         1.25        50.33        66.64        43.82        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
       49.84       108.66       100.57        27.16        19.27        20.58 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
       26.53        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 TCGA-86-7701 
       39.75        77.59       110.50        93.11        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       34.39        38.04        20.55        19.89        35.24         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       27.58        28.34        26.50        29.46         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 
       13.64        26.47        10.62         1.97         2.60        12.23 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
        7.36         1.15        16.60        14.27        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 
       17.46        23.61        19.00        41.82        12.39        27.29 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
       19.89        42.25        64.60        63.52        61.48         0.59 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       15.91         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       24.56        34.85        36.76         1.45        21.57        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       18.08        35.47        32.48        14.30        14.53         1.91 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       15.65        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        11.15        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.36               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            163.10             238.29 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             19.46              22.03 
[1] "0.4 - 163.1 (19.5)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         1       20       22        0        13        18
  16P LOSS WILD-TYPE       4      113      117        1        37        54
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16P LOSS MUTATED           20          5        7
  16P LOSS WILD-TYPE         52          6       18
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 20                113
  STAGE IB                 22                117
  STAGE II                  0                  1
  STAGE IIA                13                 37
  STAGE IIB                18                 54
  STAGE IIIA               20                 52
  STAGE IIIB                5                  6
  STAGE IV                  7                 18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED    30  60  12   5
  16P LOSS WILD-TYPE 141 218  34  14
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               30                141
  T2               60                218
  T3               12                 34
  T4                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  16P LOSS MUTATED    62  20    23
  16P LOSS WILD-TYPE 271  76    53
D69V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                  62                271
  N1                  20                 76
  N2+N3               23                 53
[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"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    71   7
  16P LOSS WILD-TYPE 278  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     71    7
  16P LOSS WILD-TYPE  278   18
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               71                278
  1                7                 18
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    52  55
  16P LOSS WILD-TYPE 224 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     52   55
  16P LOSS WILD-TYPE  224  185
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               52                224
  MALE                 55                185
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    84  13
  16P LOSS WILD-TYPE 326  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     84   13
  16P LOSS WILD-TYPE  326   47
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                84                326
  YES               13                 47
[1] 2 2
[1] FALSE
D69V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16P LOSS MUTATED                            4
  16P LOSS WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16P LOSS MUTATED                                  25
  16P LOSS WILD-TYPE                                82
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                   64
  16P LOSS WILD-TYPE                                                257
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16P LOSS MUTATED                                            0
  16P LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  16P LOSS MUTATED                                               5
  16P LOSS WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  16P LOSS MUTATED                                1
  16P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  16P LOSS MUTATED                                    1
  16P LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  16P LOSS MUTATED                              0                             3
  16P LOSS WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  16P LOSS MUTATED                                 0
  16P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  16P LOSS MUTATED                                               2
  16P LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  16P LOSS MUTATED                              2
  16P LOSS WILD-TYPE                            8
D69V10, multiclass
                                                    clus
vv                                                   16P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               64
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   16P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                257
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
D69V12, continuous
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    70   1   1   4
  16P LOSS WILD-TYPE 274  12   3  22
D69V13, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               70                274
  R1                1                 12
  R2                1                  3
  RX                4                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     1
  16P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                          11    81
  16P LOSS WILD-TYPE                        41   309
D69V14, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                      11                 41
  WHITE                                          81                309
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  76
  16P LOSS WILD-TYPE   4 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   76
  16P LOSS WILD-TYPE    4  308
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               76                308
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    85  50
  16Q LOSS WILD-TYPE 238 131
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               135                369 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                50                131 
$`16Q LOSS MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-44-2661 TCGA-44-7661 
        8.02        20.05         9.01        26.01        38.10        18.31 
TCGA-44-8119 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-55-1595 TCGA-55-6978 
        9.37        16.04        17.16        11.64        48.62         5.79 
TCGA-55-6979 TCGA-55-8205 TCGA-55-A491 TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 
        7.79        19.69        20.58        20.65        52.60        82.68 
TCGA-91-7771 TCGA-95-7562 TCGA-95-A4VN TCGA-97-A4M3 TCGA-L9-A443 TCGA-L9-A444 
       16.18         2.86        18.18        17.75         6.35        10.09 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
       27.19         5.29         2.43        45.01        37.02        47.05 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5428 TCGA-35-4122 
        2.99        29.98        30.02        25.02        22.03         7.40 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
        5.98        97.74        49.05        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 TCGA-44-7669 TCGA-44-8117 
       33.30        23.18        32.45        19.46        18.87        12.66 
TCGA-44-A47B TCGA-49-4488 TCGA-49-4494 TCGA-49-4510 TCGA-49-6743 TCGA-50-5049 
        9.44        28.57        35.54        29.46        53.29       101.72 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5936 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 
       47.41        49.28         8.45        53.16         3.91        11.05 
TCGA-50-8457 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6968 
       36.99        34.29        13.94        35.21        30.58        42.51 
TCGA-55-6971 TCGA-55-6986 TCGA-55-7281 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 
       46.03       107.21        28.67        22.03         3.91        18.64 
TCGA-55-7913 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8616 TCGA-55-8620 
       18.44        14.47         0.36        13.74         1.58        12.33 
TCGA-55-A48Z TCGA-55-A493 TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46U 
       21.40         0.92         4.57        42.38        47.80        67.96 
TCGA-62-A470 TCGA-62-A472 TCGA-64-5774 TCGA-64-5778 TCGA-67-3770 TCGA-67-3771 
       39.25        29.92        87.98        42.90        20.05        20.05 
TCGA-69-7763 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
       22.68         6.05         4.41        13.41         4.24        19.43 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-6214 TCGA-78-7143 TCGA-78-7146 
       11.18        66.64        77.85        36.66       163.10         5.69 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
      129.53        21.90        39.95        88.14        31.20         8.02 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 
       27.09         5.88        34.39        38.04        32.78        37.74 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8359 TCGA-86-8672 TCGA-91-6829 TCGA-91-6847 
       24.33        22.82        14.60         0.62        41.36        27.68 
TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7567 TCGA-95-8494 TCGA-97-7546 
        1.18        17.46         1.08        18.67         2.76        42.25 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A7SV 
       25.48        18.54        18.67        32.48        19.00        18.58 
TCGA-MP-A4TI TCGA-NJ-A4YI TCGA-NJ-A4YP 
       14.10         0.13         1.64 

$`16Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 
       19.96        14.01         9.96        15.02        15.02        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2662 
       35.28        11.64        14.73        26.30        43.53        42.08 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F 
       23.93        27.78        86.01        29.00        29.23        11.08 
TCGA-49-4501 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       46.72       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
       23.05         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 
        6.15        19.66        19.73        17.98        16.93        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF 
       18.15        13.68        16.93        22.65        19.59        20.19 
TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       13.87        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 
       13.71         1.45         6.12        17.29        16.54        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 
       15.65        21.40        17.92        20.19        20.52        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A743 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 
       24.30        23.80        21.83        31.23        10.09        50.07 
TCGA-05-4250 TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 
        3.98         0.00        24.03        19.00        14.96        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       21.99        26.01        25.02        24.00         4.96        29.00 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        9.04         2.04         0.46         8.68       120.79        37.71 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 
       44.61         4.37        46.98        44.42        44.94        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-5644 
        3.19        25.02        37.15        38.24        38.89        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 
       28.01        23.77        19.56        23.15        21.63        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7672 TCGA-44-8120 
       16.44        22.72         7.17        36.07        23.64         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.98        15.32        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 
       28.11        12.66        14.07        32.84         8.81        29.75 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       55.89        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        40.41       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 
        9.86        20.52        71.47        15.72        60.16         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        14.27        78.67        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       57.53        42.35        25.55        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 
       10.13        36.79        27.25        30.54        38.73        67.89 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       14.30        80.52         5.62        40.73        15.25        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 
       40.54        70.26        20.02        27.09        32.71        23.15 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
       25.41        11.28        34.19        17.65        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       14.66        20.71         3.25        15.81        19.99        17.95 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       39.98        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 
       54.35        72.30        13.61        40.96        56.81        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       81.80        37.02        38.37         2.04        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       28.47        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        4.64         6.64         6.12        13.61         5.42         7.56 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 
       13.51        14.01        13.45        26.73         8.42        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       50.33        43.82        85.15        49.84       108.66       100.57 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       27.16        19.27        20.58       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
      238.29        26.53        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 
      232.18        39.75        77.59       110.50        93.11        12.36 
TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       31.13        20.55        19.89        35.24         4.08         4.57 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        0.79        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
       11.61        13.91        30.84        27.58        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       29.46         3.81        24.23        13.64        26.47        10.62 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
        1.97        10.19         2.60        12.23         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP 
       16.60        14.27        19.82        22.45        23.61        19.00 
TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       41.82        12.39        27.29        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
       61.48         0.59        15.91         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W 
       21.57        21.63        18.08        35.47        14.30        14.53 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        1.91        15.65        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       71.05        74.33        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.13               0.00 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            163.10             238.29 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             21.40              21.63 
[1] "0.1 - 163.1 (21.4)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         1       31       34        0        15        21
  16Q LOSS WILD-TYPE       4      102      105        1        35        51
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16Q LOSS MUTATED           21          6        7
  16Q LOSS WILD-TYPE         51          5       18
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 31                102
  STAGE IB                 34                105
  STAGE II                  0                  1
  STAGE IIA                15                 35
  STAGE IIB                21                 51
  STAGE IIIA               21                 51
  STAGE IIIB                6                  5
  STAGE IV                  7                 18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED    44  76  12   5
  16Q LOSS WILD-TYPE 127 202  34  14
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               44                127
  T2               76                202
  T3               12                 34
  T4                5                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  16Q LOSS MUTATED    83  26    26
  16Q LOSS WILD-TYPE 250  70    50
D70V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                  83                250
  N1                  26                 70
  N2+N3               26                 50
[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"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    96   7
  16Q LOSS WILD-TYPE 253  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     96    7
  16Q LOSS WILD-TYPE  253   18
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               96                253
  1                7                 18
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    69  68
  16Q LOSS WILD-TYPE 207 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     69   68
  16Q LOSS WILD-TYPE  207  172
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               69                207
  MALE                 68                172
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   110  16
  16Q LOSS WILD-TYPE 300  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    110   16
  16Q LOSS WILD-TYPE  300   44
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               110                300
  YES               16                 44
[1] 2 2
[1] FALSE
D70V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16Q LOSS MUTATED                            5
  16Q LOSS WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16Q LOSS MUTATED                                  31
  16Q LOSS WILD-TYPE                                76
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                   83
  16Q LOSS WILD-TYPE                                                238
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16Q LOSS MUTATED                                            0
  16Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  16Q LOSS MUTATED                                               6
  16Q LOSS WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  16Q LOSS MUTATED                                2
  16Q LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  16Q LOSS MUTATED                                    1
  16Q LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  16Q LOSS MUTATED                              0                             5
  16Q LOSS WILD-TYPE                            2                            18
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  16Q LOSS MUTATED                                 0
  16Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  16Q LOSS MUTATED                                               2
  16Q LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  16Q LOSS MUTATED                              2
  16Q LOSS WILD-TYPE                            8
D70V10, multiclass
                                                    clus
vv                                                   16Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               83
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     5
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   16Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                238
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      18
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
D70V12, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    92   1   1   5
  16Q LOSS WILD-TYPE 252  12   3  21
D70V13, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               92                252
  R1                1                 12
  R2                1                  3
  RX                5                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     2
  16Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                          13   104
  16Q LOSS WILD-TYPE                        39   286
D70V14, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  5
  BLACK OR AFRICAN AMERICAN                      13                 39
  WHITE                                         104                286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V15, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5  97
  16Q LOSS WILD-TYPE   2 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   97
  16Q LOSS WILD-TYPE    2  287
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  2
  NOT HISPANIC OR LATINO               97                287
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   138  77
  17P LOSS WILD-TYPE 185 104
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               215                289 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                77                104 
$`17P LOSS MUTATED`
TCGA-05-4396 TCGA-05-4402 TCGA-05-4427 TCGA-05-5420 TCGA-38-4631 TCGA-38-6178 
        9.96         8.02        26.01        15.02        11.64        14.73 
TCGA-44-2662 TCGA-44-6147 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-49-6745 
       42.08        27.78        18.31        29.00         9.37        17.16 
TCGA-49-6761 TCGA-49-AARN TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
       11.64        37.32        41.69        23.05        48.62         5.79 
TCGA-55-7573 TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8205 TCGA-55-8207 
       16.01        21.44         6.15        19.73        19.69        32.12 
TCGA-55-8511 TCGA-55-A48X TCGA-55-A491 TCGA-67-6217 TCGA-73-4658 TCGA-91-7771 
       18.15        22.65        20.58        13.87        52.60        16.18 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       17.29         2.86        15.68        15.65        21.40        18.18 
TCGA-J2-8192 TCGA-MP-A4T8 TCGA-05-4249 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 
       24.30         5.29        50.07        45.01         0.00        24.03 
TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5428 
       29.98        21.99        26.01        25.02        24.00        22.03 
TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4632 TCGA-44-2656 
        9.04         7.40         5.98        97.74        44.61        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       44.42        44.94        42.77        38.89        34.06        33.73 
TCGA-44-5643 TCGA-44-6144 TCGA-44-6775 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 
       33.30        23.77        23.18        16.44        19.46         7.17 
TCGA-44-7667 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47B TCGA-49-4488 TCGA-49-4490 
       36.07        12.66         8.55         9.44        28.57        12.66 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 
       14.07         8.81        29.46        29.75        53.29        55.33 
TCGA-49-6767 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-50-5051 
       22.26         8.55        40.41       123.58       221.33        15.72 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 
       49.28        14.27         8.45        48.46        57.53         3.91 
TCGA-50-6594 TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       12.16         0.72        10.13        34.29        30.54        13.94 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 
       38.73        67.89         5.62        42.51        53.65         3.88 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-7281 TCGA-55-7576 
       45.34        32.71        24.99        40.54        28.67        22.03 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 
