[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/19775350/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/19782226/transformed.cor.cli.txt"

nPatients in clinical file=521, in cluster file=516, common to both=515
[1]  82 515
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              150               365 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              150               365 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              309               206 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              309               206 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              153               362 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              153               362 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              141               374 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              141               374 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               40               475 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               40               475 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               88               427 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               88               427 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               77               438 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               77               438 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               44               471 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               44               471 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              270               245 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              270               245 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              125               390 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              125               390 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              143               372 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              143               372 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               61               454 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               61               454 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              258               257 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              258               257 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              211               304 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              211               304 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              129               386 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              129               386 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              243               272 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              243               272 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               45               470 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               45               470 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               32               483 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               32               483 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               111                404 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               111                404 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                77                438 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                77                438 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                94                421 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                94                421 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               114                401 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               114                401 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               137                378 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               137                378 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               130                385 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               130                385 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                44                471 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                44                471 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               130                385 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               130                385 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                38                477 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                38                477 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               131                384 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               131                384 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                99                416 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                99                416 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                83                432 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                83                432 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               191                324 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               191                324 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                91                424 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                91                424 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                69                446 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                69                446 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                30                485 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                30                485 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                75                440 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                75                440 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               172                343 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               172                343 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               191                324 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               191                324 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                96                419 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                96                419 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                62                453 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                62                453 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               51               464 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               51               464 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               83               432 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               83               432 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               82               433 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               82               433 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               33               482 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               33               482 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               28               487 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               28               487 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               29               486 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               29               486 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              212               303 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              212               303 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              146               369 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              146               369 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              123               392 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              123               392 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              140               375 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              140               375 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               52               463 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               52               463 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              152               363 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              152               363 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              106               409 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              106               409 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              216               299 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              216               299 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               39               476 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               39               476 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               47               468 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               47               468 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              202               313 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              202               313 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               60               455 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               60               455 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              270               245 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              270               245 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              254               261 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              254               261 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               114                401 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               114                401 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               136                379 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               136                379 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               116                399 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               116                399 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                91                424 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                91                424 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               114                401 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               114                401 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               102                413 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               102                413 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               257                258 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               257                258 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               114                401 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               114                401 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               241                274 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               241                274 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               117                398 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               117                398 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               144                371 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               144                371 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               216                299 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               216                299 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                57                458 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                57                458 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               177                338 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               177                338 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               212                303 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               212                303 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               247                268 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               247                268 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               160                355 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               160                355 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               113                402 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               113                402 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                69                446 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                69                446 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               167                348 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               167                348 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               217                298 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               217                298 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              104               411 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              104               411 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               62               453 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               62               453 
[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 515 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=160,	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=326,	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=23,	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=95,	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 515 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 
170 278  46  19 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
170 278  46  19 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
170 278  46  19 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
170 278  46  19 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
332  96  74   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  332    96    76 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
332  96  74   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  332    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=95, 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    91  54
  1P GAIN WILD-TYPE 234 113
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              145               347 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               113 
$`1P GAIN MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 
       19.96         8.02        29.98        30.02        26.01        25.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-38-4628 TCGA-38-4632 
        4.96        29.00        22.03         9.04        49.05        44.61 
TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       14.73        46.98        44.94        61.28        16.44        19.46 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47B 
        7.17        18.87        13.74        12.66         3.25         9.44 
TCGA-44-A4SU TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-6742 
       13.45        12.66        46.72        14.07        29.46        16.04 
TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AARO 
       53.29        55.33        22.26       156.66        62.24       123.58 
TCGA-49-AARQ TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5068 TCGA-50-5072 
      221.33        20.52        71.47        70.55        49.28         8.09 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       14.27        78.67         9.37        25.12        22.55         3.91 
TCGA-50-6593 TCGA-50-6597 TCGA-55-1592 TCGA-55-6712 TCGA-55-6969 TCGA-55-6979 
       11.05        41.69        23.05         0.79        40.73         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-7281 TCGA-55-7573 
        2.20        45.34        32.71        60.03         0.59         0.13 
TCGA-55-7576 TCGA-55-7907 TCGA-55-7911 TCGA-55-8089 TCGA-55-8096 TCGA-55-8206 
        1.32         0.53        17.65         3.29        23.64         1.51 
TCGA-55-8514 TCGA-55-A48X TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B 
        6.64        22.65        15.81        20.19        19.99        17.95 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
       14.60        88.64        47.80        56.81        81.80        38.37 
TCGA-64-5781 TCGA-67-3772 TCGA-67-6217 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
       51.25        18.84        13.87        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
        4.24        17.16         2.01        15.35         4.31         9.24 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 
       11.18       163.10        27.16        19.27        19.50        38.50 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7542 TCGA-78-7633 
        9.57       104.19        88.14        31.20        10.55        50.24 
TCGA-78-8640 TCGA-78-8655 TCGA-86-7953 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 
      232.18        77.59        32.78         4.08         0.79        22.82 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 
       31.20        23.05         1.15        28.34        29.46        13.64 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JN TCGA-93-A4JO 
       10.62        10.19        12.23        27.68        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-8494 
       19.00        41.82        16.54         2.86        12.39         2.76 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8176 TCGA-97-8177 TCGA-97-8552 
       31.69        43.79         5.95        15.39        16.41        20.58 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 TCGA-J2-A4AG TCGA-L9-A743 TCGA-L9-A7SV 
       19.76        20.84        24.56        32.48        21.83        18.58 
TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-NJ-A55O 
       27.19        58.45        58.85         2.43        11.05         0.43 
TCGA-O1-A52J 
       59.11 

$`1P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03        47.05        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       14.96         9.01        12.00        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
       24.00        15.02        15.02         2.04         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
        5.98         8.68        97.74       120.79        37.71        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
       35.28        11.64        26.30         4.37        43.53        44.42 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       38.10        42.08        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-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 
       23.15        21.63        23.18        63.72        32.45        22.72 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 
       12.03        36.07        29.00        29.23         8.55        15.98 
TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 
       15.32        11.08        11.54        13.64        76.21        28.11 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