        3.91        18.64        34.19        17.65        19.82        23.08 
TCGA-55-8092 TCGA-55-8097 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48Y 
        5.06        15.65        17.72        17.10        17.62        20.71 
TCGA-55-A48Z TCGA-62-8397 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       21.40        42.38        47.80        56.71        54.35        67.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5815 
       29.92        56.81        81.80        38.37        87.98        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 
       20.05        20.05        14.04         5.72         6.64         6.12 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-8255 TCGA-69-8453 
       13.61         5.42         6.05         4.41         4.24        26.73 
TCGA-69-A59K TCGA-73-4659 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5147 
       19.43        23.38        50.33        11.18        66.64        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 
       85.15        49.84        36.66       108.66       163.10        27.16 
TCGA-78-7146 TCGA-78-7150 TCGA-78-7159 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
        5.69        21.90        64.90        31.20         8.02        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-80-5608 TCGA-86-7701 
       39.35        10.55       232.18        77.59        93.11        31.13 
TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       34.39        32.78        19.89        37.74         4.57        24.33 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 
       22.82        31.04        31.20        23.05        21.47        13.91 
TCGA-86-A4JF TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-93-7347 TCGA-93-A4JO 
       24.23        10.19        12.23        27.68        22.45         1.08 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8175 TCGA-97-8547 TCGA-99-7458 
       25.48        18.54         0.59        18.12        21.60        24.56 
TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W 
       34.85        21.57        18.08        35.47        19.00        14.53 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4TE TCGA-MP-A4TF 
       15.65        38.63        86.04        58.85        29.46        11.05 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-O1-A52J 
       73.91        71.05         0.13        47.08        59.11 

$`17P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 TCGA-38-4629 
       19.96        14.01        20.05         9.01        15.02        28.41 
TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 
       35.28        26.30        43.53        38.10        23.93        86.01 
TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-AAR0 TCGA-50-5932 
       29.23        11.08        46.72        16.04       156.66        40.60 
TCGA-50-5935 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-8090 
       21.47         7.79         7.99        23.18        14.53        19.66 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 TCGA-55-A4DF 
       17.98        16.93        13.68        16.93        19.59        20.19 
TCGA-64-1677 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       20.65        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-97-8172 
       85.32        13.71         1.45         6.12        16.54        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A443 
       20.19        20.52        17.75        20.68        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        21.83        27.19        31.23         2.43        10.09 
TCGA-05-4250 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        3.98        37.02        47.05        19.00         2.99        14.96 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-05-5715 
       12.00        30.02        25.02         4.96        29.00         2.04 
TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F 
        0.46         8.68       120.79        37.71        49.05         4.37 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5644 
        3.19        25.02        37.15        38.24        26.56        28.37 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 
       28.01        19.56        23.15        21.63        32.45        61.28 
TCGA-44-7659 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G 
       22.72        18.87        23.64        15.98        15.32        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4506 
       13.64        13.45        76.21        28.11        35.54        32.84 
TCGA-49-4514 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARR 
       55.89        22.26        73.12        62.24        28.90       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
        9.86        20.52        71.47       101.72        60.16        47.41 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 
        8.22         9.27        78.67        15.12        60.72        53.16 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 
       42.35        25.55        11.05         6.21        36.99        36.79 
TCGA-50-8460 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
       27.25        35.21        30.58        14.30        80.52        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 
       15.25        46.03        69.34        92.81       107.21        70.26 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
       20.02        27.09        32.71        23.15        25.41        11.28 
TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8094 TCGA-55-8096 
       18.44        29.23        29.72        15.19        17.79        23.64 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
        0.36        13.74        20.28        19.96        26.01        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
        1.58        12.33         3.25         0.92        15.81        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       17.95         4.57        39.98        14.60        88.64        49.25 
TCGA-62-A46P TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 
       19.53        72.30        13.61        39.25        40.96        39.09 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3772 
       37.02         2.04        42.90        28.41        51.25        18.84 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 TCGA-69-7979 
       12.66        14.73         4.64        22.68         7.56        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 
       13.51        14.01        13.45         8.42        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5146 TCGA-75-7027 
        4.31        30.31         9.24         1.25        77.85       100.57 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       19.27        20.58       129.53        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-8648 TCGA-78-8662 
      238.29        88.14        26.53        53.33        39.75       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 
       27.09        12.36         5.88        38.04        20.55        35.24 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8076 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
        4.08         0.79        32.65        14.60        11.61        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       27.58         0.62        28.34        26.50        29.46         3.81 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
       13.64        26.47        10.62        41.36         1.97         2.60 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       17.46        23.61        19.00        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 
       61.48        15.91        18.67         5.39        15.39        16.41 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       14.30        20.58        21.44        19.76        20.84        18.67 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP 
       36.76         1.45        21.63        32.48        14.30         1.91 
TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       18.58         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
        5.49        41.59        24.36        14.10        11.15        19.13 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       74.33         1.64         0.49         0.43        19.82        20.28 
TCGA-S2-AA1A 
       16.87 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.00               0.36 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            232.18             238.29 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             23.05              20.52 
[1] "0.0 - 232.2 (23.1)" "0.4 - 238.3 (20.5)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         3       48       59        0        24        37
  17P LOSS WILD-TYPE       2       85       80        1        26        35
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17P LOSS MUTATED           34          4        9
  17P LOSS WILD-TYPE         38          7       16
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 48                 85
  STAGE IB                 59                 80
  STAGE II                  0                  1
  STAGE IIA                24                 26
  STAGE IIB                37                 35
  STAGE IIIA               34                 38
  STAGE IIIB                4                  7
  STAGE IV                  9                 16
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED    65 126  20   7
  17P LOSS WILD-TYPE 106 152  26  12
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               65                106
  T2              126                152
  T3               20                 26
  T4                7                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  17P LOSS MUTATED   139  42    33
  17P LOSS WILD-TYPE 194  54    43
D71V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                 139                194
  N1                  42                 54
  N2+N3               33                 43
[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"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   148   9
  17P LOSS WILD-TYPE 201  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    148    9
  17P LOSS WILD-TYPE  201   16
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              148                201
  1                9                 16
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   128  91
  17P LOSS WILD-TYPE 148 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    128   91
  17P LOSS WILD-TYPE  148  149
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              128                148
  MALE                 91                149
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   181  19
  17P LOSS WILD-TYPE 229  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    181   19
  17P LOSS WILD-TYPE  229   41
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               181                229
  YES               19                 41
[1] 2 2
[1] FALSE
D71V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17P LOSS MUTATED                            7
  17P LOSS WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17P LOSS MUTATED                                  41
  17P LOSS WILD-TYPE                                66
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                  148
  17P LOSS WILD-TYPE                                                173
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17P LOSS MUTATED                                            2
  17P LOSS WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  17P LOSS MUTATED                                               7
  17P LOSS WILD-TYPE                                            12
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  17P LOSS MUTATED                                2
  17P LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  17P LOSS MUTATED                                    2
  17P LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  17P LOSS MUTATED                              0                             5
  17P LOSS WILD-TYPE                            2                            18
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  17P LOSS MUTATED                                 0
  17P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  17P LOSS MUTATED                                               3
  17P LOSS WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17P LOSS MUTATED                              2
  17P LOSS WILD-TYPE                            8
D71V10, multiclass
                                                    clus
vv                                                   17P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              148
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     7
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     5
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   17P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                173
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      12
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      18
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
D71V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   149   5   1  12
  17P LOSS WILD-TYPE 195   8   3  14
D71V13, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              149                195
  R1                5                  8
  R2                1                  3
  RX               12                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     2
  17P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          22   165
  17P LOSS WILD-TYPE                        30   225
D71V14, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  5
  BLACK OR AFRICAN AMERICAN                      22                 30
  WHITE                                         165                225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     5 159
  17P LOSS WILD-TYPE   2 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5  159
  17P LOSS WILD-TYPE    2  225
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  2
  NOT HISPANIC OR LATINO              159                225
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    33  25
  17Q LOSS WILD-TYPE 290 156
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                58                446 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                156 
$`17Q LOSS MUTATED`
TCGA-05-4396 TCGA-38-4631 TCGA-38-6178 TCGA-49-6761 TCGA-55-8091 TCGA-55-8207 
        9.96        11.64        14.73        11.64        19.73        32.12 
TCGA-55-8511 TCGA-67-6217 TCGA-91-7771 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK 
       18.15        13.87        16.18         2.86        15.65        21.40 
TCGA-J2-8192 TCGA-05-4395 TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3918 
       24.30         0.00        46.98        44.42        42.77        34.06 
TCGA-44-7660 TCGA-49-4488 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-AARQ 
       19.46        28.57        14.07         8.81        29.75       221.33 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5936 TCGA-50-6673 TCGA-53-7624 TCGA-55-1596 
       15.72        49.28         8.45         0.72        34.29        67.89 
TCGA-55-6712 TCGA-55-6975 TCGA-55-7576 TCGA-55-8092 TCGA-55-8514 TCGA-55-8614 
        5.62         3.88        22.03         5.06        17.10        17.62 
TCGA-62-8397 TCGA-64-1676 TCGA-69-7764 TCGA-69-A59K TCGA-73-A9RS TCGA-75-6212 
       42.38        56.81        13.61        19.43        11.18        49.84 
TCGA-75-7025 TCGA-78-7146 TCGA-78-7535 TCGA-78-7536 TCGA-78-8655 TCGA-86-7701 
      108.66         5.69        31.20         8.02        77.59        31.13 
TCGA-86-8280 TCGA-86-A4JF TCGA-91-6840 TCGA-95-A4VP TCGA-J2-A4AD TCGA-L4-A4E5 
       23.05        24.23        12.23        19.89        18.08        19.00 
TCGA-L9-A8F4 TCGA-MP-A4T6 TCGA-MP-A5C7 TCGA-NJ-A4YI 
       15.65        58.85        73.91         0.13 

$`17Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 
       15.02        15.02        28.41        35.28        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       17.16       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 
       23.18        14.53        21.44         6.15        19.66        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       16.93        19.69        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 
       19.59        20.19        20.65        52.60        82.68        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC 
        8.48        50.24        10.55        85.32        13.71         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VN TCGA-97-8172 
        6.12        17.29        16.54        15.68        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A443 
       20.19        20.52        17.75        20.68        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       10.09        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 
       10.09        50.07         3.98        45.01        37.02        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
        4.96        29.00        22.03         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 
       49.05        44.61         4.37        44.94         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        38.89        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 
       23.18        32.45        61.28        16.44        22.72         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 
       28.11        12.66        35.54        32.84        29.46        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       53.29        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V 
       28.90         8.55        40.41       123.58       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
       20.52        71.47       101.72        60.16        47.41         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        14.27        78.67        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21        10.13        36.99        36.79        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 
       30.54        13.94        35.21        38.73        30.58        14.30 
TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       80.52        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        3.91        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       23.08        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 
       20.28        17.72        19.96        26.01        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
       19.99        17.95         4.57        39.98        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 
       72.30        13.61        39.25        40.96        29.92        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       81.80        37.02        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       28.41        51.25        28.47        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
       13.41        13.51        14.01        13.45         4.24        26.73 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        8.42        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       85.15        36.66       100.57       163.10        27.16        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 
      104.19       238.29        88.14        26.53        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 
       39.35        10.55       232.18        39.75       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36         5.88        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
        0.62        28.34        26.50        29.46         3.81        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 
       41.82        18.67        12.39        27.29         2.76        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       21.63        35.47        32.48        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       18.58        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       37.35        86.04         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        11.15        19.13        71.05        74.33 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        47.08         0.49         0.43        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.00               0.36 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            221.33             238.29 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            19.215             22.010 
[1] "0.0 - 221.3 (19.2)" "0.4 - 238.3 (22.0)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         3        7       16        0         5        12
  17Q LOSS WILD-TYPE       2      126      123        1        45        60
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17Q LOSS MUTATED           13          2        2
  17Q LOSS WILD-TYPE         59          9       23
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                  7                126
  STAGE IB                 16                123
  STAGE II                  0                  1
  STAGE IIA                 5                 45
  STAGE IIB                12                 60
  STAGE IIIA               13                 59
  STAGE IIIB                2                  9
  STAGE IV                  2                 23
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED    11  40   7   2
  17Q LOSS WILD-TYPE 160 238  39  17
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               11                160
  T2               40                238
  T3                7                 39
  T4                2                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  17Q LOSS MUTATED    34  12    13
  17Q LOSS WILD-TYPE 299  84    63
D72V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                  34                299
  N1                  12                 84
  N2+N3               13                 63
[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"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    39   2
  17Q LOSS WILD-TYPE 310  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     39    2
  17Q LOSS WILD-TYPE  310   23
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               39                310
  1                2                 23
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    36  24
  17Q LOSS WILD-TYPE 240 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     36   24
  17Q LOSS WILD-TYPE  240  216
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               36                240
  MALE                 24                216
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    51   7
  17Q LOSS WILD-TYPE 359  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     51    7
  17Q LOSS WILD-TYPE  359   53
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                51                359
  YES                7                 53
[1] 2 2
[1] FALSE
D72V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17Q LOSS MUTATED                            2
  17Q LOSS WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17Q LOSS MUTATED                                  10
  17Q LOSS WILD-TYPE                                97
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                   44
  17Q LOSS WILD-TYPE                                                277
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17Q LOSS MUTATED                                            0
  17Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  17Q LOSS MUTATED                                               1
  17Q LOSS WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  17Q LOSS MUTATED                                0
  17Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  17Q LOSS MUTATED                                    1
  17Q LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  17Q LOSS MUTATED                              0                             1
  17Q LOSS WILD-TYPE                            2                            22
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  17Q LOSS MUTATED                                 0
  17Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  17Q LOSS MUTATED                                               0
  17Q LOSS WILD-TYPE                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17Q LOSS MUTATED                              1
  17Q LOSS WILD-TYPE                            9
D72V10, multiclass
                                                    clus
vv                                                   17Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               44
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     1
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   17Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      22
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       5
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
D72V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    43   3   0   3
  17Q LOSS WILD-TYPE 301  10   4  23
D72V13, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               43                301
  R1                3                 10