       28.57        35.54        32.84         8.81        29.75        55.89 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 
       17.16        11.64        22.26        73.12        28.90         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARR TCGA-4B-A93V TCGA-50-5051 TCGA-50-5055 
       40.41        37.32       164.12         9.86        15.72        60.16 
TCGA-50-5066 TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       31.04         9.27        40.60        21.47         8.45        15.12 
TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       29.03        42.35        25.55        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         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
       13.94        35.21        38.73        48.62        45.21         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.07        32.65        42.51        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        3.88         5.49        24.99        40.54       107.21        70.26 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
        1.15         7.99         0.20         3.12        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
        1.28         1.12         0.79         1.78        18.64         6.48 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06         0.13        15.65        17.98         1.08 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       16.93        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46P 
        0.92         4.57        39.98        42.38        49.25        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-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
       40.96        29.92        20.65        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         1.02        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-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.41         2.93        25.91        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7146 
       26.30        30.31         1.25        39.09        50.33         5.69 
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-78-7163 TCGA-78-7166 TCGA-78-7220 
        5.88        64.90        22.92       238.29         8.48        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8660 
        8.02        53.33        26.01        39.35        39.75        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        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-86-8056 
       38.04        20.55        19.89        35.24        37.74         4.57 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       24.33        32.65        31.04        21.47        14.60        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF 
       30.84        27.58         0.62        26.50         3.81        24.23 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6848 
       26.47        41.36         1.97         2.60        13.71         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7567 
       19.82        22.45        17.46         6.12        17.29        18.67 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.68        15.65        27.29        21.40        18.18        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         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX 
       17.92         5.39        18.12        14.30        21.60        20.19 
TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 
       21.44        20.52        17.75        18.67        20.68        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       36.76         1.45        21.57        21.63        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       18.08        35.47        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.53         1.91        15.65        38.63         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        86.04         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       31.23        10.09        29.46        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        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       29.13         0.26        19.82        20.28        16.87 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.13              0.00 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           232.18            238.29 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            19.96             20.05 
[1] "0.1 - 232.2 (20.0)" "0.0 - 238.3 (20.1)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         3       37       36        1        22        23
  1P GAIN WILD-TYPE       2       98      103        0        30        49
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1P GAIN MUTATED           17          2        8
  1P GAIN WILD-TYPE         55          9       18
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                37                98
  STAGE IB                36               103
  STAGE II                 1                 0
  STAGE IIA               22                30
  STAGE IIB               23                49
  STAGE IIIA              17                55
  STAGE IIIB               2                 9
  STAGE IV                 8                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    51  84  10   4
  1P GAIN WILD-TYPE 119 194  36  15
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              51               119
  T2              84               194
  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
  1P GAIN MUTATED    88  43    16
  1P GAIN WILD-TYPE 244  53    60
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                 88               244
  N1                 43                53
  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"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   103   8
  1P GAIN WILD-TYPE 246  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    103    8
  1P GAIN WILD-TYPE  246   17
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0             103               246
  1               8                17
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    78  72
  1P GAIN WILD-TYPE 197 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     78   72
  1P GAIN WILD-TYPE  197  168
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              78               197
  MALE                72               168
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   103  16
  1P GAIN WILD-TYPE 257  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    103   16
  1P GAIN WILD-TYPE  257   38
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO              103               257
  YES              16                38
[1] 2 2
[1] FALSE
D1V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1P GAIN MUTATED                            4
  1P GAIN WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1P GAIN MUTATED                                  28
  1P GAIN WILD-TYPE                                78
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                   97
  1P GAIN WILD-TYPE                                                223
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1P GAIN MUTATED                                            0
  1P GAIN WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1P GAIN MUTATED                                               7
  1P GAIN WILD-TYPE                                            12
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1P GAIN MUTATED                                1
  1P GAIN WILD-TYPE                              1
                   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                             6
  1P GAIN WILD-TYPE                            2                            17
                   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                              3
  1P GAIN WILD-TYPE                            7
D1V10, multiclass
                                                    clus
vv                                                   1P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              97
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    7
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    6
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     3
                                                    clus
vv                                                   1P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               223
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     12
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  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"
D1V11, continuous
D1V12, continuous
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    94   4   1   6
  1P GAIN WILD-TYPE 249   8   3  20
D1V13, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              94               249
  R1               4                 8
  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
  1P GAIN MUTATED                                  1     3
  1P GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          20   109
  1P GAIN WILD-TYPE                        31   280
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                     20                31
  WHITE                                        109               280
[1] 4 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     1 107
  1P GAIN WILD-TYPE   6 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1  107
  1P GAIN WILD-TYPE    6  275
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO             107               275
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   199 100
  1Q GAIN WILD-TYPE 126  67
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              299               193 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              100                67 
$`1Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
        0.00         8.02         2.99        14.96        29.98        30.02 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 
        9.04         2.04         0.46        97.74        49.05        28.41 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-44-2656 TCGA-44-2659 TCGA-44-3917 
       44.61        14.73        26.30        46.98        44.94        38.89 
TCGA-44-6144 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.77        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       19.46         7.17        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS 
       12.66         3.25        15.32         9.44        11.08        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        76.21        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       14.07        32.84        29.46        16.04        53.29        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN 
       22.26        22.26       156.66        62.24         8.55        37.32 
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        70.55 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
       15.72        49.28         8.09        14.27        78.67        21.47 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6597 
        9.37        25.12        22.55         3.91        11.05        41.69 
TCGA-50-8457 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1596 
       36.99        27.25        30.54        13.94        23.05        45.21 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6979 
       32.65         0.79        40.73        15.25        48.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 
        2.20        45.34        32.71        60.03        24.99        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        0.59         1.15         7.99         0.13         3.12         1.32 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        1.28         1.12         1.78        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15         0.16        29.72        15.19         3.29 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8206 TCGA-55-8301 
        5.06         0.13        23.64        17.98         1.51         1.45 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 
        0.36         0.49        17.72         0.30         6.64         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 
        1.58         1.61        22.65        20.71        21.40        20.58 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8398 
       19.59        15.81        20.19        19.99        17.95        14.60 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A470 
       88.64        47.80        19.53        56.71        54.35        39.25 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 
       56.81        81.80        37.02        38.37        28.41        51.25 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6217 
       20.05        18.84        12.66        14.73         5.72        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 
        6.64         6.12        13.61         5.42         7.56         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        82.68        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        11.18       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 
       19.27        20.58       129.53        21.90       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-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 
      104.19        88.14        31.20        53.33        26.01        50.24 
TCGA-78-8640 TCGA-78-8655 TCGA-86-6562 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
      232.18        77.59        12.36        38.04        32.78        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
       37.74         4.08         0.79        22.82        32.65        31.20 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 TCGA-86-8674 
       23.05        14.60         1.15        30.84        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 
       29.46         3.81        24.23        13.64        10.62        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
        2.60        12.23        27.68         1.15        16.18        16.60 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       17.46         6.12        23.61         1.08        19.00        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
       16.54         2.86        18.67        12.39        15.68        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8172 TCGA-97-8176 
       43.79        25.48         5.95         0.59        17.92        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        20.58        20.19        21.44        19.76 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8032 
       17.75        20.84        18.67        20.68        24.56         1.45 
TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A443 TCGA-L9-A444 
       21.57        23.80        18.08        32.48         6.35        10.09 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       21.83        18.58        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
       58.45        58.85         5.49         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       24.36        73.91        62.60         0.13         1.64        29.13 
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 

$`1Q GAIN WILD-TYPE`
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4418 
        9.96        24.03        47.05        19.00        20.05         9.01 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 
       12.00        21.99        26.01        26.01        24.00        15.02 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 
        7.40         5.98         8.68       120.79        37.71        35.28 
TCGA-38-4631 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
       11.64         4.37        43.53        44.42        38.10        42.08 
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-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
       33.73        26.56        33.30        28.37        28.01        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-7661 
        9.93        27.78        23.15        21.63        23.18        12.03 
TCGA-44-7667 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-49-4487 TCGA-49-4507 
       36.07         8.55        15.98        11.54        28.11         8.81 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR2 TCGA-49-AAR4 
       29.75        55.89        17.16        11.64        73.12        28.90 
TCGA-49-AARE TCGA-49-AARR TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5932 
       40.41       164.12        60.16        31.04         9.27        40.60 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 
        8.45        15.12        29.03        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         7.59        34.29        35.21 
TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6968 TCGA-55-6971 
       38.73        48.62         2.86         0.07        42.51         0.82 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6985 TCGA-55-6986 TCGA-55-7570 TCGA-55-7724 
        3.88         5.49        40.54       107.21         0.20        23.18 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7994 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 
        1.28         0.79        19.82        19.66        19.73        15.65 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 
        1.08         2.17        22.16        15.42         0.76         0.95 
TCGA-55-8507 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8620 TCGA-55-8621 
        0.26         0.10         4.80        17.62         2.17        16.93 
TCGA-55-A490 TCGA-55-A493 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 
        1.58         0.92         4.57        39.98        42.38        49.25 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
       67.96        72.30        13.61        40.96        29.92        20.65 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 
       39.09        87.98         2.04        42.90        28.47         1.02 
TCGA-67-3773 TCGA-67-6216 TCGA-69-7763 TCGA-69-7974 TCGA-69-7978 TCGA-69-8453 
       14.04         4.64        22.68         6.05         4.41        25.91 
TCGA-73-4666 TCGA-73-7499 TCGA-78-7146 TCGA-78-7152 TCGA-78-7163 TCGA-78-7166 
       26.30        50.33         5.69        39.95       238.29         8.48 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 
       26.53         8.02        39.35        10.55        39.75        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
      110.50        27.09         5.88        31.13        34.39        20.55 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8278 TCGA-86-8358 TCGA-86-8668 
       35.24         4.57        24.33        31.04        21.47        13.91 
TCGA-86-8671 TCGA-86-8672 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 
       27.58         0.62        26.47        41.36         1.97        13.71 
TCGA-91-6848 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
        7.36        14.27         1.18         1.45        19.82        22.45 
TCGA-93-A4JQ TCGA-95-7948 TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       17.29        15.65        63.52         0.72        18.67         5.39 
TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R 
       18.12        21.60        20.52        34.85        36.76        21.63 
TCGA-J2-8192 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       24.30        35.47        19.00        14.30        14.53         1.91 
TCGA-L9-A8F4 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
       15.65        49.35        37.35        86.04         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF 
       31.23        11.05        14.10        11.15        19.13        71.05 
TCGA-NJ-A55A 
        0.26 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.00              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           232.18            238.29 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            19.89             20.55 
[1] "0.0 - 232.2 (19.9)" "0.1 - 238.3 (20.6)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         3       87       81        1        34        41
  1Q GAIN WILD-TYPE       2       48       58        0        18        31
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1Q GAIN MUTATED           37          8       15
  1Q GAIN WILD-TYPE         35          3       11
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                87                48
  STAGE IB                81                58
  STAGE II                 1                 0
  STAGE IIA               34                18
  STAGE IIB               41                31
  STAGE IIIA              37                35
  STAGE IIIB               8                 3
  STAGE IV                15                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
  1Q GAIN MUTATED   105 161  28  13
  1Q GAIN WILD-TYPE  65 117  18   6
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1             105                65
  T2             161               117
  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   201  61    39
  1Q GAIN WILD-TYPE 131  35    37
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                201               131
  N1                 61                35
  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"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   210  14
  1Q GAIN WILD-TYPE 139  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    210   14
  1Q GAIN WILD-TYPE  139   11
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             210               139
  1              14                11
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   158 151
  1Q GAIN WILD-TYPE 117  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    158  151
  1Q GAIN WILD-TYPE  117   89
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE             158               117
  MALE               151                89
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   217  29
  1Q GAIN WILD-TYPE 143  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    217   29
  1Q GAIN WILD-TYPE  143   25
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              217               143
  YES              29                25
[1] 2 2
[1] FALSE
D2V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1Q GAIN MUTATED                           14
  1Q GAIN WILD-TYPE                          5
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1Q GAIN MUTATED                                  64
  1Q GAIN WILD-TYPE                                42
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                  187
  1Q GAIN WILD-TYPE                                                133
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1Q GAIN MUTATED                                            1
  1Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1Q GAIN MUTATED                                              14
  1Q GAIN WILD-TYPE                                             5
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1Q GAIN MUTATED                                1
  1Q GAIN WILD-TYPE                              1
                   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                                      14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               64
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             187
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   14
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  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)               133
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      5
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  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   198   8   2  18
  1Q GAIN WILD-TYPE 145   4   2   8
D2V13, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             198               145
  R1               8                 4
  R2               2                 2
  RX              18                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1     5
  1Q GAIN WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          32   236
  1Q GAIN WILD-TYPE                        19   153
D2V14, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          5                 2
  BLACK OR AFRICAN AMERICAN                     32                19
  WHITE                                        236               153
[1] 4 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     2 230
  1Q GAIN WILD-TYPE   5 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2  230
  1Q GAIN WILD-TYPE    5  152
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             230               152
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    94  51
  2P GAIN WILD-TYPE 231 116
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              145               347 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               51               116 
$`2P GAIN MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 
        3.98        19.96        45.01        37.02         0.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 
       14.96         9.01        29.98        30.02        25.02        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       22.03         7.40         5.98        35.28        11.64        44.61 
TCGA-38-6178 TCGA-44-2657 TCGA-44-6779 TCGA-44-7667 TCGA-44-7670 TCGA-44-A47A 
       14.73        44.42        16.44        36.07        29.00        15.32 
TCGA-44-A47G TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4507 TCGA-49-4510 
       11.54        28.11        28.57        12.66         8.81        29.46 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ 
       16.04        53.29        55.33         8.55       123.58       221.33 
TCGA-50-5072 TCGA-50-5946 TCGA-50-6592 TCGA-50-6593 TCGA-50-6597 TCGA-50-6673 
        8.09        22.55        25.55        11.05        41.69         0.72 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
       34.29        13.94        35.21        23.05        38.73        48.62 
TCGA-55-1596 TCGA-55-6970 TCGA-55-6981 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 
       45.21        15.25        45.34        60.03         0.59         1.15 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 
        0.13         1.32         0.53         6.48        17.65         0.16 
TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 
       23.64        17.98         1.08        22.16         0.76         0.26 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A493 
       17.72         0.30         0.49         1.58         2.17         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R 
       15.81        19.99        17.95        49.25        47.80        56.71 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-67-3770 TCGA-67-6217 TCGA-69-7764 
       39.09        37.02        87.98         1.02        13.87        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 TCGA-73-4662 
        7.56         6.05         4.41        12.56         4.24        82.68 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-78-7145 TCGA-78-7149 TCGA-78-7150 
       15.35        30.31         9.24        27.16       129.53        21.90 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7539 
       38.50        64.90        22.92         9.57       238.29        26.01 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-86-6562 TCGA-86-7711 
       50.24       232.18        77.59       110.50        12.36        34.39 
TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8359 TCGA-86-8585 
       38.04        35.24        37.74         4.08        14.60         1.15 
TCGA-86-8669 TCGA-86-8673 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       30.84        28.34        41.36        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7043 TCGA-95-7567 
       12.23        27.68        23.61         1.08        16.54        18.67 
TCGA-95-7944 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7938 TCGA-97-8179 TCGA-99-8025 
       12.39        21.40        64.60         0.59        14.30        34.85 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP 
        1.45        21.57        23.80         6.35        10.09         1.91 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TK TCGA-NJ-A4YQ 
       27.19         2.76        41.59         2.43        19.13        29.13 
TCGA-O1-A52J 
       59.11 

$`2P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
       50.07        14.01         9.96        24.03        47.05         8.02 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       19.00        20.05        12.00        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 
       25.02        24.00        15.02        15.02         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         0.46         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       49.05        28.41        26.30         4.37        43.53        46.98 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.94        38.10        42.08        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-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
       61.28        22.72        19.46        12.03         7.17        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.23        13.74        12.66         3.25         8.55        15.98 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
        9.44        11.08        13.64        13.45        76.21        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 TCGA-49-6745 
       46.72        14.07        32.84        29.75        55.89        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       11.64        22.26        22.26       156.66        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       28.90        40.41        37.32       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        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 
       15.12         9.37        29.03        25.12        42.35         3.91 
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         7.59        27.25 
TCGA-53-7626 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       30.54         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        2.20        32.71        24.99        40.54       107.21        70.26 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.99         0.20         3.12        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 
        1.12         0.79         1.78        18.64         6.15        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
        0.13        15.65         1.51         2.17        15.42         1.45 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.95         0.36         0.49         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
       17.62         1.61        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 
        1.58        20.58        19.59        20.19         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U 
       42.38        14.60        88.64        19.53        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-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       20.65        81.80        38.37         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 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-69-7763 
       14.73         5.72         4.64         6.64         6.12        22.68 
TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K 
        5.42         2.93        14.01        13.45        25.91        17.16 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 
        2.01        52.60        23.38        26.30         4.31         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33        11.18       163.10         5.69        19.27 
TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       20.58        39.95       119.51        19.50        32.09         5.88 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 TCGA-83-5908 
       53.33        39.35        10.55        39.75        10.55        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-91-7771 TCGA-91-8496 TCGA-91-8497 
        1.97         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
       19.00        17.29        41.82         2.86        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 
       27.29         2.76        18.18        19.89        31.69        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       43.79        25.48         5.95         0.72        18.67        17.92 
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-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-8192 
       18.67        20.68        24.56        36.76        21.63        24.30 
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-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
       21.83        18.58        15.65        38.63        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23        10.09        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        62.60         0.13         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.26         0.43        19.82        20.28        16.87 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.00              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           238.29            164.12 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            19.13             20.05 
[1] "0.0 - 238.3 (19.1)" "0.1 - 164.1 (20.1)"
[1] "hr=" "1"  
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         3       40       38        0        17        18
  2P GAIN WILD-TYPE       2       95      101        1        35        54
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2P GAIN MUTATED           23          4       10
  2P GAIN WILD-TYPE         49          7       16
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                40                95
  STAGE IB                38               101
  STAGE II                 0                 1
  STAGE IIA               17                35
  STAGE IIB               18                54
  STAGE IIIA              23                49
  STAGE IIIB               4                 7
  STAGE IV                10                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
  2P GAIN MUTATED    49  81  16   6
  2P GAIN WILD-TYPE 121 197  30  13
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              49               121
  T2              81               197
  T3              16                30
  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    93  31    26
  2P GAIN WILD-TYPE 239  65    50
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                 93               239
  N1                 31                65
  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   102  10
  2P GAIN WILD-TYPE 247  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    102   10
  2P GAIN WILD-TYPE  247   15
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0             102               247
  1              10                15
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    85  68
  2P GAIN WILD-TYPE 190 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     85   68
  2P GAIN WILD-TYPE  190  172
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              85               190
  MALE                68               172
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    98  23
  2P GAIN WILD-TYPE 262  31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     98   23
  2P GAIN WILD-TYPE  262   31
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               98               262
  YES              23                31
[1] 2 2
[1] FALSE
D3V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2P GAIN MUTATED                            4
  2P GAIN WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2P GAIN MUTATED                                  35
  2P GAIN WILD-TYPE                                71
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                   97
  2P GAIN WILD-TYPE                                                223
                   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                               35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              97
  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                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               223
  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   107   7   2   9
  2P GAIN WILD-TYPE 236   5   2  17
D3V13, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0             107               236
  R1               7                 5
  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                          11   114
  2P GAIN WILD-TYPE                        40   275
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                     11                40
  WHITE                                        114               275
[1] 4 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     5 105
  2P GAIN WILD-TYPE   2 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5  105
  2P GAIN WILD-TYPE    2  277
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             105               277
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    87  46
  2Q GAIN WILD-TYPE 238 121
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              133               359 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               46               121 
$`2Q GAIN MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4405 
        3.98        19.96        45.01        37.02         0.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 
        2.99        14.96         9.01        30.02        25.02        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       22.03         7.40         8.68        35.28        44.61        14.73 
TCGA-44-2657 TCGA-44-7662 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47G TCGA-49-4487 
       44.42         7.17        29.00        15.32        11.54        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-6742 
       28.57        12.66        14.07         8.81        29.46        16.04 
TCGA-49-6744 TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5072 TCGA-50-6592 TCGA-50-6593 
       55.33       221.33         9.86         8.09        25.55        11.05 
TCGA-50-6597 TCGA-50-6673 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       41.69         0.72        34.29        13.94        35.21        23.05 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6970 TCGA-55-6975 TCGA-55-6983 TCGA-55-7281 
       38.73        45.21        15.25         3.88        60.03         0.59 
TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 
        1.15         0.13         1.32         1.28         0.53         6.48 
TCGA-55-7911 TCGA-55-7995 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 
       17.65         0.16        23.64        17.98         1.08         2.17 
TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 
       22.16         0.76         0.26        17.72         6.64         0.49 
TCGA-55-8620 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8402 
        2.17         0.92        15.81        19.99        17.95        49.25 
TCGA-62-A46R TCGA-62-A471 TCGA-64-1678 TCGA-64-1680 TCGA-67-3770 TCGA-67-3771 
       56.71        40.96        39.09        37.02         1.02        20.05 
TCGA-67-6217 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
       13.87        13.61         7.56         6.05         4.41        12.56 
TCGA-69-8255 TCGA-73-4662 TCGA-73-4675 TCGA-78-7149 TCGA-78-7150 TCGA-78-7155 
        4.24        82.68        30.31       129.53        21.90        38.50 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 
       22.92       104.19       238.29        88.14        26.53        26.01 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 
       50.24       232.18        77.59       110.50        12.36         5.88 
TCGA-86-7713 TCGA-86-8055 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 
       38.04         4.08        14.60         1.15        30.84        28.34 
TCGA-91-6829 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JN 
       41.36         2.60        13.71        12.23        27.68        23.61 
TCGA-93-A4JO TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-97-7547 TCGA-97-7938 
        1.08        16.54        18.67        12.39        64.60         0.59 
TCGA-97-8179 TCGA-97-A4M3 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8194 TCGA-L9-A444 
       14.30        17.75        34.85        21.57        23.80        10.09 
TCGA-L9-A5IP TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-NJ-A4YQ 
        1.91        27.19         2.76        41.59         2.43        29.13 
TCGA-O1-A52J 
       59.11 

$`2Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
       50.07        14.01         9.96        24.03        47.05         8.02 
TCGA-05-4403 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       19.00        29.98        12.00        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 