  R2                0                  4
  RX                3                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     1
  17Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           7    45
  17Q LOSS WILD-TYPE                        45   345
D72V14, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                       7                 45
  WHITE                                          45                345
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  45
  17Q LOSS WILD-TYPE   6 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   45
  17Q LOSS WILD-TYPE    6  339
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               45                339
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   110  67
  18P LOSS WILD-TYPE 213 114
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               177                327 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                67                114 
$`18P LOSS MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 TCGA-38-4631 
        8.02        20.05         9.01        26.01        15.02        11.64 
TCGA-44-7670 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-AARN TCGA-50-6597 
       29.00        11.08        46.72        16.04        37.32        41.69 
TCGA-55-6979 TCGA-55-7573 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 
        7.79        16.01        21.44        19.66        19.73        32.12 
TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-78-8660 TCGA-91-6836 TCGA-91-7771 
       20.58        19.59        13.87        10.55        13.71        16.18 
TCGA-95-7948 TCGA-95-A4VN TCGA-97-A4LX TCGA-J2-8192 TCGA-J2-8194 TCGA-05-4249 
       15.65        18.18        20.19        24.30        23.80        50.07 
TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4417 TCGA-05-4425 
        3.98        37.02         0.00        47.05        14.96        21.99 
TCGA-05-4426 TCGA-05-5425 TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
       26.01        29.00         2.04         5.98         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2665 TCGA-44-3918 
       37.71        49.05        44.61        46.98        42.77        34.06 
TCGA-44-6145 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7667 
       19.56        23.18        32.45        61.28        16.44        36.07 
TCGA-44-7669 TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 
       18.87        13.45        28.57        12.66        14.07        32.84 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       29.75        53.29        22.26        73.12        62.24        28.90 
TCGA-49-AARE TCGA-49-AARO TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 
       40.41       123.58         8.22        78.67         8.45        48.46 
TCGA-50-5946 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
       53.16        36.99        36.79        34.29        30.54        38.73 
TCGA-55-1596 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6985 
       67.89        42.51        46.03        53.65         3.88        40.54 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7910 
       28.67        20.02        32.71        22.03        23.15        34.19 
TCGA-55-7913 TCGA-55-8087 TCGA-55-8097 TCGA-55-8507 TCGA-55-8616 TCGA-55-8620 
       18.44        15.19        15.65        13.74         1.58        12.33 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 
       21.40         3.25         0.92        17.95         4.57        42.38 
TCGA-62-A46O TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       47.80        54.35        39.25        40.96        29.92        56.81 
TCGA-64-1679 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       81.80        51.25        28.47        20.05        20.05        18.84 
TCGA-67-6216 TCGA-69-7765 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 
        4.64         5.42        13.41        19.43         8.42        26.30 
TCGA-73-4670 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-6212 TCGA-75-6214 
        4.31        50.33        11.18        66.64        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7150 TCGA-78-7161 TCGA-78-7167 
      108.66       100.57         5.69        21.90         9.57        88.14 
TCGA-78-7535 TCGA-83-5908 TCGA-86-6851 TCGA-86-7714 TCGA-86-7954 TCGA-86-8073 
       31.20        27.09         5.88        20.55        19.89        24.33 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8672 TCGA-91-6830 
       31.04        31.20        23.05        21.47         0.62         1.97 
TCGA-91-6847 TCGA-91-6848 TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JP TCGA-95-7039 
       27.68         7.36        19.82        17.46        19.00        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 
       18.67        27.29         2.76        64.60        63.52        18.54 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4M0 TCGA-J2-A4AD 
       15.91         5.39        15.39        21.60        21.44        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SW 
       35.47        19.00        14.53        18.58        15.65        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ 
       37.35        58.85         5.49        11.05        14.10        11.15 
TCGA-NJ-A4YF TCGA-NJ-A55O TCGA-O1-A52J 
       71.05         0.43        59.11 

$`18P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 
       19.96        14.01         9.96        15.02        28.41        35.28 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-49-6745 
       27.78        86.01        18.31        29.23         9.37        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-1595 
       11.64       156.66        40.60        21.47        23.05        48.62 
TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8203 
        5.79         7.99        23.18        14.53         6.15        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       16.93        19.69        18.15        13.68        16.93        22.65 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.19        20.65        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-80-5611 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       50.24        85.32         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 
        2.86        15.68        21.40        17.92        20.52        17.75 
TCGA-97-A4M7 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       20.68         6.35        10.09        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4397 TCGA-05-4403 
       31.23         2.43        10.09        45.01        24.03        19.00 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 
        2.99        29.98        12.00        30.02        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 
       24.00         4.96        22.03         9.04         0.46         7.40 
TCGA-38-4626 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 
      120.79         4.37        44.42        44.94         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        38.89        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 TCGA-44-7659 
       28.37        28.01        23.77        23.15        21.63        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       19.46         7.17        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 
       15.32         9.44        11.54        13.64        76.21        28.11 
TCGA-49-4494 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-AAQV 
       35.54         8.81        29.46        55.89        55.33        22.26 
TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
        8.55       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
      101.72        15.72        60.16        47.41        49.28         9.27 
TCGA-50-5931 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 
       14.27        15.12        60.72        57.53        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       27.25        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        5.62        40.73        15.25        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7727 
       92.81        24.99       107.21        70.26        27.09         3.91 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
       25.41        18.64        11.28        17.65        19.82        29.23 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 
       29.72        23.08         5.06        17.79        23.64        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-A48Y TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 
       14.66        20.71        15.81        19.99        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V 
       88.64        49.25        19.53        56.71        67.96        72.30 
TCGA-62-A46Y TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       13.61        39.09        37.02        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       42.90        28.41        14.04        12.66        14.73         5.72 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
        6.64         6.12        22.68        13.61         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        4.41        13.51        14.01        13.45         4.24        26.73 
TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5146 
       23.38        15.35        30.31         9.24         1.25        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
       43.82        85.15       163.10        27.16        19.27        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
      129.53        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 
        5.88        64.90        22.92       104.19       238.29        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 TCGA-86-7701 
       39.75        77.59       110.50        93.11        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       34.39        38.04        32.78        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8359 TCGA-86-8585 
        4.57         0.79        22.82        32.65        14.60        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       10.19         2.60        12.23         1.15        16.60        14.27 
TCGA-91-8499 TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7944 TCGA-95-A4VP 
        1.18        22.45        23.61         1.08        12.39        19.89 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-8171 TCGA-97-8175 
       42.25        61.48        25.48         0.59        18.67        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       16.41        14.30        20.58        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       24.56        34.85        36.76         1.45        21.57        21.63 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        14.30         1.91        38.63         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK 
       49.35        86.04        41.59        29.46        24.36        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       19.82        20.28        16.87 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.00               0.13 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            123.58             238.29 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             21.90              21.57 
[1] "0.0 - 123.6 (21.9)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         1       35       50        0        22        33
  18P LOSS WILD-TYPE       4       98       89        1        28        39
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18P LOSS MUTATED           21          5       12
  18P LOSS WILD-TYPE         51          6       13
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 35                 98
  STAGE IB                 50                 89
  STAGE II                  0                  1
  STAGE IIA                22                 28
  STAGE IIB                33                 39
  STAGE IIIA               21                 51
  STAGE IIIB                5                  6
  STAGE IV                 12                 13
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    53 103  17   6
  18P LOSS WILD-TYPE 118 175  29  13
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               53                118
  T2              103                175
  T3               17                 29
  T4                6                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  18P LOSS MUTATED   110  43    24
  18P LOSS WILD-TYPE 223  53    52
D73V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                 110                223
  N1                  43                 53
  N2+N3               24                 52
[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"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   110  12
  18P LOSS WILD-TYPE 239  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    110   12
  18P LOSS WILD-TYPE  239   13
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              110                239
  1               12                 13
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   110  70
  18P LOSS WILD-TYPE 166 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    110   70
  18P LOSS WILD-TYPE  166  170
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              110                166
  MALE                 70                170
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   143  20
  18P LOSS WILD-TYPE 267  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    143   20
  18P LOSS WILD-TYPE  267   40
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               143                267
  YES               20                 40
[1] 2 2
[1] FALSE
D73V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18P LOSS MUTATED                            7
  18P LOSS WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18P LOSS MUTATED                                  37
  18P LOSS WILD-TYPE                                70
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                  113
  18P LOSS WILD-TYPE                                                208
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18P LOSS MUTATED                                            1
  18P LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  18P LOSS MUTATED                                               4
  18P LOSS WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  18P LOSS MUTATED                                1
  18P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  18P LOSS MUTATED                                    2
  18P LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  18P LOSS MUTATED                              0                             8
  18P LOSS WILD-TYPE                            2                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  18P LOSS MUTATED                                 1
  18P LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  18P LOSS MUTATED                                               1
  18P LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  18P LOSS MUTATED                              5
  18P LOSS WILD-TYPE                            5
D73V10, multiclass
                                                    clus
vv                                                   18P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              113
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     8
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      5
                                                    clus
vv                                                   18P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                208
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, continuous
D73V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   118   5   3   6
  18P LOSS WILD-TYPE 226   8   1  20
D73V13, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              118                226
  R1                5                  8
  R2                3                  1
  RX                6                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     3
  18P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          23   127
  18P LOSS WILD-TYPE                        29   263
D73V14, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                      23                 29
  WHITE                                         127                263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3 133
  18P LOSS WILD-TYPE   4 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3  133
  18P LOSS WILD-TYPE    4  251
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              133                251
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   131  81
  18Q LOSS WILD-TYPE 192 100
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               212                292 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                81                100 
$`18Q LOSS MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 TCGA-38-4631 
        8.02        20.05         9.01        26.01        15.02        11.64 
TCGA-38-6178 TCGA-44-2662 TCGA-44-6146 TCGA-44-7670 TCGA-44-A47F TCGA-49-4501 
       14.73        42.08        23.93        29.00        11.08        46.72 
TCGA-49-6742 TCGA-49-6761 TCGA-49-AARN TCGA-50-6597 TCGA-55-1595 TCGA-55-6979 
       16.04        11.64        37.32        41.69        48.62         7.79 
TCGA-55-7573 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 
       16.01        14.53        21.44        19.66        19.73        32.12 
TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-78-8660 TCGA-91-6836 
       20.58        19.59        13.87        82.68        10.55        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7947 TCGA-95-A4VN TCGA-97-A4LX 
       16.18         1.45        17.29        15.68        18.18        20.19 
TCGA-J2-8192 TCGA-J2-8194 TCGA-05-4249 TCGA-05-4250 TCGA-05-4395 TCGA-05-4398 
       24.30        23.80        50.07         3.98         0.00        47.05 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 
       14.96        12.00        30.02        21.99        26.01        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 
        4.96        29.00         9.04         2.04         5.98         8.68 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       37.71        49.05        44.61        46.98        44.42        42.77 
TCGA-44-3918 TCGA-44-6145 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7662 
       34.06        19.56        23.18        32.45        16.44         7.17 
TCGA-44-7669 TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 
       18.87        13.45        28.11        28.57        12.66        14.07 
TCGA-49-4506 TCGA-49-4512 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR4 
       32.84        29.75        53.29        22.26        62.24        28.90 
TCGA-49-AARE TCGA-49-AARO TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5933 
       40.41       123.58        47.41        49.28         8.22        78.67 
TCGA-50-5936 TCGA-50-5941 TCGA-50-5946 TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 
        8.45        48.46        53.16        11.05        12.16        36.99 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 
       36.79        34.29        30.54        38.73        67.89         5.62 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6982 
       42.51        46.03        53.65         3.88        69.34        32.71 
TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 
       40.54        28.67        20.02        32.71        22.03        23.15 
TCGA-55-7910 TCGA-55-7994 TCGA-55-8087 TCGA-55-8094 TCGA-55-8097 TCGA-55-8507 
       34.19        19.82        15.19        17.79        15.65        13.74 
TCGA-55-8616 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A57B TCGA-62-8394 
        1.58        21.40         3.25         0.92        17.95         4.57 
TCGA-62-8397 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 
       42.38        47.80        56.71        54.35        67.96        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
       40.96        29.92        56.81        81.80        38.37         2.04 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       42.90        51.25        28.47        20.05        20.05        18.84 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-69-7979 TCGA-69-8254 TCGA-69-8453 
        4.64         6.64         5.42        13.41        13.45        26.73 
TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 
       19.43        26.30         4.31        50.33        11.18        66.64 
TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       43.82        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7161 TCGA-78-7535 
       27.16         5.69        19.27        21.90         9.57        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        8.02        26.01        27.09         5.88        31.13        34.39 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       20.55        19.89         0.79        31.04        31.20        23.05 
TCGA-86-8672 TCGA-91-6829 TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-A4BD 
        0.62        41.36         1.97        27.68         7.36        19.82 
TCGA-93-7348 TCGA-93-A4JP TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7547 
       17.46        19.00        18.67        27.29         2.76        64.60 
TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 
       63.52        18.54        15.91         5.39        15.39        16.41 
TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M6 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
       21.60        21.44        18.67        18.08        35.47        19.00 
TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 
       14.53        15.65        38.63        58.45        37.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF 
        5.49        11.05        14.10        11.15        19.13        71.05 
TCGA-NJ-A55O TCGA-O1-A52J 
        0.43        59.11 

$`18Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 
       19.96        14.01         9.96        15.02        28.41        35.28 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        43.53        38.10        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-8119 TCGA-49-6745 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 
       29.23         9.37        17.16       156.66        40.60        21.47 
TCGA-55-1592 TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7914 TCGA-55-8203 
       23.05         5.79         7.99        23.18         6.15        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       16.93        19.69        18.15        13.68        16.93        22.65 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       20.19        20.65        52.60        39.09         8.48        50.24 
TCGA-80-5611 TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK 
       85.32         6.12        16.54         2.86        15.65        21.40 
TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-L9-A443 TCGA-L9-A444 
       17.92        20.52        17.75        20.68         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       21.83        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 
       45.01        37.02        24.03        19.00         2.99        29.98 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 
       25.02        25.02        22.03         0.46         7.40        97.74 
TCGA-38-4626 TCGA-38-A44F TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
      120.79         4.37        44.94         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        38.89        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 TCGA-44-7659 
       28.01        23.77        23.15        21.63        61.28        22.72 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       19.46        36.07        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 
       15.32         9.44        11.54        13.64        76.21        35.54 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 
        8.81        29.46        55.89        55.33        22.26        73.12 
TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
        8.55       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5930 TCGA-50-5931 TCGA-50-5939 
      101.72        15.72        60.16         9.27        14.27        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 
       60.72        57.53        42.35         3.91        25.55         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
        0.72        10.13        27.25        13.94        35.21        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6981 TCGA-55-6983 
       14.30        80.52        40.73        15.25        45.34        92.81 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7727 TCGA-55-7815 
       24.99       107.21        70.26        27.09         3.91        25.41 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 
       18.64        11.28        17.65        18.44        29.23        29.72 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       23.08         5.06        23.64        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