       25.02        24.00        15.02        15.02         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         0.46         5.98        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       49.05        28.41        11.64        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       46.98        44.94        38.10        42.08        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-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU 
        8.55        15.98         9.44        11.08        13.64        13.45 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 
       76.21        35.54        46.72        32.84        29.75        55.89 
TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       53.29        17.16        11.64        22.26        22.26       156.66 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
       73.12        62.24        28.90         8.55        40.41        37.32 
TCGA-49-AARO TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      123.58       164.12        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 TCGA-50-6595 
       25.12        22.55        42.35         3.91        12.16         6.21 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1595 
       10.13        36.99         7.59        27.25        30.54        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        0.82        48.49         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 
       32.71        24.99        40.54       107.21        70.26         7.99 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        0.20         3.12        23.18         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
        1.78        18.64         6.15        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
        3.29        19.66        19.73         5.06         0.13        15.65 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
        1.51        15.42         1.45         0.95         0.36         0.49 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
        0.30         0.10         4.80        17.62         1.58         1.61 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       19.59        20.19         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       88.64        47.80        19.53        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       13.61        39.25        29.92        56.81        20.65        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-67-3772 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-69-7763 TCGA-69-7765 TCGA-69-7979 
        4.64         6.64         6.12        22.68         5.42         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
       14.01        13.45        25.91        17.16         2.01        52.60 
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-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       39.09        50.33        11.18       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       19.27        20.58        39.95       119.51        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 
        5.88        64.90         9.57         8.48        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 TCGA-83-5908 
       53.33        39.35        10.55        39.75        10.55        27.09 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        20.55        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       37.74         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 
       31.04        31.20        23.05        21.47        13.91        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-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 
       26.47        10.62         1.97        10.19         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
       22.45        17.46         6.12        19.00        17.29        41.82 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
        2.86        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       18.18        19.89        31.69        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        5.95         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       19.76        20.52        20.84        18.67        20.68        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        21.63        24.30        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 
       32.48        19.00        14.30         6.35        14.53        21.83 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       18.58        15.65        38.63        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA 
       37.35        86.04        58.85         5.49         5.29        31.23 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       10.09        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        62.60         0.13         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.26         0.43        19.82        20.28        16.87 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.00              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           238.29            164.12 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            17.75             20.52 
[1] "0.0 - 238.3 (17.8)" "0.1 - 164.1 (20.5)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         3       38       35        0        16        14
  2Q GAIN WILD-TYPE       2       97      104        1        36        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2Q GAIN MUTATED           22          4        9
  2Q GAIN WILD-TYPE         50          7       17
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                38                97
  STAGE IB                35               104
  STAGE II                 0                 1
  STAGE IIA               16                36
  STAGE IIB               14                58
  STAGE IIIA              22                50
  STAGE IIIB               4                 7
  STAGE IV                 9                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
  2Q GAIN MUTATED    46  76  13   5
  2Q GAIN WILD-TYPE 124 202  33  14
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              46               124
  T2              76               202
  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
  2Q GAIN MUTATED    87  28    24
  2Q GAIN WILD-TYPE 245  68    52
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                 87               245
  N1                 28                68
  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    97   9
  2Q GAIN WILD-TYPE 252  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     97    9
  2Q GAIN WILD-TYPE  252   16
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              97               252
  1               9                16
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    76  65
  2Q GAIN WILD-TYPE 199 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     76   65
  2Q GAIN WILD-TYPE  199  175
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              76               199
  MALE                65               175
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    87  21
  2Q GAIN WILD-TYPE 273  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     87   21
  2Q GAIN WILD-TYPE  273   33
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               87               273
  YES              21                33
[1] 2 2
[1] FALSE
D4V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2Q GAIN MUTATED                            4
  2Q GAIN WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2Q GAIN MUTATED                                  38
  2Q GAIN WILD-TYPE                                68
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                   85
  2Q GAIN WILD-TYPE                                                235
                   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                                    0
  2Q GAIN WILD-TYPE                                  3
                   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                               38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              85
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  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                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               235
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     14
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  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   101   5   2   7
  2Q GAIN WILD-TYPE 242   7   2  19
D4V13, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0             101               242
  R1               5                 7
  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                          12   104
  2Q GAIN WILD-TYPE                        39   285
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                     12                39
  WHITE                                        104               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"
D4V15, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4  98
  2Q GAIN WILD-TYPE   3 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   98
  2Q GAIN WILD-TYPE    3  284
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO              98               284
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    23  15
  3P GAIN WILD-TYPE 302 152
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               38               454 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               15               152 
$`3P GAIN MUTATED`
TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4434 TCGA-05-5428 TCGA-35-5375 
       29.98        30.02        26.01        15.02        22.03         8.68 
TCGA-44-A47B TCGA-49-4487 TCGA-49-4488 TCGA-49-4507 TCGA-49-AARQ TCGA-50-5946 
        9.44        28.11        28.57         8.81       221.33        22.55 
TCGA-53-A4EZ TCGA-55-6972 TCGA-55-7903 TCGA-55-7995 TCGA-64-1677 TCGA-64-5775 
       35.21        48.49        18.64         0.16        20.65         2.04 
TCGA-69-7760 TCGA-69-7974 TCGA-69-7978 TCGA-69-A59K TCGA-73-4676 TCGA-78-7143 
        6.64         6.05         4.41        17.16         9.24       163.10 
TCGA-78-7145 TCGA-78-8662 TCGA-86-7711 TCGA-86-7953 TCGA-86-8074 TCGA-86-8075 
       27.16       110.50        34.39        32.78         0.79        22.82 
TCGA-91-6828 TCGA-93-A4JQ TCGA-95-8494 TCGA-97-8176 TCGA-J2-A4AD TCGA-L9-A443 
       10.62        17.29         2.76        15.39        18.08         6.35 
TCGA-L9-A444 TCGA-MN-A4N4 
       10.09        38.63 

$`3P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 
       20.05         2.99        14.96         9.01        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        25.02        24.00        15.02         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-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       11.64        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
       46.98        44.42        44.94        38.10        42.08        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-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 
       11.08        11.54        13.64        13.45        76.21        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
       35.54        46.72        14.07        32.84        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       22.26        22.26       156.66        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41        37.32       123.58       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        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
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-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
       34.29        30.54        13.94        23.05        38.73        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       45.21         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.12         0.79         1.78         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15        19.82        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       20.19        19.99        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-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-64-1676 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         1.02 
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-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64        13.87         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        7.56         2.93        12.56        14.01        13.45         4.24 
TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
       25.91         2.01        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31        30.31         1.25        39.09        50.33 
TCGA-73-A9RS TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       11.18         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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 
       10.55        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         1.15        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-91-6836 
       26.47        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7043 
        6.12        23.61         1.08        19.00        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       17.92         5.39        18.12        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
        1.45        21.57        21.63        24.30        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       32.48        19.00        14.30        14.53         1.91        21.83 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       18.58        15.65        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        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 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.16              0.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           221.33            238.29 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            18.36             20.02 
[1] "0.2 - 221.3 (18.4)" "0.0 - 238.3 (20.0)"
[1] "hr=" "1.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         1       12        7        0         6         6
  3P GAIN WILD-TYPE       4      123      132        1        46        66
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3P GAIN MUTATED            6          0        2
  3P GAIN WILD-TYPE         66         11       24
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                12               123
  STAGE IB                 7               132
  STAGE II                 0                 1
  STAGE IIA                6                46
  STAGE IIB                6                66
  STAGE IIIA               6                66
  STAGE IIIB               0                11
  STAGE IV                 2                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
  3P GAIN MUTATED    14  18   5   3
  3P GAIN WILD-TYPE 156 260  41  16
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              14               156
  T2              18               260
  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
  3P GAIN MUTATED    24  13     3
  3P GAIN WILD-TYPE 308  83    73
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                 24               308
  N1                 13                83
  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"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    27   2
  3P GAIN WILD-TYPE 322  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     27    2
  3P GAIN WILD-TYPE  322   23
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              27               322
  1               2                23
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    19  21
  3P GAIN WILD-TYPE 256 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     19   21
  3P GAIN WILD-TYPE  256  219
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              19               256
  MALE                21               219
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    26   8
  3P GAIN WILD-TYPE 334  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26    8
  3P GAIN WILD-TYPE  334   46
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               26               334
  YES               8                46
[1] 2 2
[1] FALSE
D5V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3P GAIN MUTATED                            4
  3P GAIN WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3P GAIN MUTATED                                  10
  3P GAIN WILD-TYPE                                96
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                   24
  3P GAIN WILD-TYPE                                                296
                   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                                0
  3P GAIN WILD-TYPE                              2
                   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                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              24
  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                                     0
                                                    clus
vv                                                   3P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               296
  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                                      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 317  10   3  21
D5V13, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              26               317
  R1               2                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
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           2    30
  3P GAIN WILD-TYPE                        49   359
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                      2                49
  WHITE                                         30               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"
D5V15, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  27
  3P GAIN WILD-TYPE   5 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   27
  3P GAIN WILD-TYPE    5  355
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              27               355
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    57  28
  3Q GAIN WILD-TYPE 268 139
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               85               407 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               28               139 
$`3Q GAIN MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4402 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 
       19.96        45.01         8.02        29.98        30.02        26.01 
TCGA-05-4434 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-5375 TCGA-38-4626 
       15.02        29.00        22.03         9.04         8.68       120.79 
TCGA-38-4630 TCGA-44-5643 TCGA-44-6145 TCGA-44-7660 TCGA-44-7670 TCGA-44-A47B 
       35.28        33.30        19.56        19.46        29.00         9.44 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4507 TCGA-49-6743 TCGA-49-AAR0 TCGA-49-AARN 
       28.11        28.57         8.81        53.29       156.66        37.32 
TCGA-49-AARQ TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5946 TCGA-53-A4EZ 
      221.33         8.09        14.27         9.37        22.55        35.21 
TCGA-55-1594 TCGA-55-6972 TCGA-55-6984 TCGA-55-7724 TCGA-55-7726 TCGA-55-7903 
       38.73        48.49        24.99        23.18         1.28        18.64 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8205 TCGA-55-8614 TCGA-55-A490 TCGA-55-A491 
        0.16        29.72         1.08        17.62         1.58        20.58 
TCGA-62-A46O TCGA-64-1677 TCGA-64-1679 TCGA-64-5815 TCGA-69-7760 TCGA-69-7978 
       47.80        20.65        81.80        28.47         6.64         4.41 
TCGA-69-7980 TCGA-69-A59K TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
       12.56        17.16         9.24        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7154 TCGA-78-8662 TCGA-86-7711 TCGA-86-7953 TCGA-86-8074 
        5.69        19.50       110.50        34.39        32.78         0.79 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 TCGA-91-6828 
       22.82        31.04        21.47        30.84        28.34        10.62 
TCGA-91-6830 TCGA-91-6835 TCGA-93-A4JN TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
        1.97         2.60        23.61        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-8494 TCGA-97-8176 TCGA-97-A4LX TCGA-J2-A4AD TCGA-L9-A443 