       17.56        15.72        14.47         0.36        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 
       19.96        26.01        17.10        17.62        14.66        12.33 
TCGA-55-A48Y TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
       20.71        15.81        19.99        39.98        14.60        88.64 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46V TCGA-62-A46Y TCGA-64-1678 TCGA-64-1680 
       49.25        19.53        72.30        13.61        39.09        37.02 
TCGA-64-5774 TCGA-64-5779 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       87.98        28.41        14.04        12.66        14.73         5.72 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         7.56         6.05         4.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 
       13.51        14.01         4.24         8.42        23.38        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5146 TCGA-75-6206 TCGA-78-7148 
       30.31         9.24         1.25        77.85        85.15        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
      129.53        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
        5.88        64.90        22.92       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       26.53        53.33        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 TCGA-86-7713 TCGA-86-7953 
       77.59       110.50        93.11        12.36        38.04        32.78 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
       35.24        37.74         4.08         4.57        24.33        22.82 
TCGA-86-8076 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       32.65        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       27.58        28.34        26.50        29.46         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       13.64        26.47        10.62        10.19         2.60        12.23 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-7347 TCGA-93-A4JN 
        1.15        16.60        14.27         1.18        22.45        23.61 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-7944 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7553 
        1.08        41.82        12.39        19.89        42.25        61.48 
TCGA-97-7554 TCGA-97-7938 TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 
       25.48         0.59        18.67        18.12        14.30        20.58 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       19.76        20.84        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A7SV 
       21.57        21.63        32.48        14.30         1.91        18.58 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TE 
        2.76        86.14        49.35        86.04        41.59        29.46 
TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       24.36        73.91        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.49        19.82        20.28        16.87 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.00               0.13 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            163.10             238.29 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             21.75              21.60 
[1] "0.0 - 163.1 (21.8)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1.2"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         1       43       55        0        26        42
  18Q LOSS WILD-TYPE       4       90       84        1        24        30
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18Q LOSS MUTATED           28          5       13
  18Q LOSS WILD-TYPE         44          6       12
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 43                 90
  STAGE IB                 55                 84
  STAGE II                  0                  1
  STAGE IIA                26                 24
  STAGE IIB                42                 30
  STAGE IIIA               28                 44
  STAGE IIIB                5                  6
  STAGE IV                 13                 12
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED    63 121  22   8
  18Q LOSS WILD-TYPE 108 157  24  11
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               63                108
  T2              121                157
  T3               22                 24
  T4                8                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  18Q LOSS MUTATED   129  51    30
  18Q LOSS WILD-TYPE 204  45    46
D74V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                 129                204
  N1                  51                 45
  N2+N3               30                 46
[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"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   136  13
  18Q LOSS WILD-TYPE 213  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    136   13
  18Q LOSS WILD-TYPE  213   12
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              136                213
  1               13                 12
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   126  89
  18Q LOSS WILD-TYPE 150 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    126   89
  18Q LOSS WILD-TYPE  150  151
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              126                150
  MALE                 89                151
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   168  24
  18Q LOSS WILD-TYPE 242  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    168   24
  18Q LOSS WILD-TYPE  242   36
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               168                242
  YES               24                 36
[1] 2 2
[1] FALSE
D74V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18Q LOSS MUTATED                            7
  18Q LOSS WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18Q LOSS MUTATED                                  49
  18Q LOSS WILD-TYPE                                58
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                  132
  18Q LOSS WILD-TYPE                                                189
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18Q LOSS MUTATED                                            1
  18Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  18Q LOSS MUTATED                                               7
  18Q LOSS WILD-TYPE                                            12
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  18Q LOSS MUTATED                                2
  18Q LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  18Q LOSS MUTATED                                    2
  18Q LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  18Q LOSS MUTATED                              1                             6
  18Q LOSS WILD-TYPE                            1                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  18Q LOSS MUTATED                                 1
  18Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  18Q LOSS MUTATED                                               1
  18Q LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  18Q LOSS MUTATED                              6
  18Q LOSS WILD-TYPE                            4
D74V10, multiclass
                                                    clus
vv                                                   18Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              132
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     7
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      6
                                                    clus
vv                                                   18Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  58
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                189
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      12
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, continuous
D74V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   140   9   3   6
  18Q LOSS WILD-TYPE 204   4   1  20
D74V13, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              140                204
  R1                9                  4
  R2                3                  1
  RX                6                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     3
  18Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          21   158
  18Q LOSS WILD-TYPE                        31   232
D74V14, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                      21                 31
  WHITE                                         158                232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4 155
  18Q LOSS WILD-TYPE   3 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4  155
  18Q LOSS WILD-TYPE    3  229
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              155                229
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED   145  96
  19P LOSS WILD-TYPE 178  85
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               241                263 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                96                 85 
$`19P LOSS MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-2655 
       15.02        15.02        35.28        11.64        14.73        43.53 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 
       23.93        86.01        29.00        29.23         9.37        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 
       16.04        17.16       156.66        40.60        41.69        23.05 
TCGA-55-6978 TCGA-55-7914 TCGA-55-8203 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF 
        5.79         6.15        17.98        22.65        20.58        20.19 
TCGA-73-7498 TCGA-78-7166 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ 
       39.09         8.48        13.71        16.18         1.45        17.29 
TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-J2-8192 
       16.54        15.65        21.40        18.18        20.19        24.30 
TCGA-L9-A443 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 
        6.35         5.29        31.23         2.43         3.98        45.01 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4432 
        0.00        47.05         2.99        29.98        12.00        25.02 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       24.00        29.00        22.03         7.40         5.98         8.68 
TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-3917 TCGA-44-5644 TCGA-44-6144 
       49.05        44.61        46.98        38.89        28.37        23.77 
TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       21.63        61.28        16.44        19.46        36.07        18.87 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 
       12.66         8.55        13.64        13.45        76.21        12.66 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       14.07         8.81        29.46        53.29        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 
       22.26        73.12         8.55        40.41       123.58        15.72 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 
        8.22        14.27         8.45        15.12        48.46        57.53 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ 
       53.16         3.91        11.05        10.13        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 
       38.73        67.89        30.58        42.51        46.03        53.65 
TCGA-55-6975 TCGA-55-6981 TCGA-55-6982 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 
        3.88        45.34        32.71        27.09        22.03         3.91 
TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
       34.19        18.44        19.82        29.23        29.72        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
        5.06        17.79        15.72        13.74        20.28        19.96 
TCGA-55-8614 TCGA-55-8616 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       17.62         1.58         0.92        15.81        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R 
       39.98        42.38        14.60        49.25        47.80        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 
       54.35        67.96        39.25        40.96        56.81        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 
       87.98        42.90        28.41        20.05        18.84        12.66 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 
        6.12        22.68        13.61         4.41        13.51         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       26.73        19.43         8.42        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        4.31         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 
       85.15        49.84        36.66       108.66       100.57        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7156 
        5.69        19.27        20.58       129.53       119.51        32.09 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
       64.90       104.19        88.14        26.53        31.20         8.02 
TCGA-78-7539 TCGA-78-7542 TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
       26.01        10.55        93.11        31.13        38.04        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       19.89        35.24         4.08        24.33         0.79        22.82 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4D0 
       31.20        23.05        30.84         0.62        29.46         3.81 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 
       10.62        41.36         1.97        10.19        12.23         7.36 
TCGA-91-6849 TCGA-95-7039 TCGA-95-7567 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 
        1.15        41.82        18.67        18.67         5.39        15.39 
TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD 
       19.76        18.67        24.56        34.85        21.57        18.08 
TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY 
       19.00        18.58        15.65         2.76        86.14        49.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       86.04        58.85         5.49        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-NJ-A7XG 
       19.13        73.91        71.05        47.08        19.82        20.28 
TCGA-O1-A52J 
       59.11 

$`19P LOSS WILD-TYPE`
TCGA-05-4405 TCGA-38-4629 TCGA-38-7271 TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 
       20.05        28.41        26.30        38.10        42.08        27.78 
TCGA-44-7661 TCGA-44-A47F TCGA-49-6761 TCGA-49-AARN TCGA-50-5935 TCGA-55-1595 
       18.31        11.08        11.64        37.32        21.47        48.62 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
       19.66        19.73        16.93        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       13.68        16.93        19.59        20.65        13.87        52.60 
TCGA-73-4662 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-93-8067 TCGA-95-7562 
       82.68        50.24        10.55        85.32         6.12         2.86 
TCGA-95-7947 TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 
       15.68        17.92        20.52        17.75        20.68        23.80 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4390 
       10.09        21.83        27.19        10.09        50.07        37.02 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       24.03        19.00        14.96        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 
       25.02         4.96         9.04         2.04         0.46        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 
      120.79        37.71         4.37        44.42        44.94        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
        3.19        25.02        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 
       26.56        33.30        28.01        19.56        23.15        23.18 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A 
       32.45        22.72         7.17        23.64        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 
        9.44        11.54        28.11        28.57        35.54        32.84 
TCGA-49-4512 TCGA-49-4514 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ TCGA-49-AARR 
       29.75        55.89        62.24        28.90       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
        9.86        20.52        71.47       101.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5933 TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 
       49.28         9.27        78.67        60.72        42.35        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21         0.72        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       34.29        30.54        14.30        80.52         5.62        40.73 
TCGA-55-6970 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       15.25        69.34        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 
       70.26        28.67        20.02        32.71        23.15        25.41 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-8087 TCGA-55-8096 TCGA-55-8097 
       18.64        11.28        17.65        15.19        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
       29.19        22.16        15.42        17.56        14.47         0.36 
TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y 
       17.72        26.01        17.10        14.66        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A57B TCGA-62-8399 TCGA-62-A46P TCGA-62-A46V 
       21.40         3.25        17.95        88.64        19.53        72.30 
TCGA-62-A46Y TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 
       13.61        29.92        39.09        81.80        37.02         2.04 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       51.25        28.47        20.05        14.04        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
        4.64         6.64         5.42         7.56         6.05        13.41 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-78-7143 
       14.01        13.45        30.31         9.24        11.18       163.10 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 
       21.90        39.95        19.50        38.50         5.88        22.92 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 
        9.57       238.29        53.33        39.35       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 
       77.59       110.50        27.09        12.36         5.88        34.39 
TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 
       20.55        37.74         4.57        32.65        31.04        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
       14.60        11.61        13.91        27.58        28.34        26.50 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 
       24.23        13.64        26.47         2.60        27.68        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
        1.08        19.00        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        0.59        15.91        18.12        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       20.58        21.44        20.84        36.76         1.45        21.63 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N4 
       35.47        32.48        14.30        14.53         1.91        38.63 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TJ TCGA-NJ-A4YG 
       58.45        37.35        41.59        29.46        11.15        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
        0.13         1.64         0.49         0.43        16.87 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.00               0.13 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            156.66             238.29 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             21.57              21.63 
[1] "0.0 - 156.7 (21.6)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1.2"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         2       56       59        1        26        38
  19P LOSS WILD-TYPE       3       77       80        0        24        34
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19P LOSS MUTATED           38          7       16
  19P LOSS WILD-TYPE         34          4        9
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 56                 77
  STAGE IB                 59                 80
  STAGE II                  1                  0
  STAGE IIA                26                 24
  STAGE IIB                38                 34
  STAGE IIIA               38                 34
  STAGE IIIB                7                  4
  STAGE IV                 16                  9
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED    76 136  20  12
  19P LOSS WILD-TYPE  95 142  26   7
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               76                 95
  T2              136                142
  T3               20                 26
  T4               12                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  19P LOSS MUTATED   150  53    38
  19P LOSS WILD-TYPE 183  43    38
D75V5, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                 150                183
  N1                  53                 43
  N2+N3               38                 38
[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"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   171  16
  19P LOSS WILD-TYPE 178   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    171   16
  19P LOSS WILD-TYPE  178    9
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              171                178
  1               16                  9
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   119 126
  19P LOSS WILD-TYPE 157 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    119  126
  19P LOSS WILD-TYPE  157  114
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE              119                157
  MALE                126                114
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   193  27
  19P LOSS WILD-TYPE 217  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    193   27
  19P LOSS WILD-TYPE  217   33
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO               193                217
  YES               27                 33
[1] 2 2
[1] FALSE
D75V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19P LOSS MUTATED                            8
  19P LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19P LOSS MUTATED                                  54
  19P LOSS WILD-TYPE                                53
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                  154
  19P LOSS WILD-TYPE                                                167
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19P LOSS MUTATED                                            0
  19P LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  19P LOSS MUTATED                                               9
  19P LOSS WILD-TYPE                                            10
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  19P LOSS MUTATED                                1
  19P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  19P LOSS MUTATED                                    2
  19P LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  19P LOSS MUTATED                              1                            10
  19P LOSS WILD-TYPE                            1                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  19P LOSS MUTATED                                 0
  19P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  19P LOSS MUTATED                                               2
  19P LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  19P LOSS MUTATED                              4
  19P LOSS WILD-TYPE                            6
D75V10, multiclass
                                                    clus
vv                                                   19P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              154
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     9
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                    10
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      4
                                                    clus
vv                                                   19P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                167
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      10
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
D75V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED   165   3   3  12
  19P LOSS WILD-TYPE 179  10   1  14
D75V13, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0              165                179
  R1                3                 10
  R2                3                  1
  RX               12                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  1     4
  19P LOSS WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                          24   181
  19P LOSS WILD-TYPE                        28   209
D75V14, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  3
  BLACK OR AFRICAN AMERICAN                      24                 28
  WHITE                                         181                209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V15, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3 177
  19P LOSS WILD-TYPE   4 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3  177
  19P LOSS WILD-TYPE    4  207
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              177                207
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    91  65
  19Q LOSS WILD-TYPE 232 116
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               156                348 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                65                116 
$`19Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4402 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-6178 
        9.96         8.02        15.02        15.02        35.28        14.73 
TCGA-44-2655 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-49-6742 TCGA-49-6745 
       43.53        29.00        29.23         9.37        16.04        17.16 
TCGA-49-AAR0 TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 TCGA-55-8203 
      156.66        40.60        41.69        23.05         5.79        17.98 
TCGA-55-8511 TCGA-55-A48X TCGA-55-A491 TCGA-73-7498 TCGA-80-5611 TCGA-91-6836 
       18.15        22.65        20.58        39.09        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-95-7948 TCGA-95-A4VN TCGA-97-A4LX TCGA-J2-8192 
       16.18         1.45        15.65        18.18        20.19        24.30 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4250 TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 
        5.29        31.23         3.98         0.00        47.05         2.99 
TCGA-05-4420 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-38-4632 TCGA-44-2656 
       29.98        25.02        29.00        22.03        44.61        46.98 
TCGA-44-3917 TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 TCGA-44-8117 TCGA-44-8120 
       38.89        28.37        61.28        16.44        12.66         8.55 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-6767 
       13.45        76.21        12.66        14.07         8.81        22.26 
TCGA-49-AAQV TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 TCGA-50-5072 TCGA-50-5939 
       22.26        40.41       123.58        15.72         8.22        15.12 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-55-1594 
       48.46        57.53        53.16         3.91        11.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 TCGA-55-6982 
       67.89        30.58        42.51        53.65         3.88        32.71 
TCGA-55-7570 TCGA-55-7727 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8507 
       27.09         3.91        19.82        29.23        29.72        13.74 
TCGA-55-8616 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 
        1.58        19.99         4.57        39.98        42.38        49.25 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 
       47.80        56.71        39.25        40.96        56.81        38.37 
TCGA-67-3770 TCGA-67-3772 TCGA-69-7978 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       20.05        18.84         4.41         4.24        19.43         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
       23.38        26.30         4.31         1.25        50.33        66.64 
TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 
       43.82        49.84        36.66       100.57         5.69        20.58 
TCGA-78-7149 TCGA-78-7153 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      129.53       119.51       104.19        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7542 TCGA-86-7701 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
        8.02        10.55        31.13        32.78        19.89        35.24 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 
        0.79        22.82        31.20        30.84         0.62        29.46 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 
        3.81        10.62        41.36        10.19        12.23         7.36 
TCGA-91-6849 TCGA-95-7039 TCGA-95-7567 TCGA-95-8494 TCGA-97-8171 TCGA-97-8176 
        1.15        41.82        18.67         2.76        18.67        15.39 
TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 
       19.76        18.67        24.56        21.57        18.08        19.00 
TCGA-L9-A7SV TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4TI TCGA-MP-A4TK 
       18.58        86.14        49.35        58.85        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       73.91        71.05        47.08        19.82        20.28        59.11 

$`19Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 
       19.96        14.01        20.05         9.01        26.01        28.41 
TCGA-38-4631 TCGA-38-7271 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 
       11.64        26.30        38.10        42.08        23.93        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-A47F TCGA-49-4501 TCGA-49-6761 TCGA-49-AARN 
       86.01        18.31        11.08        46.72        11.64        37.32 
TCGA-50-5935 TCGA-55-1595 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       21.47        48.62         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 
       14.53        21.44         6.15        19.66        19.73        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 TCGA-55-A4DF 
       19.69        32.12        13.68        16.93        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 
       20.65        13.87        52.60        82.68         8.48        50.24 
TCGA-78-8660 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
       10.55         6.12        17.29        16.54         2.86        15.68 
TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 
       21.40        17.92        20.52        17.75        20.68        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-MP-A4TD 
        6.35        10.09        21.83        27.19         2.43        10.09 
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 
       50.07        45.01        37.02        24.03        19.00        14.96 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 
       12.00        30.02        21.99        26.01        25.02        24.00 
TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
        4.96         9.04         2.04         0.46         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F 
        8.68        97.74       120.79        37.71        49.05         4.37 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       38.24        34.06        33.73        26.56        33.30        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4487 
       15.98        15.32         9.44        11.54        13.64        28.11 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       28.57        35.54        32.84        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       53.29        55.33        73.12        62.24        28.90         8.55 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      221.33       164.12         9.86        20.52        71.47       101.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        47.41        49.28         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
        8.45        60.72        42.35        25.55        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       30.54        13.94        35.21        14.30        80.52         5.62 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 
       40.73        15.25        46.03        69.34        45.34        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
       24.99        40.54       107.21        70.26        28.67        20.02 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       32.71        22.03        23.15        25.41        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       34.19        17.65        18.44        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
       17.56        15.72        14.47         0.36        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 
       19.96        26.01        17.10        17.62        14.66        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B 
       20.71        21.40         3.25         0.92        15.81        17.95 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       14.60        88.64        19.53        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
       13.61        29.92        39.09        81.80        37.02        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4668 
       13.41        13.51        14.01        13.45        26.73        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-75-5146 TCGA-75-6206 TCGA-75-7025 
       30.31         9.24        11.18        77.85        85.15       108.66 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
      163.10        27.16        19.27        21.90        39.95        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7163 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 
      238.29        53.33        26.01        39.35       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       34.39        38.04        20.55        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       24.33        32.65        31.04        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF 
       11.61        13.91        27.58        28.34        26.50        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 
       13.64        26.47         1.97         2.60        27.68        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 
        1.08        19.00        12.39        27.29        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       15.91         5.39        18.12        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.58        21.44        20.84        34.85        36.76         1.45 
TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       21.63        35.47        32.48        14.30        14.53         1.91 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
       15.65        38.63         2.76        58.45        37.35        86.04 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ 
        5.49        41.59        29.46        11.05        24.36        11.15 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
       74.33         0.13         1.64         0.49         0.43        16.87 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.00               0.13 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            156.66             238.29 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             22.26              21.47 
[1] "0.0 - 156.7 (22.3)" "0.1 - 238.3 (21.5)"
[1] "hr=" "1.2"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         1       36       37        1        14        25
  19Q LOSS WILD-TYPE       4       97      102        0        36        47
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19Q LOSS MUTATED           26          6       11
  19Q LOSS WILD-TYPE         46          5       14
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 36                 97
  STAGE IB                 37                102
  STAGE II                  1                  0
  STAGE IIA                14                 36
  STAGE IIB                25                 47
  STAGE IIIA               26                 46
  STAGE IIIB                6                  5
  STAGE IV                 11                 14
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED    47  89  13   9
  19Q LOSS WILD-TYPE 124 189  33  10
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               47                124
  T2               89                189
  T3               13                 33
  T4                9                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  19Q LOSS MUTATED    95  36    26
  19Q LOSS WILD-TYPE 238  60    50
D76V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                  95                238
  N1                  36                 60
  N2+N3               26                 50
[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"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   114  11
  19Q LOSS WILD-TYPE 235  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    114   11
  19Q LOSS WILD-TYPE  235   14
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0              114                235
  1               11                 14
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    80  79
  19Q LOSS WILD-TYPE 196 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     80   79
  19Q LOSS WILD-TYPE  196  161
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               80                196
  MALE                 79                161
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   127  16
  19Q LOSS WILD-TYPE 283  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    127   16
  19Q LOSS WILD-TYPE  283   44
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO               127                283
  YES               16                 44
[1] 2 2
[1] FALSE
D76V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19Q LOSS MUTATED                            3
  19Q LOSS WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19Q LOSS MUTATED                                  37
  19Q LOSS WILD-TYPE                                70
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                  102
  19Q LOSS WILD-TYPE                                                219
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19Q LOSS MUTATED                                            0
  19Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  19Q LOSS MUTATED                                               4
  19Q LOSS WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  19Q LOSS MUTATED                                0
  19Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  19Q LOSS MUTATED                                    1
  19Q LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  19Q LOSS MUTATED                              0                             8
  19Q LOSS WILD-TYPE                            2                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  19Q LOSS MUTATED                                 0
  19Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  19Q LOSS MUTATED                                               3
  19Q LOSS WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  19Q LOSS MUTATED                              1
  19Q LOSS WILD-TYPE                            9
D76V10, multiclass
                                                    clus
vv                                                   19Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              102
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     8
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   19Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                219
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
D76V12, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED   105   2   3   6
  19Q LOSS WILD-TYPE 239  11   1  20
D76V13, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0              105                239
  R1                2                 11
  R2                3                  1
  RX                6                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     4
  19Q LOSS WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                          14   117
  19Q LOSS WILD-TYPE                        38   273
D76V14, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  3
  BLACK OR AFRICAN AMERICAN                      14                 38
  WHITE                                         117                273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V15, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2 115
  19Q LOSS WILD-TYPE   5 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2  115
  19Q LOSS WILD-TYPE    5  269
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              115                269
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    60  50
  20P LOSS WILD-TYPE 263 131
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               110                394 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                50                131 
$`20P LOSS MUTATED`
TCGA-05-4405 TCGA-44-2662 TCGA-49-4501 TCGA-49-6745 TCGA-50-6597 TCGA-55-1595 
       20.05        42.08        46.72        17.16        41.69        48.62 
TCGA-55-7725 TCGA-55-8090 TCGA-55-8207 TCGA-78-8660 TCGA-80-5611 TCGA-95-7562 
       14.53        19.66        32.12        10.55        85.32         2.86 
TCGA-L9-A444 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4395 TCGA-05-4415 TCGA-05-4422 
       10.09         5.29         2.43         0.00         2.99        12.00 
TCGA-05-5423 TCGA-05-5428 TCGA-44-2656 TCGA-44-2665 TCGA-44-3919 TCGA-44-6779 
        4.96        22.03        46.98        42.77        33.73        16.44 
TCGA-44-A47A TCGA-44-A47G TCGA-49-4505 TCGA-49-4512 TCGA-49-6743 TCGA-49-AARE 
       15.32        11.54        14.07        29.75        53.29        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-50-5051 TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 
      123.58       221.33        15.72         8.22        78.67         8.45 
TCGA-50-5939 TCGA-50-5944 TCGA-50-6593 TCGA-50-6594 TCGA-53-7624 TCGA-55-1594 
       15.12        57.53        11.05        12.16        34.29        38.73 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6980 TCGA-55-6984 TCGA-55-7727 TCGA-55-7903 
        5.62        42.51        69.34        24.99         3.91        18.64 
TCGA-55-7907 TCGA-55-7994 TCGA-55-8092 TCGA-55-8506 TCGA-55-8616 TCGA-62-8397 
       11.28        19.82         5.06         0.36         1.58        42.38 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 
       47.80        19.53        67.96        72.30        13.61        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1681 TCGA-64-5781 TCGA-67-3770 
       29.92        56.81        39.09        38.37        51.25        20.05 
TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 TCGA-69-7974 TCGA-69-8453 TCGA-69-A59K 
       14.04         4.64         6.12         6.05        26.73        19.43 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       26.30         4.31        30.31        50.33        66.64        77.85 
TCGA-75-6212 TCGA-75-6214 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
       49.84        36.66       163.10        27.16         5.69        20.58 
TCGA-78-7158 TCGA-78-7535 TCGA-78-7537 TCGA-86-6562 TCGA-86-6851 TCGA-86-7953 
        5.88        31.20        53.33        12.36         5.88        32.78 
TCGA-86-8280 TCGA-86-8673 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6848 
       23.05        28.34        10.62        10.19         2.60         7.36 
TCGA-93-7347 TCGA-95-7039 TCGA-97-8177 TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8033 
       22.45        41.82        16.41        21.44        24.56        21.57 
TCGA-L4-A4E5 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4TI TCGA-NJ-A4YF 
       19.00        38.63        86.14        58.45        14.10        71.05 
TCGA-NJ-A4YI TCGA-O1-A52J 
        0.13        59.11 

$`20P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       26.30        43.53        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 
       18.31        29.00        29.23         9.37        11.08        16.04 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 
       11.64       156.66        37.32        40.60        21.47        23.05 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 
        5.79         7.79         7.99        16.01        23.18        21.44 
TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 
        6.15        19.73        17.98        16.93        19.69        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       13.68        16.93        22.65        20.58        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       50.24        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
       16.54        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 
        6.35        21.83        27.19        31.23        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
        3.98        45.01        37.02        24.03        47.05        19.00 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       14.96        29.98        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       25.02        24.00        29.00         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2666 
       49.05        44.61         4.37        44.42        44.94         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 
       25.02        37.15        38.24        38.89        34.06        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        32.45        61.28        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       15.98         9.44        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       28.57        12.66        35.54        32.84         8.81        29.46 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       55.89        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
       28.90         8.55       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
      101.72        60.16        47.41        49.28         9.27        14.27 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       48.46        60.72        53.16        42.35         3.91        25.55 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
       30.54        13.94        35.21        67.89        30.58        14.30 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       80.52        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       45.34        32.71        92.81        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 
       28.67        20.02        27.09        32.71        22.03        23.15 
TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 
       25.41        34.19        17.65        18.44        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19        23.08        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42        17.56        15.72        14.47        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
       14.66        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
       15.81        19.99        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46R TCGA-62-A46S TCGA-62-A470 TCGA-64-1679 
       88.64        49.25        56.71        54.35        39.25        81.80 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       37.02        87.98         2.04        42.90        28.41        28.47 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-69-7760 
       20.05        18.84        12.66        14.73         5.72         6.64 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         5.42         7.56         4.41        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4659 
       13.51        14.01        13.45         4.24         8.42        23.38 
TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5147 TCGA-75-6206 
       15.35         9.24         1.25        11.18        43.82        85.15 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      108.66       100.57        19.27       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 
      119.51        19.50        38.50        32.09        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        9.57       104.19       238.29        88.14        26.53         8.02 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        93.11        27.09        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        26.50        29.46         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
       26.47        41.36         1.97        12.23        27.68         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN 
       16.60        14.27         1.18        19.82        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 
       15.39        14.30        21.60        20.58        19.76        20.84 
TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD 
       18.67        34.85        36.76         1.45        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV 
       35.47        32.48        14.30        14.53         1.91        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       15.65         2.76        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ 
        5.49        41.59        29.46        11.05        24.36        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       19.13        73.91        74.33         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.43        19.82        20.28        16.87 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.00               0.43 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            221.33             238.29 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            21.800             21.615 
[1] "0.0 - 221.3 (21.8)" "0.4 - 238.3 (21.6)"
[1] "hr=" "1.3"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         2       22       28        0         8        20
  20P LOSS WILD-TYPE       3      111      111        1        42        52
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20P LOSS MUTATED           22          4        6
  20P LOSS WILD-TYPE         50          7       19
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 22                111
  STAGE IB                 28                111