       15.68         2.76        15.39        20.19        18.08         6.35 
TCGA-L9-A444 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4TF TCGA-NJ-A4YF 
       10.09        15.65        38.63        86.14        11.05        71.05 
TCGA-S2-AA1A 
       16.87 

$`3Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       24.03        47.05        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
        9.01        12.00        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
       24.00        15.02         4.96         2.04         0.46         7.40 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 
        5.98        97.74        37.71        49.05        28.41        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       44.61        14.73        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       44.42        44.94        38.10        42.08        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-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6147 
       26.56        28.37        28.01        23.77         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        12.03         7.17        36.07        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.23        13.74        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
       12.66        35.54        46.72        14.07        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        16.04        55.33        17.16        11.64 
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 
       70.55        15.72        60.16        31.04        49.28         9.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       40.60        78.67        21.47         8.45        15.12        29.03 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 
       27.25        34.29        30.54        13.94        23.05        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       45.21         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        2.20        45.34        32.71        60.03        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
       70.26         0.59         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        3.12         1.32         1.28         1.12         0.79         1.78 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 
        0.53         6.48        17.65         6.15        19.82        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 
       17.72         0.30         0.10         4.80         6.64         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       21.40        19.59         0.92        15.81        20.19        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       17.95         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        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-64-1680 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-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       51.25         1.02        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64        13.87         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 
       13.61         5.42         7.56         6.05         2.93        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
       13.45         4.24        25.91         2.01        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       82.68        26.30        15.35         4.31        30.31         1.25 
TCGA-73-7498 TCGA-73-A9RS TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       39.09        11.18        19.27        20.58       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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36         5.88        31.13        38.04        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-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       32.65        31.20        23.05        14.60         1.15        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-91-6829 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
       13.64        26.47        41.36        10.19        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 
        1.08        19.00        41.82        18.67        12.39        15.65 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       27.29        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92         5.39        18.12        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.58        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
        1.45        21.57        21.63        24.30        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       32.48        19.00        14.30        14.53         1.91        21.83 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       18.58        27.19         2.76        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
        2.43        10.09        29.46        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.26         0.43        19.82        20.28        59.11 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.16              0.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           221.33            238.29 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            20.58             19.89 
[1] "0.2 - 221.3 (20.6)" "0.0 - 238.3 (19.9)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         2       25       21        0        12        11
  3Q GAIN WILD-TYPE       3      110      118        1        40        61
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3Q GAIN MUTATED           13          0        4
  3Q GAIN WILD-TYPE         59         11       22
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                25               110
  STAGE IB                21               118
  STAGE II                 0                 1
  STAGE IIA               12                40
  STAGE IIB               11                61
  STAGE IIIA              13                59
  STAGE IIIB               0                11
  STAGE IV                 4                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
  3Q GAIN MUTATED    32  47   7   2
  3Q GAIN WILD-TYPE 138 231  39  17
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              32               138
  T2              47               231
  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
  3Q GAIN MUTATED    56  20    11
  3Q GAIN WILD-TYPE 276  76    65
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                 56               276
  N1                 20                76
  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"
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  42
  3Q GAIN WILD-TYPE 229 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     46   42
  3Q GAIN WILD-TYPE  229  198
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              46               229
  MALE                42               198
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    61  11
  3Q GAIN WILD-TYPE 299  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     61   11
  3Q GAIN WILD-TYPE  299   43
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               61               299
  YES              11                43
[1] 2 2
[1] FALSE
D6V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3Q GAIN MUTATED                            5
  3Q GAIN WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3Q GAIN MUTATED                                  20
  3Q GAIN WILD-TYPE                                86
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                   56
  3Q GAIN WILD-TYPE                                                264
                   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                             3
  3Q GAIN WILD-TYPE                            2                            20
                   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                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              56
  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                                    3
  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)               264
  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                                     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"
D6V11, continuous
D6V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    58   3   2   7
  3Q GAIN WILD-TYPE 285   9   2  19
D6V13, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              58               285
  R1               3                 9
  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                           9    64
  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                      9                42
  WHITE                                         64               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  63
  3Q GAIN WILD-TYPE   4 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   63
  3Q GAIN WILD-TYPE    4  319
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              63               319
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    42  29
  4P GAIN WILD-TYPE 283 138
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               71               421 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               29               138 
$`4P GAIN MUTATED`
TCGA-05-4432 TCGA-05-5423 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-44-7661 
       25.02         4.96        49.05        28.41        11.64        12.03 
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-55-1595 
       12.16        10.13        34.29        13.94        38.73        48.62 
TCGA-55-6712 TCGA-55-7573 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
        0.79         0.13         3.29        19.73         0.13        23.64 
TCGA-55-8302 TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A57B TCGA-62-8402 
        0.76         1.58        19.59         0.92        17.95        49.25 
TCGA-62-A46O TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 TCGA-64-1681 TCGA-69-7980 
       47.80        40.96        56.81        37.02        38.37        12.56 
TCGA-69-8253 TCGA-78-7143 TCGA-78-7145 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 
       14.01       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-91-6836 TCGA-91-6848 TCGA-93-A4JP TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VP 
       13.71         7.36        19.00        15.65         2.76        19.89 
TCGA-97-7937 TCGA-97-8179 TCGA-97-8552 TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4SW 
        5.95        14.30        20.58         1.91         2.76        58.45 
TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4TF TCGA-NJ-A4YF 
       49.35        86.04        58.85        11.05        71.05 

$`4P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       30.02        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02        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-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       37.71        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
       43.53        46.98        44.42        44.94        38.10        42.08 
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-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 
        9.44        11.08        11.54        13.64        76.21        28.11 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       17.16        11.64        22.26       156.66        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARR 
       28.90         8.55        40.41        37.32       123.58       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        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 
       25.12        22.55        42.35        11.05         6.21        41.69 
TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ 
        0.72        36.99         7.59        27.25        30.54        35.21 
TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       23.05        45.21         2.86         0.07        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.20         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        1.12         0.79         1.78        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
       19.66         5.06        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16        15.42         1.45         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 
       16.93        22.65        20.71        21.40        20.58        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       88.64        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
       13.61        39.25        29.92        20.65        39.09        81.80 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
        1.02        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
       13.45         4.24        25.91        17.16         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 
        9.24         1.25        39.09        50.33        11.18         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 
       19.27        20.58       129.53        39.95        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7536 
       64.90        22.92         9.57       104.19         8.48         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       53.33        39.35        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       34.39        38.04        20.55        19.89        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 
        4.57        24.33         0.79        22.82        32.65        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        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-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        17.29        41.82        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
       18.67        12.39        15.68        27.29        21.40        18.18 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       31.69        64.60        63.52        43.79        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       16.41        21.60        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       36.76         1.45        21.57        21.63        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
       10.09        14.53        21.83        18.58        15.65        27.19 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       38.63        86.14        37.35         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23         2.43        10.09        29.46        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       11.15        19.13        73.91        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.13              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           238.29            232.18 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            22.26             19.82 
[1] "0.1 - 238.3 (22.3)" "0.0 - 232.2 (19.8)"
[1] "hr=" "1"  
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         3       15       22        0         7        12
  4P GAIN WILD-TYPE       2      120      117        1        45        60
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4P GAIN MUTATED            9          1        8
  4P GAIN WILD-TYPE         63         10       18
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                15               120
  STAGE IB                22               117
  STAGE II                 0                 1
  STAGE IIA                7                45
  STAGE IIB               12                60
  STAGE IIIA               9                63
  STAGE IIIB               1                10
  STAGE IV                 8                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
  4P GAIN MUTATED    19  49   6   2
  4P GAIN WILD-TYPE 151 229  40  17
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              19               151
  T2              49               229
  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    51  14    11
  4P GAIN WILD-TYPE 281  82    65
D7V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0                 51               281
  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    52   8
  4P GAIN WILD-TYPE 297  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     52    8
  4P GAIN WILD-TYPE  297   17
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              52               297
  1               8                17
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    42  35
  4P GAIN WILD-TYPE 233 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     42   35
  4P GAIN WILD-TYPE  233  205
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              42               233
  MALE                35               205
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    56   5
  4P GAIN WILD-TYPE 304  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     56    5
  4P GAIN WILD-TYPE  304   49
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               56               304
  YES               5                49
[1] 2 2
[1] FALSE
D7V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4P GAIN MUTATED                            2
  4P GAIN WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4P GAIN MUTATED                                  11
  4P GAIN WILD-TYPE                                95
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                   56
  4P GAIN WILD-TYPE                                                264
                   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                                               0
  4P GAIN WILD-TYPE                                             5
                   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)              56
  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                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   4P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               264
  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                      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"
D7V11, continuous
D7V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    52   2   0   3
  4P GAIN WILD-TYPE 291  10   4  23
D7V13, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              52               291
  R1               2                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
  4P GAIN MUTATED                                  0     3
  4P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           6    60
  4P GAIN WILD-TYPE                        45   329
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                      6                45
  WHITE                                         60               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"
D7V15, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  50
  4P GAIN WILD-TYPE   6 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   50
  4P GAIN WILD-TYPE    6  332
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              50               332
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    25  12
  4Q GAIN WILD-TYPE 300 155
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               37               455 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               12               155 
$`4Q GAIN MUTATED`
TCGA-38-4628 TCGA-38-4629 TCGA-44-2659 TCGA-44-7661 TCGA-50-6591 TCGA-50-6594 
       49.05        28.41        44.94        12.03         3.91        12.16 
TCGA-55-6712 TCGA-55-8089 TCGA-55-8091 TCGA-55-8096 TCGA-55-8614 TCGA-55-8615 
        0.79         3.29        19.73        23.64        17.62         0.49 
TCGA-55-A493 TCGA-55-A57B TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 
        0.92        17.95        49.25        40.96        56.81        37.02 
TCGA-69-7980 TCGA-69-8253 TCGA-78-7143 TCGA-78-7154 TCGA-78-7163 TCGA-78-7542 
       12.56        14.01       163.10        19.50       238.29        10.55 
TCGA-86-7953 TCGA-86-8278 TCGA-86-A456 TCGA-91-6836 TCGA-91-6848 TCGA-93-A4JP 
       32.78        31.04        29.46        13.71         7.36        19.00 
TCGA-95-7948 TCGA-95-8494 TCGA-97-8552 TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T4 
       15.65         2.76        20.58         2.76        49.35        86.04 
TCGA-MP-A4T6 
       58.85 

$`4Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         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-38-4630 TCGA-38-4631 TCGA-38-4632 