  STAGE II                  0                  1
  STAGE IIA                 8                 42
  STAGE IIB                20                 52
  STAGE IIIA               22                 50
  STAGE IIIB                4                  7
  STAGE IV                  6                 19
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED    31  64  11   6
  20P LOSS WILD-TYPE 140 214  35  13
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               31                140
  T2               64                214
  T3               11                 35
  T4                6                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  20P LOSS MUTATED    67  21    24
  20P LOSS WILD-TYPE 266  75    52
D77V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                  67                266
  N1                  21                 75
  N2+N3               24                 52
[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"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    82   6
  20P LOSS WILD-TYPE 267  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     82    6
  20P LOSS WILD-TYPE  267   19
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               82                267
  1                6                 19
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    63  50
  20P LOSS WILD-TYPE 213 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     63   50
  20P LOSS WILD-TYPE  213  190
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               63                213
  MALE                 50                190
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    92  12
  20P LOSS WILD-TYPE 318  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     92   12
  20P LOSS WILD-TYPE  318   48
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                92                318
  YES               12                 48
[1] 2 2
[1] FALSE
D77V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20P LOSS MUTATED                            3
  20P LOSS WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20P LOSS MUTATED                                  26
  20P LOSS WILD-TYPE                                81
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                   70
  20P LOSS WILD-TYPE                                                251
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20P LOSS MUTATED                                            0
  20P LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20P LOSS MUTATED                                               5
  20P LOSS WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  20P LOSS MUTATED                                2
  20P LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  20P LOSS MUTATED                                    1
  20P LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  20P LOSS MUTATED                              0                             3
  20P LOSS WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  20P LOSS MUTATED                                 0
  20P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  20P LOSS MUTATED                                               1
  20P LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  20P LOSS MUTATED                              2
  20P LOSS WILD-TYPE                            8
D77V10, multiclass
                                                    clus
vv                                                   20P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               70
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   20P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                251
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, continuous
D77V12, continuous
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    80   4   1   3
  20P LOSS WILD-TYPE 264   9   3  23
D77V13, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               80                264
  R1                4                  9
  R2                1                  3
  RX                3                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           7    87
  20P LOSS WILD-TYPE                        45   303
D77V14, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                       7                 45
  WHITE                                          87                303
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  80
  20P LOSS WILD-TYPE   6 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   80
  20P LOSS WILD-TYPE    6  304
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               80                304
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    37  29
  20Q LOSS WILD-TYPE 286 152
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                66                438 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                29                152 
$`20Q LOSS MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-49-4501 TCGA-49-6745 TCGA-55-1595 TCGA-55-8090 
        8.02        20.05        46.72        17.16        48.62        19.66 
TCGA-55-8207 TCGA-80-5611 TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4415 TCGA-05-4422 
       32.12        85.32         2.43        50.07         2.99        12.00 
TCGA-05-5428 TCGA-44-2656 TCGA-44-3919 TCGA-44-A47B TCGA-44-A47G TCGA-49-4507 
       22.03        46.98        33.73         9.44        11.54         8.81 
TCGA-49-4512 TCGA-49-6743 TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 TCGA-50-5072 
       29.75        53.29        40.41       123.58        15.72         8.22 
TCGA-50-5936 TCGA-50-6593 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-8087 TCGA-55-8097 
        8.45        11.05        34.29        35.21        15.19        15.65 
TCGA-62-8397 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A472 
       42.38        47.80        19.53        54.35        67.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-67-3770 TCGA-67-3773 TCGA-67-6216 TCGA-69-8453 
       56.81        39.09        20.05        14.04         4.64        26.73 
TCGA-69-A59K TCGA-73-4675 TCGA-73-7499 TCGA-75-5146 TCGA-75-6212 TCGA-78-7143 
       19.43        30.31        50.33        77.85        49.84       163.10 
TCGA-78-7146 TCGA-78-7158 TCGA-78-7160 TCGA-78-7537 TCGA-86-6851 TCGA-86-7953 
        5.69         5.88        22.92        53.33         5.88        32.78 
TCGA-86-8280 TCGA-86-8358 TCGA-91-6828 TCGA-91-6831 TCGA-93-7347 TCGA-97-8174 
       23.05        21.47        10.62        10.19        22.45         5.39 
TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8033 TCGA-MP-A4SW TCGA-MP-A4TI TCGA-NJ-A4YF 
       21.44        24.56        21.57        58.45        14.10        71.05 

$`20Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       43.53        38.10        42.08        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 
       18.31        29.00        29.23         9.37        11.08        16.04 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       11.64       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       23.05         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       14.53        21.44         6.15        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       19.69        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 TCGA-91-7771 
       39.09         8.48        50.24        10.55        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
        1.45         6.12        17.29        16.54         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.65        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       17.75        20.68        24.30        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4250 
       21.83        27.19         5.29        31.23        10.09         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       14.96        29.98        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
       25.02        24.00         4.96        29.00         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        0.46         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 
       37.71        49.05        44.61         4.37        44.42        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       34.06        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A4SS 
       23.64        12.66         8.55        15.98        15.32        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 
       14.07        32.84        29.46        55.89        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARQ 
       22.26        73.12        62.24        28.90         8.55       221.33 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
      164.12         9.86        20.52        71.47       101.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 
       47.41        49.28         9.27        14.27        78.67        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       25.55        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 
       36.79        27.25        30.54        13.94        38.73        67.89 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       23.15        25.41        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
       18.44        19.82        29.23        29.72        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.79        23.64        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
       19.99        17.95         4.57        39.98        14.60        88.64 
TCGA-62-8402 TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       49.25        56.71        72.30        13.61        39.25        40.96 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       81.80        37.02        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
       28.41        51.25        28.47        20.05        18.84        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
       14.73         5.72         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
       14.01        13.45         4.24         8.42        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5125 
       15.35         4.31         9.24         1.25        11.18        66.64 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 
       43.82        85.15        36.66       108.66       100.57        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 
       19.50        38.50        32.09        64.90         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
      238.29        88.14        26.53        31.20         8.02        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       93.11        27.09        12.36        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       28.34        26.50        29.46         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       26.47        41.36         1.97         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       18.67        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 
       20.58        19.76        20.84        18.67        34.85        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.63        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.30        14.53         1.91        18.58        15.65        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        86.14        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ 
        5.49        41.59        29.46        11.05        24.36        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.49         0.43        19.82        20.28        59.11        16.87 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.43               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            163.10             238.29 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            22.685             21.455 
[1] "2.4 - 163.1 (22.7)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0       14       21        0         6         7
  20Q LOSS WILD-TYPE       5      119      118        1        44        65
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20Q LOSS MUTATED           12          2        4
  20Q LOSS WILD-TYPE         60          9       21
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 14                119
  STAGE IB                 21                118
  STAGE II                  0                  1
  STAGE IIA                 6                 44
  STAGE IIB                 7                 65
  STAGE IIIA               12                 60
  STAGE IIIB                2                  9
  STAGE IV                  4                 21
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED    19  37   6   4
  20Q LOSS WILD-TYPE 152 241  40  15
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1               19                152
  T2               37                241
  T3                6                 40
  T4                4                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  20Q LOSS MUTATED    44   9    12
  20Q LOSS WILD-TYPE 289  87    64
D78V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                  44                289
  N1                   9                 87
  N2+N3               12                 64
[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"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    52   4
  20Q LOSS WILD-TYPE 297  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     52    4
  20Q LOSS WILD-TYPE  297   21
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               52                297
  1                4                 21
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    38  29
  20Q LOSS WILD-TYPE 238 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     38   29
  20Q LOSS WILD-TYPE  238  211
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               38                238
  MALE                 29                211
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    55   8
  20Q LOSS WILD-TYPE 355  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     55    8
  20Q LOSS WILD-TYPE  355   52
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                55                355
  YES                8                 52
[1] 2 2
[1] FALSE
D78V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20Q LOSS MUTATED                            2
  20Q LOSS WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20Q LOSS MUTATED                                  19
  20Q LOSS WILD-TYPE                                88
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q LOSS MUTATED                                                   34
  20Q LOSS WILD-TYPE                                                287
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20Q LOSS MUTATED                                            0
  20Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20Q LOSS MUTATED                                               3
  20Q LOSS WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  20Q LOSS MUTATED                                2
  20Q LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  20Q LOSS MUTATED                                    1
  20Q LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  20Q LOSS MUTATED                              0                             3
  20Q LOSS WILD-TYPE                            2                            20
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  20Q LOSS MUTATED                                 0
  20Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  20Q LOSS MUTATED                                               1
  20Q LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  20Q LOSS MUTATED                              2
  20Q LOSS WILD-TYPE                            8
D78V10, multiclass
                                                    clus
vv                                                   20Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               34
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   20Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  88
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      20
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, continuous
D78V12, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED    48   2   1   3
  20Q LOSS WILD-TYPE 296  11   3  23
D78V13, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               48                296
  R1                2                 11
  R2                1                  3
  RX                3                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     1
  20Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           4    51
  20Q LOSS WILD-TYPE                        48   339
D78V14, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                       4                 48
  WHITE                                          51                339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2  47
  20Q LOSS WILD-TYPE   5 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2   47
  20Q LOSS WILD-TYPE    5  337
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               47                337
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   104  60
  21Q LOSS WILD-TYPE 219 121
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               164                340 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                60                121 
$`21Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4427 TCGA-05-5420 TCGA-44-7661 
       19.96         9.96         8.02        26.01        15.02        18.31 
TCGA-44-7670 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 
       29.00        11.08        17.16        11.64        40.60        21.47 
TCGA-55-1592 TCGA-55-6978 TCGA-55-7724 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 
       23.05         5.79        23.18        19.66        17.98        16.93 
TCGA-55-8205 TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-78-8660 
       19.69        20.58        20.19        20.65        52.60        10.55 
TCGA-91-7771 TCGA-95-7043 TCGA-95-7562 TCGA-97-8172 TCGA-05-4249 TCGA-05-4389 
       16.18        16.54         2.86        17.92        50.07        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       37.02         0.00        47.05        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 
       30.02        25.02        25.02         9.04         7.40         5.98 
TCGA-38-4627 TCGA-44-2659 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
       37.71        44.94        38.89        33.30        28.37        23.77 
TCGA-44-6145 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       19.56        61.28        16.44        19.46         7.17        36.07 
TCGA-44-7672 TCGA-44-A479 TCGA-44-A47B TCGA-44-A4SS TCGA-49-4506 TCGA-49-4507 
       23.64        15.98         9.44        13.64        32.84         8.81 
TCGA-49-4510 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-4B-A93V 
       29.46        73.12        28.90         8.55        40.41         9.86 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5068 TCGA-50-5072 TCGA-50-5933 TCGA-50-5944 
       71.47        15.72        49.28         8.22        78.67        57.53 
TCGA-50-5946 TCGA-50-6592 TCGA-50-6595 TCGA-50-7109 TCGA-53-7813 TCGA-55-1594 
       53.16        25.55         6.21        10.13        13.94        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 
       67.89        30.58        42.51        46.03        53.65        92.81 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 
       40.54       107.21        22.03        23.15        25.41        34.19 
TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 TCGA-55-8092 TCGA-55-8302 TCGA-55-8507 
       17.65        19.82        23.08         5.06        15.72        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 TCGA-55-A490 TCGA-62-8402 TCGA-62-A46S 
       20.28        17.72        17.10         3.25        49.25        54.35 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 
       39.25        40.96        81.80        87.98         2.04        51.25 
TCGA-67-3770 TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 
       20.05         6.64         6.12         6.05        13.41        13.51 
TCGA-69-8255 TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        4.24        26.73        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-A9RS TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 TCGA-78-7153 
       30.31        11.18       100.57         5.69        20.58       119.51 
TCGA-78-7154 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-8640 
       19.50        64.90        88.14        26.53         8.02       232.18 
TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8359 
       93.11        31.13        38.04        32.78        37.74        14.60 
TCGA-86-8585 TCGA-86-8669 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6840 TCGA-95-8494 
       11.61        30.84        24.23        10.62        12.23         2.76 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-8174 TCGA-97-8175 TCGA-99-8025 TCGA-99-8028 
       19.89        64.60         5.39        18.12        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AE TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
        1.45        21.57        35.47        15.65        38.63        86.14 
TCGA-MP-A4SY TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YQ TCGA-NJ-A55O 
       49.35        29.46        11.05        11.15        47.08         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG 
       19.82        20.28 

$`21Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 
       14.01        20.05         9.01        15.02        28.41        35.28 
TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       11.64        14.73        26.30        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 
       23.93        27.78        86.01        29.23         9.37        46.72 
TCGA-49-6742 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-6597 TCGA-55-1595 TCGA-55-6979 
       16.04       156.66        37.32        41.69        48.62         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 
        7.99        16.01        14.53        21.44         6.15        19.73 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 
       32.12        18.15        13.68        16.93        22.65        19.59 
TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 
       13.87        82.68        39.09         8.48        50.24        85.32 
TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7947 TCGA-95-7948 
       13.71         1.45         6.12        17.29        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       21.40        18.18        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       24.30        23.80         6.35        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4397 
        5.29        31.23         2.43        10.09         3.98        24.03 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 
       19.00         2.99        21.99        26.01        24.00         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 
       29.00        22.03         2.04         0.46         8.68        97.74 
TCGA-38-4626 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
      120.79        49.05        44.61         4.37        46.98        44.42 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       42.77         3.19        25.02        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       33.73        26.56        28.01        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A 
       32.45        22.72        18.87        12.66         8.55        15.32 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
       35.54        14.07        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       22.26        22.26        62.24       123.58       221.33       164.12 
TCGA-50-5044 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 
       20.52       101.72        60.16        47.41         9.27        14.27 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 
        8.45        15.12        48.46        60.72        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       11.05        12.16         0.72        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       34.29        30.54        35.21        14.30        80.52         5.62 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       40.73        15.25         3.88        69.34        45.34        32.71 
TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       24.99        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 
        3.91        18.64        11.28        18.44        29.23        29.72 
TCGA-55-8087 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       15.19        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8512 TCGA-55-8513 
       15.42        17.56        14.47         0.36        19.96        26.01 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        19.99        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        47.80        19.53        56.71 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
       67.96        72.30        13.61        29.92        56.81        39.09 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
       37.02        38.37        42.90        28.41        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-8253 
       22.68        13.61         5.42         7.56         4.41        14.01 
TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       13.45        19.43         8.42         9.24         1.25        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
      108.66       163.10        27.16        19.27       129.53        21.90 
TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 
       39.95        38.50        32.09         5.88        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
      104.19       238.29        31.20        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       10.55        39.75        77.59       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
        5.88        34.39        20.55        19.89        35.24         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       31.20        23.05        21.47        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46         3.81        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
       41.36         1.97        10.19         2.60        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       12.39        27.29        42.25        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8176 TCGA-97-8177 
       18.54         0.59        15.91        18.67        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
       18.67        24.56        21.63        18.08        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SW 
       14.30        14.53         1.91        18.58         2.76        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH 
       37.35        86.04        58.85         5.49        41.59        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-O1-A52J TCGA-S2-AA1A 
        1.64         0.49        59.11        16.87 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.00               0.13 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            232.18             238.29 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             21.52              21.63 
[1] "0.0 - 232.2 (21.5)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1"  
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         1       38       45        0        15        27
  21Q LOSS WILD-TYPE       4       95       94        1        35        45
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  21Q LOSS MUTATED           26          5        7
  21Q LOSS WILD-TYPE         46          6       18
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 38                 95
  STAGE IB                 45                 94
  STAGE II                  0                  1
  STAGE IIA                15                 35
  STAGE IIB                27                 45
  STAGE IIIA               26                 46
  STAGE IIIB                5                  6
  STAGE IV                  7                 18
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q LOSS MUTATED    48  94  16   7
  21Q LOSS WILD-TYPE 123 184  30  12
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               48                123
  T2               94                184
  T3               16                 30
  T4                7                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  21Q LOSS MUTATED   108  30    25
  21Q LOSS WILD-TYPE 225  66    51
D79V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                 108                225
  N1                  30                 66
  N2+N3               25                 51
[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"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   116   7
  21Q LOSS WILD-TYPE 233  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    116    7
  21Q LOSS WILD-TYPE  233   18
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              116                233
  1                7                 18
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    80  86
  21Q LOSS WILD-TYPE 196 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     80   86
  21Q LOSS WILD-TYPE  196  154
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               80                196
  MALE                 86                154
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   130  24
  21Q LOSS WILD-TYPE 280  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    130   24
  21Q LOSS WILD-TYPE  280   36
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               130                280
  YES               24                 36
[1] 2 2
[1] FALSE
D79V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  21Q LOSS MUTATED                            8
  21Q LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  21Q LOSS MUTATED                                  26
  21Q LOSS WILD-TYPE                                81
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                  115
  21Q LOSS WILD-TYPE                                                206
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  21Q LOSS MUTATED                                            0
  21Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  21Q LOSS MUTATED                                               2
  21Q LOSS WILD-TYPE                                            17
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  21Q LOSS MUTATED                                0
  21Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  21Q LOSS MUTATED                                    1
  21Q LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  21Q LOSS MUTATED                              0                             5
  21Q LOSS WILD-TYPE                            2                            18
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  21Q LOSS MUTATED                                 1
  21Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  21Q LOSS MUTATED                                               3
  21Q LOSS WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  21Q LOSS MUTATED                              5
  21Q LOSS WILD-TYPE                            5
D79V10, multiclass
                                                    clus
vv                                                   21Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              115
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     5
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      5
                                                    clus
vv                                                   21Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                206
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      18
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, continuous
D79V12, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   111   2   1   6
  21Q LOSS WILD-TYPE 233  11   3  20
D79V13, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              111                233
  R1                2                 11
  R2                1                  3
  RX                6                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     1
  21Q LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          20   118
  21Q LOSS WILD-TYPE                        32   272
D79V14, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                      20                 32
  WHITE                                         118                272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2 120
  21Q LOSS WILD-TYPE   5 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2  120
  21Q LOSS WILD-TYPE    5  264
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              120                264
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   141  75
  22Q LOSS WILD-TYPE 182 106
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               216                288 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                75                106 
$`22Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-5420 TCGA-38-6178 TCGA-44-2662 
        9.96         9.01        26.01        15.02        14.73        42.08 
TCGA-44-6147 TCGA-44-7671 TCGA-49-4501 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 
       27.78        29.23        46.72        11.64        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
       21.47        41.69        17.98        19.69        32.12        18.15 
TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 TCGA-78-8660 TCGA-80-5611 
       20.19        20.65        13.87        82.68        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-95-7562 TCGA-95-A4VN TCGA-97-A4M3 
       13.71        16.18         1.45         2.86        18.18        17.75 
TCGA-L9-A444 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09         5.29        31.23        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4415 TCGA-05-4424 TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 
       24.03         2.99        30.02        26.01        25.02        24.00 
TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 
       29.00        22.03         7.40         5.98         8.68        49.05 
TCGA-44-2656 TCGA-44-2659 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       46.98        44.94        38.89        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6778 TCGA-44-7667 
       33.30        28.37        23.77        19.56        61.28        36.07 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66         8.55        13.64        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE 
       29.46        55.33        22.26        73.12         8.55        40.41 
TCGA-49-AARO TCGA-50-5051 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
      123.58        15.72         9.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6673 TCGA-50-7109 
       48.46        42.35         3.91        25.55         0.72        10.13 
TCGA-50-8457 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6642 
       36.99        34.29        13.94        35.21        30.58        80.52 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6985 
       42.51        46.03        53.65         3.88        69.34        40.54 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7903 
       28.67        20.02        27.09        32.71        22.03        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-8092 TCGA-55-8094 TCGA-55-8505 TCGA-55-8507 
       34.19        17.65         5.06        17.79        14.47        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       20.28        17.72        19.96        14.66         1.58        12.33 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-62-A46S TCGA-62-A46U 
       21.40         3.25         0.92        19.99        54.35        67.96 
TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       13.61        29.92        56.81        81.80        38.37        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       42.90        28.41        51.25         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       13.61         7.56         4.41        13.41        13.51        14.01 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 
       26.73        19.43         8.42        23.38        15.35         4.31 
TCGA-73-4677 TCGA-73-A9RS TCGA-75-5147 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 
        1.25        11.18        43.82        36.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7152 TCGA-78-7159 TCGA-78-7163 TCGA-78-7167 
       27.16         5.69        39.95        64.90       238.29        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
       31.20         8.02       232.18        93.11        27.09         5.88 
TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8074 
       34.39        32.78        19.89        37.74         4.57         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
       22.82        31.20        21.47        14.60        11.61        30.84 
TCGA-86-8672 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
        0.62         3.81        24.23        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 TCGA-93-A4JN TCGA-95-7039 TCGA-95-7567 
       10.19        12.23         1.18        23.61        41.82        18.67 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
        2.76        19.89        42.25        63.52        25.48        18.54 
TCGA-97-7938 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8032 
        0.59        18.12        21.60        21.44        24.56         1.45 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        18.58        15.65         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ 
       49.35        37.35        58.85        29.46        11.05        11.15 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       71.05         0.13        47.08        19.82        20.28        59.11 

$`22Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4434 TCGA-38-4629 
       19.96        14.01         8.02        20.05        15.02        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 
       35.28        11.64        26.30        43.53        38.10        23.93 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 
       86.01        18.31        29.00         9.37        11.08        16.04 
TCGA-49-6745 TCGA-49-AAR0 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       17.16       156.66        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.66        19.73        16.93        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       20.58        19.59        52.60        39.09         8.48        50.24 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
        6.12        17.29        16.54        15.68        15.65        21.40 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       17.92        20.19        20.52        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
        6.35        21.83        27.19         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
        3.98        47.05        19.00        14.96        29.98        12.00 
TCGA-05-4425 TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       21.99        25.02         4.96         9.04         2.04         0.46 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 
       97.74       120.79        37.71        44.61         4.37        44.42 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-5645 
       42.77         3.19        25.02        37.15        38.24        28.01 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       23.15        21.63        23.18        32.45        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A 
       19.46         7.17        18.87        23.64        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
        9.44        11.54        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-AAQV 
       12.66        35.54        29.75        55.89        53.29        22.26 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       62.24        28.90       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       71.47       101.72        60.16        47.41        49.28         8.22 
TCGA-50-5931 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6593 TCGA-50-6594 
       14.27        60.72        57.53        53.16        11.05        12.16 
TCGA-50-6595 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 
        6.21        36.79        27.25        30.54        38.73        67.89 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6981 TCGA-55-6982 
       14.30         5.62        40.73        15.25        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7727 TCGA-55-7728 
       92.81        24.99       107.21        70.26         3.91        23.15 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       25.41        11.28        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       15.19        23.08        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8513 TCGA-55-8514 
       15.42        17.56        15.72         0.36        26.01        17.10 
TCGA-55-8614 TCGA-55-A48Y TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       17.62        20.71        15.81        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-1680 
       56.71        72.30        39.25        40.96        39.09        37.02 
TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        2.04        28.47        20.05        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7765 TCGA-69-7974 
       12.66        14.73         5.72         4.64         5.42         6.05 
TCGA-69-8254 TCGA-69-8255 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
       13.45         4.24        26.30        30.31         9.24        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-78-7147 
       66.64        77.85        85.15        49.84       108.66        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       20.58       129.53        21.90       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7220 
       32.09         5.88        22.92         9.57       104.19        26.53 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35        10.55        39.75        77.59 
TCGA-78-8662 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 
      110.50        12.36        31.13        38.04        20.55        35.24 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8668 
        4.08        24.33        32.65        31.04        23.05        13.91 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
       27.58        28.34        26.50        29.46        13.64        26.47 
TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
        2.60        27.68         7.36         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 
       19.82        22.45        17.46         1.08        19.00        12.39 
TCGA-95-8039 TCGA-97-7547 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       27.29        64.60        61.48        15.91        18.67         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 
       15.39        16.41        14.30        20.58        19.76        20.84 
TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       18.67        34.85        36.76        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MP-A4SW 
       35.47        14.30        14.53         1.91        38.63        58.45 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       86.04         5.49        41.59        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
       73.91        74.33         1.64         0.49         0.43        16.87 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.00               0.36 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            238.29             221.33 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            21.815             21.600 
[1] "0.0 - 238.3 (21.8)" "0.4 - 221.3 (21.6)"
[1] "hr=" "1"  
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         3       52       58        0        23        32
  22Q LOSS WILD-TYPE       2       81       81        1        27        40
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  22Q LOSS MUTATED           34          6       11
  22Q LOSS WILD-TYPE         38          5       14
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 52                 81
  STAGE IB                 58                 81
  STAGE II                  0                  1
  STAGE IIA                23                 27
  STAGE IIB                32                 40
  STAGE IIIA               34                 38
  STAGE IIIB                6                  5
  STAGE IV                 11                 14
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED    71 121  20   9
  22Q LOSS WILD-TYPE 100 157  26  10
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               71                100
  T2              121                157
  T3               20                 26
  T4                9                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1 N2+N3
  22Q LOSS MUTATED   143  41    35
  22Q LOSS WILD-TYPE 190  55    41
D80V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                 143                190
  N1                  41                 55
  N2+N3               35                 41
[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"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   153  11
  22Q LOSS WILD-TYPE 196  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    153   11
  22Q LOSS WILD-TYPE  196   14
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              153                196
  1               11                 14
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   111 110
  22Q LOSS WILD-TYPE 165 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    111  110
  22Q LOSS WILD-TYPE  165  130
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE              111                165
  MALE                110                130
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   175  28
  22Q LOSS WILD-TYPE 235  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    175   28
  22Q LOSS WILD-TYPE  235   32
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               175                235
  YES               28                 32
[1] 2 2
[1] FALSE
D80V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  22Q LOSS MUTATED                           10
  22Q LOSS WILD-TYPE                          8
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  22Q LOSS MUTATED                                  41
  22Q LOSS WILD-TYPE                                66
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                  141
  22Q LOSS WILD-TYPE                                                180
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  22Q LOSS MUTATED                                            1
  22Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  22Q LOSS MUTATED                                              10
  22Q LOSS WILD-TYPE                                             9
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  22Q LOSS MUTATED                                0
  22Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  22Q LOSS MUTATED                                    2
  22Q LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  22Q LOSS MUTATED                              0                             8
  22Q LOSS WILD-TYPE                            2                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  22Q LOSS MUTATED                                 1
  22Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  22Q LOSS MUTATED                                               4
  22Q LOSS WILD-TYPE                                             1
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  22Q LOSS MUTATED                              3
  22Q LOSS WILD-TYPE                            7
D80V10, multiclass
                                                    clus
vv                                                   22Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              141
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    10
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     8
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     4
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   22Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                180
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                       9
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       1
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, continuous
D80V12, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED   146   5   1   9
  22Q LOSS WILD-TYPE 198   8   3  17
D80V13, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              146                198
  R1                5                  8
  R2                1                  3
  RX                9                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     1
  22Q LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          23   165
  22Q LOSS WILD-TYPE                        29   225
D80V14, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  6
  BLACK OR AFRICAN AMERICAN                      23                 29
  WHITE                                         165                225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V15, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3 166
  22Q LOSS WILD-TYPE   4 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3  166
  22Q LOSS WILD-TYPE    4  218
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              166                218
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    73  31
  XP LOSS WILD-TYPE 250 150
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              104               400 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               31               150 
$`XP LOSS MUTATED`
TCGA-05-4396 TCGA-05-4405 TCGA-38-6178 TCGA-44-6146 TCGA-50-5932 TCGA-50-6597 
        9.96        20.05        14.73        23.93        40.60        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-7726 TCGA-55-8090 TCGA-55-8203 TCGA-55-A492 
       23.05        48.62        21.44        19.66        17.98        19.59 
TCGA-67-6217 TCGA-78-7166 TCGA-78-8660 TCGA-93-A4JQ TCGA-95-7043 TCGA-97-8172 