       97.74       120.79        37.71        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       38.10        42.08        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-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        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-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        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-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       22.26        22.26       156.66        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
        8.55        40.41        37.32       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        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       25.12        22.55        42.35        25.55        11.05         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       34.29        30.54        13.94        35.21        23.05        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       48.62        45.21         2.86         0.07        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1.28         1.12         0.79         1.78        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 
       15.19        19.66         5.06         0.13        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 
        0.30         0.10         4.80         6.64         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       20.58        19.59        15.81        20.19        19.99         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-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       29.92        20.65        39.09        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         1.02 
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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 
        5.42         7.56         6.05         4.41         2.93        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
        4.24        25.91        17.16         2.01        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        50.33        11.18        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-78-7155 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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        38.04        20.55        19.89        35.24 
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-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       32.65        31.20        23.05        21.47        14.60         1.15 
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-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-91-6849 
        1.97        10.19         2.60        12.23        27.68         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JQ 
       22.45        17.46         6.12        23.61         1.08        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       27.29        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       14.30        21.60        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       36.76         1.45        21.57        21.63        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
       10.09        14.53         1.91        21.83        18.58        15.65 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 
       27.19        38.63        86.14        58.45        37.35         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        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        62.60         0.13         1.64        29.13         0.26 
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 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.49              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           238.29            232.18 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            19.50             20.05 
[1] "0.5 - 238.3 (19.5)" "0.0 - 232.2 (20.1)"
[1] "hr=" "1.3"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         2        6       15        0         3         9
  4Q GAIN WILD-TYPE       3      129      124        1        49        63
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4Q GAIN MUTATED            6          0        3
  4Q GAIN WILD-TYPE         66         11       23
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 6               129
  STAGE IB                15               124
  STAGE II                 0                 1
  STAGE IIA                3                49
  STAGE IIB                9                63
  STAGE IIIA               6                66
  STAGE IIIB               0                11
  STAGE IV                 3                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
  4Q GAIN MUTATED    11  27   5   0
  4Q GAIN WILD-TYPE 159 251  41  19
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              11               159
  T2              27               251
  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    26  10     7
  4Q GAIN WILD-TYPE 306  86    69
D8V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0                 26               306
  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    31   3
  4Q GAIN WILD-TYPE 318  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     31    3
  4Q GAIN WILD-TYPE  318   22
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              31               318
  1               3                22
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    22  22
  4Q GAIN WILD-TYPE 253 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     22   22
  4Q GAIN WILD-TYPE  253  218
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              22               253
  MALE                22               218
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    35   1
  4Q GAIN WILD-TYPE 325  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     35    1
  4Q GAIN WILD-TYPE  325   53
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               35               325
  YES               1                53
[1] 2 2
[1] FALSE
D8V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4Q GAIN MUTATED                            0
  4Q GAIN WILD-TYPE                         19
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4Q GAIN MUTATED                                   5
  4Q GAIN WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                   34
  4Q GAIN WILD-TYPE                                                286
                   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)              34
  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                                        19
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               286
  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    31   0   0   2
  4Q GAIN WILD-TYPE 312  12   4  24
D8V13, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              31               312
  R1               0                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
  4Q GAIN MUTATED                                  0     2
  4Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           3    32
  4Q GAIN WILD-TYPE                        48   357
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                      3                48
  WHITE                                         32               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"
D8V15, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0  31
  4Q GAIN WILD-TYPE   7 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   31
  4Q GAIN WILD-TYPE    7  351
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              31               351
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   168  88
  5P GAIN WILD-TYPE 157  79
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              256               236 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               88                79 
$`5P GAIN MUTATED`
TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4422 
        0.00        47.05         8.02        20.05         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-38-4629 
        0.46         8.68       120.79        37.71        49.05        28.41 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-44-2659 TCGA-44-3398 
       11.64        44.61        14.73        26.30        44.94        38.24 
TCGA-44-3919 TCGA-44-5644 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       33.73        28.37        21.63        32.45        61.28        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 
       19.46         7.17        36.07        18.87        29.00        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SS TCGA-49-4487 
       12.66         3.25        15.32        11.08        13.64        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
       28.57        12.66        46.72        14.07        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AAR4 
       55.89        53.29        55.33        11.64       156.66        28.90 
TCGA-49-AAR9 TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
        8.55         9.86        71.47        70.55        15.72        31.04 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 
       49.28         9.27        78.67        21.47         9.37        22.55 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 
        3.91        25.55        11.05        41.69        10.13        36.99 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
       34.29        30.54        13.94        23.05        38.73        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6970 TCGA-55-6972 TCGA-55-6979 TCGA-55-6980 
        2.86         0.07        15.25        48.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 
       45.34        60.03        40.54        70.26         0.20         0.13 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 
        3.12        23.18         1.28         1.28         1.12        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 
        6.48        17.65        19.73         0.13        23.64         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
        2.17        22.16         1.45         0.76         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.49        17.72         0.30         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.58         2.17        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       20.58         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8395 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U 
       39.98        88.64        49.25        47.80        54.35        67.96 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
       13.61        39.25        40.96        81.80        37.02        87.98 
TCGA-64-5778 TCGA-64-5781 TCGA-67-3770 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       42.90        51.25         1.02        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       13.87         6.64        22.68        13.61         5.42         7.56 
TCGA-69-8253 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4668 TCGA-73-4670 
       14.01        17.16         2.01        52.60        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 TCGA-78-7147 TCGA-78-7149 
       30.31         9.24        50.33       163.10        19.27       129.53 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7163 TCGA-78-7166 
      119.51        19.50        38.50        64.90       238.29         8.48 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 
       26.53        31.20         8.02        26.01        50.24       232.18 
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-86-7953 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         1.15         0.62        28.34 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-8499 
        3.81        10.62         1.97        13.71        12.23         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO 
        1.45        19.82        22.45        17.46         6.12         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
       19.00        17.29        41.82        18.67        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 
       27.29         2.76        31.69        64.60        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 
        5.95         0.59        17.92         5.39        15.39        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 
       20.58        21.44        19.76        20.68        34.85        21.57 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A5IP 
       24.30        18.08        35.47        19.00        10.09         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       21.83        18.58         2.76        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       86.04        58.85         5.49         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG 
       10.09        11.05        24.36        19.13        71.05        62.60 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

$`5P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 
        9.96        24.03        19.00        14.96         9.01        29.98 
TCGA-05-4425 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       21.99        26.01        25.02        24.00        15.02        15.02 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4630 
        9.04         2.04         7.40         5.98        97.74        35.28 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
        4.37        43.53        46.98        44.42        38.10        42.08 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 
       42.77         3.19        25.02        37.15        38.89        34.06 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7661 
       27.78        23.15        23.18        63.72        16.44        12.03 
TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU 
       29.23         8.55        15.98         9.44        11.54        13.45 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6742 TCGA-49-6745 
       76.21        35.54        32.84         8.81        16.04        17.16 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARE TCGA-49-AARN 
       22.26        22.26        73.12        62.24        40.41        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5055 TCGA-50-5072 
      123.58       221.33       164.12        20.52        60.16         8.09 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       14.27        40.60         8.45        15.12        29.03        25.12 
TCGA-50-6590 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8459 TCGA-50-8460 
       42.35        12.16         6.21         0.72         7.59        27.25 
TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       35.21        45.21        32.65         0.79        42.51        40.73 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6982 TCGA-55-6984 TCGA-55-6986 
        0.82         3.88         5.49        32.71        24.99       107.21 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 
        0.59         1.15         7.99         1.32         0.79         1.78 
TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        0.53         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        3.29        19.66         5.06        15.65        17.98         1.08 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 
       15.42         0.95         0.10         4.80         1.61        16.93 
TCGA-55-A492 TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 TCGA-62-A46P TCGA-62-A46R 
       19.59        17.95        42.38        14.60        19.53        56.71 
TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1681 
       72.30        29.92        56.81        20.65        39.09        38.37 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
        2.04        28.41        28.47        20.05        18.84        12.66 
TCGA-67-4679 TCGA-69-7761 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       14.73         6.12         6.05         4.41         2.93        12.56 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
       13.45         4.24        25.91        23.38        82.68        26.30 
TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
        1.25        39.09        11.18        27.16         5.69        20.58 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 
       21.90        39.95        32.09         5.88        22.92         9.57 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
      104.19        88.14        53.33        39.35        10.55        39.75 
TCGA-78-8660 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
       10.55        31.13        38.04        20.55        19.89        35.24 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8668 TCGA-86-8669 
        4.57         0.79        32.65        31.04        13.91        30.84 
TCGA-86-8671 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       27.58        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       41.36        10.19         2.60        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-93-A4JN TCGA-95-7043 TCGA-95-7562 
       16.18        16.60        14.27        23.61        16.54         2.86 
TCGA-95-7944 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7941 
       12.39        21.40        18.18        19.89        63.52         0.72 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4LX TCGA-97-A4M2 
       18.67        18.12        16.41        14.30        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       17.75        20.84        18.67        24.56        36.76         1.45 
TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W 
       21.63        23.80        32.48        14.30         6.35        14.53 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T9 TCGA-MP-A4TE 
       15.65        27.19        38.63        86.14        41.59        29.46 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       14.10        11.15        73.91         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O 
        0.26         0.43 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              0.0               0.1 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           238.29            221.33 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           20.020            19.925 
[1] "0.0 - 238.3 (20.0)" "0.1 - 221.3 (19.9)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         2       70       73        0        33        32
  5P GAIN WILD-TYPE       3       65       66        1        19        40
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5P GAIN MUTATED           38          8       14
  5P GAIN WILD-TYPE         34          3       12
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                70                65
  STAGE IB                73                66
  STAGE II                 0                 1
  STAGE IIA               33                19
  STAGE IIB               32                40
  STAGE IIIA              38                34
  STAGE IIIB               8                 3
  STAGE IV                14                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    92 147  20   9
  5P GAIN WILD-TYPE  78 131  26  10
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              92                78
  T2             147               131
  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
  5P GAIN MUTATED   170  51    44
  5P GAIN WILD-TYPE 162  45    32
D9V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                170               162
  N1                 51                45
  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   177  13
  5P GAIN WILD-TYPE 172  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    177   13
  5P GAIN WILD-TYPE  172   12
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             177               172
  1              13                12
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   151 119
  5P GAIN WILD-TYPE 124 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    151  119
  5P GAIN WILD-TYPE  124  121
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE             151               124
  MALE               119               121
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   189  29
  5P GAIN WILD-TYPE 171  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    189   29
  5P GAIN WILD-TYPE  171   25
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              189               171
  YES              29                25
[1] 2 2
[1] FALSE
D9V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5P GAIN MUTATED                            9
  5P GAIN WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5P GAIN MUTATED                                  53
  5P GAIN WILD-TYPE                                53
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                  177
  5P GAIN WILD-TYPE                                                143
                   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                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             177
  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                                 53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               143
  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   183   6   2  13
  5P GAIN WILD-TYPE 160   6   2  13
D9V13, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             183               160
  R1               6                 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
  5P GAIN MUTATED                                  1     4
  5P GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          25   208
  5P GAIN WILD-TYPE                        26   181
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                26
  WHITE                                        208               181
[1] 4 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     3 204
  5P GAIN WILD-TYPE   4 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  204
  5P GAIN WILD-TYPE    4  178
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             204               178
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    76  41
  5Q GAIN WILD-TYPE 249 126
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              117               375 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               41               126 
$`5Q GAIN MUTATED`
TCGA-05-4398 TCGA-05-4402 TCGA-05-4426 TCGA-05-5423 TCGA-35-3615 TCGA-38-6178 
       47.05         8.02        26.01         4.96         0.46        14.73 
TCGA-38-7271 TCGA-44-2659 TCGA-44-3398 TCGA-44-6774 TCGA-44-6777 TCGA-44-7659 
       26.30        44.94        38.24        21.63        32.45        22.72 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47F TCGA-49-4490 TCGA-49-4501 
       13.74         3.25        15.32        11.08        12.66        46.72 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AAR9 TCGA-50-5051 
       29.75        53.29        11.64       156.66         8.55        15.72 
TCGA-50-5935 TCGA-50-6591 TCGA-50-6592 TCGA-50-6597 TCGA-50-8457 TCGA-53-7626 
       21.47         3.91        25.55        41.69        36.99        30.54 
TCGA-53-7813 TCGA-55-1595 TCGA-55-6543 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
       13.94        48.62         0.07        48.49         2.20        60.03 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7910 TCGA-55-7911 TCGA-55-8091 TCGA-55-8206 
        0.13         3.12         6.48        17.65        19.73         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48Z 
        2.17        22.16         0.49         6.64        17.62        21.40 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-64-1680 
        0.92        19.99        54.35        67.96        13.61        37.02 
TCGA-64-5775 TCGA-64-5781 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
        2.04        51.25         5.72         4.64        13.87         6.64 
TCGA-69-7763 TCGA-69-8253 TCGA-69-A59K TCGA-73-4670 TCGA-73-4675 TCGA-78-7143 
       22.68        14.01        17.16         4.31        30.31       163.10 
TCGA-78-7147 TCGA-78-7153 TCGA-78-7154 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 
       19.27       119.51        19.50       238.29        26.53        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-83-5908 TCGA-86-7711 TCGA-86-8055 
        8.02        26.01        50.24        27.09        34.39         4.08 
TCGA-86-8075 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-A4D0 TCGA-91-6836 
       22.82        23.05        21.47        14.60         3.81        13.71 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7947 
       19.82        22.45        17.46        19.00        17.29        15.68 
TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-8172 TCGA-97-8174 
       27.29         2.76        31.69        64.60        17.92         5.39 
TCGA-97-8176 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M7 TCGA-J2-A4AE 
       15.39        20.58        21.44        19.76        20.68        35.47 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA 
       49.35        37.35        86.04         5.49         5.29        31.23 
TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A55R 
       10.09        11.05        24.36        19.13        62.60        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

$`5Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        0.00         9.96        24.03        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       35.28        11.64        44.61         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.42        38.10        42.08        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.89        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       23.15        23.18        63.72        61.28        16.44        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
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-49-4494 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-49-4514 TCGA-49-6742 TCGA-49-6744 
       32.84         8.81        29.46        55.89        16.04        55.33 
TCGA-49-6745 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       17.16        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       40.41        37.32       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        70.55        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 
        8.09         9.27        14.27        40.60        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 
       11.05        12.16         6.21         0.72        10.13         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
       27.25        34.29        35.21        23.05        38.73        45.21 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        2.86        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 
        0.82         3.88         5.49         7.79        45.34        32.71 
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         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.99         0.20         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7914 
        1.12         0.79         1.78        18.64         0.53         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        5.06         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 
       17.72         0.30         0.10         4.80         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
        1.61         2.17        16.93        22.65        20.71         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 
       20.58        19.59        15.81        20.19        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-A46R TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       19.53        56.71        72.30        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       56.81        20.65        39.09        81.80        38.37        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        28.47         1.02        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
       14.04        12.66        14.73         6.12        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
        7.56         6.05         4.41         2.93        12.56        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.24        25.91         2.01        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       26.30        15.35         9.24         1.25        39.09        50.33 
TCGA-73-A9RS TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       11.18        27.16         5.69        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       39.95        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 
        9.57       104.19         8.48        88.14        53.33        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       10.55       232.18        39.75        77.59        10.55       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-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       32.65        31.04        31.20         1.15        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-91-6831 
       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-91-7771 
        2.60        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JN 
       16.60        14.27         1.18         1.45         6.12        23.61 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
        1.08        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 
       15.65        21.40        18.18        19.89        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       25.48         5.95         0.59         0.72        18.67        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       16.41        14.30        21.60        20.19        20.52        17.75 
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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG 
       21.57        21.63        24.30        23.80        18.08        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       19.00        14.30         6.35        10.09        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       21.83        18.58        15.65        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE 
       86.14        58.45        58.85        41.59         2.43        29.46 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP 
       14.10        11.15        73.91        71.05         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       29.13         0.26         0.43 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.07              0.00 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           238.29            232.18 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            19.82             20.05 
[1] "0.1 - 238.3 (19.8)" "0.0 - 232.2 (20.1)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         1       34       32        0        14        13
  5Q GAIN WILD-TYPE       4      101      107        1        38        59
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5Q GAIN MUTATED           21          3        7
  5Q GAIN WILD-TYPE         51          8       19
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                34               101
  STAGE IB                32               107
  STAGE II                 0                 1
  STAGE IIA               14                38
  STAGE IIB               13                59
  STAGE IIIA              21                51
  STAGE IIIB               3                 8
  STAGE IV                 7                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
  5Q GAIN MUTATED    43  67  10   4
  5Q GAIN WILD-TYPE 127 211  36  15
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              43               127
  T2              67               211
  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
  5Q GAIN MUTATED    81  20    21
  5Q GAIN WILD-TYPE 251  76    55
D10V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                 81               251
  N1                 20                76
  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    84   7
  5Q GAIN WILD-TYPE 265  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     84    7
  5Q GAIN WILD-TYPE  265   18
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              84               265
  1               7                18
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    75  50
  5Q GAIN WILD-TYPE 200 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     75   50
  5Q GAIN WILD-TYPE  200  190
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              75               200
  MALE                50               190
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    93  12
  5Q GAIN WILD-TYPE 267  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     93   12
  5Q GAIN WILD-TYPE  267   42
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               93               267
  YES              12                42
[1] 2 2
[1] FALSE
D10V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5Q GAIN MUTATED                            7
  5Q GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5Q GAIN MUTATED                                  22
  5Q GAIN WILD-TYPE                                84
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                   79
  5Q GAIN WILD-TYPE                                                241
                   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                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              79
  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                                 84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               241
  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    81   3   2   7
  5Q GAIN WILD-TYPE 262   9   2  19
D10V13, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              81               262
  R1               3                 9
  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    99
  5Q GAIN WILD-TYPE                        41   290
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                41
  WHITE                                         99               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"
D10V15, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  93
  5Q GAIN WILD-TYPE   6 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   93
  5Q GAIN WILD-TYPE    6  289
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              93               289
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    97  41
  6P GAIN WILD-TYPE 228 126
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              138               354 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               41               126 
$`6P GAIN MUTATED`
TCGA-05-4249 TCGA-05-4420 TCGA-05-4430 TCGA-05-5425 TCGA-35-3615 TCGA-35-5375 
       50.07        29.98        25.02        29.00         0.46         8.68 
TCGA-38-4625 TCGA-38-4628 TCGA-44-2659 TCGA-44-6774 TCGA-44-7662 TCGA-44-7667 
       97.74        49.05        44.94        21.63         7.17        36.07 
TCGA-44-7670 TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4510 TCGA-49-6742 
       29.00        13.45        28.11        12.66        29.46        16.04 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR0 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
       11.64        22.26       156.66        14.27        78.67         9.37 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6673 TCGA-50-7109 
       25.12        22.55        42.35         3.91         0.72        10.13 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 
       34.29        13.94        35.21        23.05        48.62        45.21 
TCGA-55-6642 TCGA-55-6970 TCGA-55-7573 TCGA-55-7903 TCGA-55-7995 TCGA-55-8085 
       32.65        15.25         0.13        18.64         0.16        29.72 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8507 
       15.65        17.98         1.08         1.51        22.16         0.26 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 
        0.30         0.10         6.64        17.62         0.49         2.17 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 
       22.65        20.71         1.58         4.57        14.60        88.64 
TCGA-62-A46P TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1680 
       19.53        72.30        39.25        40.96        20.65        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-73-4662 TCGA-73-4668 
       13.61         5.42         2.93         4.24        82.68        15.35 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7147 TCGA-78-7149 
        4.31         1.25        39.09        50.33        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-78-7633 TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 
       26.01        10.55        50.24        77.59       110.50         5.88 
TCGA-86-7954 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8674 
       19.89         0.79        22.82        31.20        21.47        26.50 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 
       10.19         2.60        13.71        27.68         7.36         1.18 
TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-97-7546 
       23.61        19.00         2.86        18.67        12.39        31.69 
TCGA-97-7553 TCGA-97-7938 TCGA-97-8171 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       43.79         0.59        18.67        15.39        16.41        14.30 
TCGA-97-A4M1 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AE 
       19.76        20.68        34.85        21.57        23.80        35.47 
TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T6 
       10.09        18.58        38.63         2.76        86.14        58.85 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-O1-A52J 
       10.09        29.46         1.64         0.26        20.28        59.11 

$`6P GAIN WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96         9.01        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        26.01        25.02        24.00        15.02        15.02 
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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
      120.79        37.71        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       38.10        42.08        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-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 
       22.72        19.46        12.03        18.87        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 TCGA-49-4494 
       11.08        11.54        13.64        76.21        28.57        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
       46.72        14.07        32.84         8.81        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       53.29        55.33        17.16        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       28.90         8.55        40.41        37.32       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        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
       60.16        31.04        49.28         8.09         9.27        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6592 TCGA-50-6593 
       21.47         8.45        15.12        29.03        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21        41.69        36.99         7.59        27.25 
TCGA-53-7626 TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       30.54        38.73         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        0.79         1.78         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       19.82        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        0.13        23.64         2.17        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8513 TCGA-55-8616 
        0.95         0.36         0.49        17.72         4.80         1.58 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
        1.61        16.93        21.40        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        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         1.02        18.84        12.66 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 
        5.72         4.64        13.87         6.64         6.12         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        6.05         4.41        12.56        14.01        13.45        25.91 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 
       17.16         2.01        52.60        23.38        26.30        30.31 
TCGA-73-4676 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
        9.24        11.18       163.10        27.16         5.69        20.58 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95       119.51        19.50        32.09         5.88 
TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
       22.92       238.29         8.48        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
       39.35       232.18        39.75        10.55        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
       31.13        34.39        38.04        20.55        32.78        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
       37.74         4.08         4.57        24.33        32.65        31.04 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       23.05        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        29.46         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-91-6849 