       13.87         8.48        10.55        17.29        16.54        17.92 
TCGA-97-A4M7 TCGA-05-4426 TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       20.68        26.01        22.03         2.04         7.40         5.98 
TCGA-44-2659 TCGA-44-3918 TCGA-44-5643 TCGA-44-6778 TCGA-44-8120 TCGA-49-4507 
       44.94        34.06        33.30        61.28         8.55         8.81 
TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARQ TCGA-50-5936 TCGA-50-5941 
       22.26        73.12        62.24       221.33         8.45        48.46 
TCGA-50-5946 TCGA-50-6590 TCGA-50-7109 TCGA-53-7626 TCGA-55-1596 TCGA-55-5899 
       53.16        42.35        10.13        30.54        67.89        30.58 
TCGA-55-6968 TCGA-55-6985 TCGA-55-7281 TCGA-55-7570 TCGA-55-7903 TCGA-55-7913 
       42.51        40.54        28.67        27.09        18.64        18.44 
TCGA-55-7994 TCGA-55-8510 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8397 
       19.82        17.72         1.58        21.40        19.99        42.38 
TCGA-62-A46O TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-5778 TCGA-64-5815 
       47.80        67.96        29.92        56.81        42.90        28.47 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-69-7764 TCGA-71-6725 
       20.05        18.84        14.04        14.73        13.61         8.42 
TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-7025 
       26.30         4.31        50.33        11.18        66.64       108.66 
TCGA-78-7146 TCGA-78-7535 TCGA-78-7542 TCGA-78-8655 TCGA-86-7954 TCGA-86-7955 
        5.69        31.20        10.55        77.59        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 TCGA-86-A4P7 
       37.74         4.08        22.82        21.47        14.60        13.64 
TCGA-91-6848 TCGA-91-8496 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 
        7.36        16.60         1.08        41.82        18.67        27.29 
TCGA-95-8494 TCGA-97-7937 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M6 TCGA-L4-A4E5 
        2.76        18.54        21.60        21.44        18.67        19.00 
TCGA-L9-A50W TCGA-MN-A4N5 TCGA-MP-A4T4 TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YI 
       14.53         2.76        86.04        14.10        19.13         0.13 
TCGA-NJ-A55A TCGA-S2-AA1A 
        0.49        16.87 

$`XP LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         8.02         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 
       15.02        28.41        35.28        11.64        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        42.08        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5935 TCGA-55-6978 TCGA-55-6979 
       11.64       156.66        37.32        21.47         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8091 
        7.99        16.01        23.18        14.53         6.15        19.73 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 
       22.65        20.58        20.19        20.65        52.60        82.68 
TCGA-73-7498 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       39.09        50.24        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
        6.12         2.86        15.68        15.65        21.40        18.18 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.19        20.52        17.75        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       10.09        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       12.00        30.02        21.99        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 
        4.96        29.00         9.04         0.46         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.42        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       38.89        33.73        26.56        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       19.56        23.15        21.63        23.18        32.45        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       12.66        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       14.07        32.84        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       55.33        22.26        28.90         8.55        40.41       123.58 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 
       78.67        15.12        60.72        57.53         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 
       11.05        12.16         6.21         0.72        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6543 
       27.25        34.29        13.94        35.21        38.73        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       80.52         5.62        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
      107.21        70.26        20.02        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 
       23.15        25.41        11.28        34.19        17.65        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
       14.47         0.36        13.74        20.28        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 
       17.10        17.62        14.66        12.33        20.71         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
        0.92        15.81        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V 
       88.64        49.25        19.53        56.71        54.35        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
       13.61        39.25        40.96        39.09        81.80        37.02 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 
       38.37        87.98         2.04        28.41        51.25        20.05 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       12.66         5.72         4.64         6.64         6.12        22.68 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 
       14.01        13.45         4.24        26.73        19.43        23.38 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5146 TCGA-75-5147 
       15.35        30.31         9.24         1.25        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       85.15        49.84        36.66       100.57       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        9.57       104.19       238.29        88.14        26.53         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 
       53.33        26.01        39.35       232.18        39.75       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       38.04        20.55        32.78         4.57        24.33         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 TCGA-86-8668 
       32.65        31.04        31.20        23.05        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
        3.81        24.23        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8497 
       10.19         2.60        12.23        27.68         1.15        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP 
        1.18        19.82        22.45        17.46        23.61        19.00 
TCGA-95-7944 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       12.39        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       25.48         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 
       15.39        16.41        14.30        20.58        19.76        20.84 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       24.56        34.85        36.76         1.45        21.57        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A7SV 
       18.08        35.47        32.48        14.30         1.91        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       15.65        38.63        86.14        58.45        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       11.15        73.91        71.05        74.33         1.64        47.08 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.43        19.82        20.28        59.11 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.13              0.00 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           221.33            238.29 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           20.020            22.355 
[1] "0.1 - 221.3 (20.0)" "0.0 - 238.3 (22.4)"
[1] "hr=" "1.2"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         2       30       30        0         7        20
  XP LOSS WILD-TYPE       3      103      109        1        43        52
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XP LOSS MUTATED           10          2        3
  XP LOSS WILD-TYPE         62          9       22
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                30               103
  STAGE IB                30               109
  STAGE II                 0                 1
  STAGE IIA                7                43
  STAGE IIB               20                52
  STAGE IIIA              10                62
  STAGE IIIB               2                 9
  STAGE IV                 3                22
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP LOSS MUTATED    38  57  10   1
  XP LOSS WILD-TYPE 133 221  36  18
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              38               133
  T2              57               221
  T3              10                36
  T4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  XP LOSS MUTATED    71  23    10
  XP LOSS WILD-TYPE 262  73    66
D81V5, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  N0                 71               262
  N1                 23                73
  N2+N3              10                66
[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"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    75   3
  XP LOSS WILD-TYPE 274  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     75    3
  XP LOSS WILD-TYPE  274   22
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              75               274
  1               3                22
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    52  54
  XP LOSS WILD-TYPE 224 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     52   54
  XP LOSS WILD-TYPE  224  186
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              52               224
  MALE                54               186
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    81  10
  XP LOSS WILD-TYPE 329  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     81   10
  XP LOSS WILD-TYPE  329   50
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               81               329
  YES              10                50
[1] 2 2
[1] FALSE
D81V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XP LOSS MUTATED                            5
  XP LOSS WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XP LOSS MUTATED                                  22
  XP LOSS WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XP LOSS MUTATED                                                   69
  XP LOSS WILD-TYPE                                                252
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XP LOSS MUTATED                                            1
  XP LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  XP LOSS MUTATED                                               3
  XP LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  XP LOSS MUTATED                                1
  XP LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  XP LOSS MUTATED                                    1
  XP LOSS WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  XP LOSS MUTATED                              1                             2
  XP LOSS WILD-TYPE                            1                            21
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  XP LOSS MUTATED                                 0
  XP LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  XP LOSS MUTATED                                               0
  XP LOSS WILD-TYPE                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  XP LOSS MUTATED                              1
  XP LOSS WILD-TYPE                            9
D81V10, multiclass
                                                    clus
vv                                                   XP LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              69
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   XP LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               252
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      5
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, continuous
D81V12, continuous
                   vv
clus                 R0  R1  R2  RX
  XP LOSS MUTATED    72   1   0   5
  XP LOSS WILD-TYPE 272  12   4  21
D81V13, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              72               272
  R1               1                12
  R2               0                 4
  RX               5                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     3
  XP LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          11    80
  XP LOSS WILD-TYPE                        41   310
D81V14, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                     11                41
  WHITE                                         80               310
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V15, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0  82
  XP LOSS WILD-TYPE   7 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   82
  XP LOSS WILD-TYPE    7  302
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              82               302
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    39  21
  XQ LOSS WILD-TYPE 284 160
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               60               444 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               21               160 
$`XQ LOSS MUTATED`
TCGA-05-4396 TCGA-44-6146 TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
        9.96        23.93        40.60        41.69        23.05        48.62 
TCGA-55-8090 TCGA-55-8203 TCGA-55-A491 TCGA-78-7166 TCGA-97-A4M7 TCGA-05-5428 
       19.66        17.98        20.58         8.48        20.68        22.03 
TCGA-05-5715 TCGA-44-5643 TCGA-44-8120 TCGA-49-4507 TCGA-49-AAR2 TCGA-49-AAR3 
        2.04        33.30         8.55         8.81        73.12        62.24 
TCGA-49-AAR9 TCGA-50-5936 TCGA-50-6590 TCGA-55-1596 TCGA-55-6968 TCGA-55-7570 
        8.55         8.45        42.35        67.89        42.51        27.09 
TCGA-55-7576 TCGA-55-7903 TCGA-55-7913 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8397 
       22.03        18.64        18.44        21.40        19.99        42.38 
TCGA-62-A46O TCGA-62-A46U TCGA-62-A472 TCGA-64-5778 TCGA-64-5815 TCGA-67-3772 
       47.80        67.96        29.92        42.90        28.47        18.84 
TCGA-67-3773 TCGA-69-7764 TCGA-69-7973 TCGA-69-8255 TCGA-73-7499 TCGA-73-A9RS 
       14.04        13.61         7.56         4.24        50.33        11.18 
TCGA-78-7146 TCGA-78-7220 TCGA-78-7536 TCGA-78-8655 TCGA-86-7954 TCGA-86-7955 
        5.69        26.53         8.02        77.59        19.89        35.24 
TCGA-86-8054 TCGA-86-8359 TCGA-91-8496 TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 
       37.74        14.60        16.60        41.82        18.67        27.29 
TCGA-95-8494 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M6 TCGA-L9-A50W TCGA-NJ-A4YI 
        2.76        21.60        21.44        18.67        14.53         0.13 

$`XQ LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 TCGA-44-6776 
       26.30        43.53        38.10        42.08        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5935 
       16.04        17.16        11.64       156.66        37.32        21.47 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       21.44         6.15        19.73        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF 
       18.15        13.68        16.93        22.65        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7633 
       20.65        13.87        52.60        82.68        39.09        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 
       18.18        17.92        20.19        20.52        17.75        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       23.80         6.35        10.09        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       25.02        25.02        24.00         4.96        29.00         9.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        0.46         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.94        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 
       38.89        34.06        33.73        26.56        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       18.87        23.64        12.66        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
       12.66        35.54        14.07        32.84        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR4 
       55.89        53.29        55.33        22.26        22.26        28.90 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       40.41       123.58       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 
        8.22         9.27        14.27        78.67        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       60.72        57.53        53.16         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94        35.21        38.73 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       30.58        14.30        80.52         5.62        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
       20.02        32.71         3.91        23.15        25.41        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 
       17.62        14.66         1.58        12.33        20.71         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
        0.92        15.81        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V 
       88.64        49.25        19.53        56.71        54.35        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       13.61        39.25        40.96        56.81        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       37.02        38.37        87.98         2.04        28.41        51.25 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        20.05        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
        6.64         6.12        22.68         5.42         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K 
       13.41        13.51        14.01        13.45        26.73        19.43 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        8.42        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        9.24         1.25        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 
        9.57       104.19       238.29        88.14        31.20        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 
       26.01        39.35        10.55       232.18        39.75       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       38.04        20.55        32.78         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       21.47        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       28.34        26.50        29.46         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 
       12.23        27.68         7.36         1.15        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7944 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       12.39        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 
       18.12        15.39        16.41        14.30        20.58        19.76 
TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.84        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        1.91        18.58        15.65        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        71.05        74.33         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.49         0.43        19.82        20.28        59.11        16.87 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.13              0.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            77.59            238.29 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           21.040            21.865 
[1] "0.1 - 77.6 (21.0)"  "0.0 - 238.3 (21.9)"
[1] "hr=" "1.1"
D82V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         0       16       16        0         3        14
  XQ LOSS WILD-TYPE       5      117      123        1        47        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XQ LOSS MUTATED            9          2        1
  XQ LOSS WILD-TYPE         63          9       24
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                16               117
  STAGE IB                16               123
  STAGE II                 0                 1
  STAGE IIA                3                47
  STAGE IIB               14                58
  STAGE IIIA               9                63
  STAGE IIIB               2                 9
  STAGE IV                 1                24
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED    19  33   8   1
  XQ LOSS WILD-TYPE 152 245  38  18
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              19               152
  T2              33               245
  T3               8                38
  T4               1                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1 N2+N3
  XQ LOSS MUTATED    37  13     9
  XQ LOSS WILD-TYPE 296  83    67
D82V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                 37               296
  N1                 13                83
  N2+N3               9                67
[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"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    46   1
  XQ LOSS WILD-TYPE 303  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     46    1
  XQ LOSS WILD-TYPE  303   24
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              46               303
  1               1                24
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    26  35
  XQ LOSS WILD-TYPE 250 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     26   35
  XQ LOSS WILD-TYPE  250  205
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              26               250
  MALE                35               205
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    45  10
  XQ LOSS WILD-TYPE 365  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     45   10
  XQ LOSS WILD-TYPE  365   50
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               45               365
  YES              10                50
[1] 2 2
[1] FALSE
D82V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XQ LOSS MUTATED                            3
  XQ LOSS WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XQ LOSS MUTATED                                  19
  XQ LOSS WILD-TYPE                                88
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                   31
  XQ LOSS WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XQ LOSS MUTATED                                            0
  XQ LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  XQ LOSS MUTATED                                               3
  XQ LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  XQ LOSS MUTATED                                1
  XQ LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  XQ LOSS MUTATED                                    0
  XQ LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  XQ LOSS MUTATED                              1                             1
  XQ LOSS WILD-TYPE                            1                            22
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  XQ LOSS MUTATED                                 0
  XQ LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  XQ LOSS MUTATED                                               1
  XQ LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  XQ LOSS MUTATED                              1
  XQ LOSS WILD-TYPE                            9
D82V10, multiclass
                                                    clus
vv                                                   XQ LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              31
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   XQ LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 88
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     22
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V11, continuous
D82V12, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    38   0   0   2
  XQ LOSS WILD-TYPE 306  13   4  24
D82V13, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              38               306
  R1               0                13
  R2               0                 4
  RX               2                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     2
  XQ LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                          10    44
  XQ LOSS WILD-TYPE                        42   346
D82V14, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                     10                42
  WHITE                                         44               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V15, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1  50
  XQ LOSS WILD-TYPE   6 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   50
  XQ LOSS WILD-TYPE    6  334
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              50               334
[1] 2 2
[1] FALSE