       26.47        10.62        41.36         1.97        12.23         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       17.46         6.12         1.08        17.29        41.82        16.54 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
       19.89        64.60        63.52        25.48         5.95         0.72 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       17.92         5.39        18.12        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       21.44        20.52        17.75        20.84        18.67        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG 
       36.76         1.45        21.63        24.30        18.08        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       19.00        14.30         6.35        14.53         1.91        21.83 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       15.65        27.19        58.45        49.35        37.35        86.04 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
        5.49         5.29        41.59        31.23         2.43        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-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
       62.60         0.13        29.13         0.43        19.82        16.87 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              0.1               0.0 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           156.66            238.29 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           20.165            19.925 
[1] "0.1 - 156.7 (20.2)" "0.0 - 238.3 (19.9)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         1       42       36        0        14        14
  6P GAIN WILD-TYPE       4       93      103        1        38        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6P GAIN MUTATED           19          4       12
  6P GAIN WILD-TYPE         53          7       14
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                42                93
  STAGE IB                36               103
  STAGE II                 0                 1
  STAGE IIA               14                38
  STAGE IIB               14                58
  STAGE IIIA              19                53
  STAGE IIIB               4                 7
  STAGE IV                12                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    51  75   9   6
  6P GAIN WILD-TYPE 119 203  37  13
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              51               119
  T2              75               203
  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    21
  6P GAIN WILD-TYPE 237  73    55
D11V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                 95               237
  N1                 23                73
  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"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    97  11
  6P GAIN WILD-TYPE 252  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     97   11
  6P GAIN WILD-TYPE  252   14
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              97               252
  1              11                14
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    72  71
  6P GAIN WILD-TYPE 203 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     72   71
  6P GAIN WILD-TYPE  203  169
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              72               203
  MALE                71               169
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    98  17
  6P GAIN WILD-TYPE 262  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     98   17
  6P GAIN WILD-TYPE  262   37
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               98               262
  YES              17                37
[1] 2 2
[1] FALSE
D11V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6P GAIN MUTATED                            9
  6P GAIN WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6P GAIN MUTATED                                  28
  6P GAIN WILD-TYPE                                78
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                   88
  6P GAIN WILD-TYPE                                                232
                   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                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              88
  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                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               232
  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    97   2   0   7
  6P GAIN WILD-TYPE 246  10   4  19
D11V13, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              97               246
  R1               2                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   118
  6P GAIN WILD-TYPE                        42   271
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                42
  WHITE                                        118               271
[1] 4 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     4 109
  6P GAIN WILD-TYPE   3 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4  109
  6P GAIN WILD-TYPE    3  273
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             109               273
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    43  17
  6Q GAIN WILD-TYPE 282 150
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               60               432 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17               150 
$`6Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4420 TCGA-05-4432 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
       50.07        29.98        25.02         8.68        97.74        49.05 
TCGA-44-7667 TCGA-44-7670 TCGA-49-4490 TCGA-49-6742 TCGA-49-6767 TCGA-50-6591 
       36.07        29.00        12.66        16.04        22.26         3.91 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-7910 
       41.69         0.72        10.13        35.21        45.21         6.48 
TCGA-55-7995 TCGA-55-8097 TCGA-55-8206 TCGA-55-8507 TCGA-55-8511 TCGA-55-8514 
        0.16        15.65         1.51         0.26         0.30         6.64 
TCGA-55-8615 TCGA-55-8620 TCGA-62-8394 TCGA-62-A46P TCGA-62-A471 TCGA-67-3773 
        0.49         2.17         4.57        19.53        40.96        14.04 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-73-4677 TCGA-78-7167 
       22.68        13.61         5.42         2.93         1.25        88.14 
TCGA-78-7220 TCGA-78-7539 TCGA-78-8662 TCGA-86-6851 TCGA-86-7954 TCGA-86-8074 
       26.53        26.01       110.50         5.88        19.89         0.79 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-95-7562 TCGA-95-7944 
       13.71        27.68         7.36         1.18         2.86        12.39 
TCGA-97-7546 TCGA-97-8177 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AE 
       31.69        16.41        19.76        34.85        21.57        35.47 
TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4TD TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-O1-A52J 
       18.58        38.63        10.09         0.26        20.28        59.11 

$`6Q GAIN WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96         9.01        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        26.01        25.02        24.00        15.02        15.02 
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-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 
        7.40         5.98       120.79        37.71        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       11.64        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
       46.98        44.42        44.94        38.10        42.08        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-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       12.03         7.17        18.87        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
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-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        53.29        55.33        17.16        11.64 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26       156.66        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       40.41        37.32       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        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       22.55        42.35        25.55        11.05        12.16         6.21 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       23.05        38.73        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
       18.64         0.53        17.65         6.15        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       15.19         3.29        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       23.64        17.98         1.08         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.36         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
        0.10         4.80        17.62         1.58         1.61        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 
        0.92        15.81        20.19        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-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       56.81        20.65        39.09        81.80        37.02        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
        1.02        20.05        18.84        12.66        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 TCGA-69-7974 
        4.64        13.87         6.64         6.12         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        4.41        12.56        14.01        13.45         4.24        25.91 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
       17.16         2.01        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31        30.31         9.24        39.09        50.33 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       11.18       163.10        27.16         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-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
      238.29         8.48        31.20         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
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-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       32.78        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-86-8672 
       14.60         1.15        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-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
       12.23         1.15        16.18        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 
       19.00        17.29        41.82        16.54        18.67        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 
       14.30        21.60        20.58        20.19        21.44        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
       17.75        20.84        18.67        20.68        24.56        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG 
        1.45        21.63        24.30        23.80        18.08        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       19.00        14.30         6.35        10.09        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       21.83        15.65        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59        31.23         2.43        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        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        0.13         1.64        29.13         0.43        19.82        16.87 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.16              0.00 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           110.50            238.29 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           16.225            20.355 
[1] "0.2 - 110.5 (16.2)" "0.0 - 238.3 (20.4)"
[1] "hr=" "1"  
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         1       15       16        0         9         6
  6Q GAIN WILD-TYPE       4      120      123        1        43        66
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6Q GAIN MUTATED            8          1        5
  6Q GAIN WILD-TYPE         64         10       21
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                15               120
  STAGE IB                16               123
  STAGE II                 0                 1
  STAGE IIA                9                43
  STAGE IIB                6                66
  STAGE IIIA               8                64
  STAGE IIIB               1                10
  STAGE IV                 5                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  33   5   3
  6Q GAIN WILD-TYPE 151 245  41  16
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              19               151
  T2              33               245
  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
  6Q GAIN MUTATED    39  13     8
  6Q GAIN WILD-TYPE 293  83    68
D12V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0                 39               293
  N1                 13                83
  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"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    40   4
  6Q GAIN WILD-TYPE 309  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     40    4
  6Q GAIN WILD-TYPE  309   21
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              40               309
  1               4                21
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    34  27
  6Q GAIN WILD-TYPE 241 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     34   27
  6Q GAIN WILD-TYPE  241  213
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              34               241
  MALE                27               213
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    42   7
  6Q GAIN WILD-TYPE 318  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     42    7
  6Q GAIN WILD-TYPE  318   47
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               42               318
  YES               7                47
[1] 2 2
[1] FALSE
D12V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6Q GAIN MUTATED                            3
  6Q GAIN WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6Q GAIN MUTATED                                  12
  6Q GAIN WILD-TYPE                                94
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                   43
  6Q GAIN WILD-TYPE                                                277
                   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)              43
  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                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 94
  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                                 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 304  12   4  23
D12V13, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              39               304
  R1               0                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
  6Q GAIN MUTATED                                  0     1
  6Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           7    48
  6Q GAIN WILD-TYPE                        44   341
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                44
  WHITE                                         48               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"
D12V15, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  48
  6Q GAIN WILD-TYPE   5 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   48
  6Q GAIN WILD-TYPE    5  334
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              48               334
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   155  91
  7P GAIN WILD-TYPE 170  76
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              246               246 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               91                76 
$`7P GAIN MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 
        3.98        19.96        45.01        37.02         0.00        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 
        8.02        20.05         2.99        14.96         9.01        29.98 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
        4.96        29.00        22.03         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 
       97.74        37.71        49.05        28.41        11.64        44.61 
TCGA-38-6178 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-3396 TCGA-44-3919 
       14.73        44.42        44.94        38.10        37.15        33.73 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7660 
       28.37        23.77        23.18        32.45        16.44        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-A479 
       12.03         7.17        36.07        18.87        12.66        15.98 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       11.08        13.64        13.45        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       14.07        32.84        29.75        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ 
       22.26       156.66        28.90        40.41       123.58       221.33 
TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        9.86        71.47        70.55        60.16        31.04         8.09 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       78.67         8.45         9.37        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        11.05        12.16         6.21        41.69         0.72 
TCGA-53-7624 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 
       34.29        45.21         2.86         0.07         0.79         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 
       32.71        40.54        70.26         1.15         7.99         1.32 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 
       23.18         1.28         1.12         0.53         6.48        19.82 
TCGA-55-8085 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
       29.72        19.73         5.06        23.64         1.08         1.51 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
        1.45         0.76         0.95        17.72         0.30         6.64 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        0.49         1.58         2.17        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       19.59         0.92        15.81        19.99        17.95         4.57 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46Y 
       42.38        14.60        88.64        19.53        56.71        13.61 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 
       29.92        56.81        81.80        37.02        38.37        28.41 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 
       51.25         1.02        20.05        18.84        13.87         6.64 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
       13.61         5.42         6.05         2.93         4.24        17.16 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        2.01        52.60        82.68        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
        9.24        50.33        11.18       163.10        27.16        19.27 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 
       21.90        19.50        38.50        22.92         9.57       238.29 
TCGA-78-7535 TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
       31.20        39.35        10.55        77.59       110.50        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 
       12.36        31.13        38.04        32.78        35.24         4.08 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       24.33         0.79        22.82        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 
       14.60        13.91         0.62        28.34        29.46        13.64 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC 
       10.19         2.60        27.68         7.36        16.60         1.45 
TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 
       17.46         1.08        19.00        17.29        41.82         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7553 
       18.67        12.39        15.68         2.76        18.18        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       25.48         5.95        18.67        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 
       14.30        21.60        20.58        20.68        34.85        21.57 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A443 
       24.30        23.80        18.08        35.47        19.00         6.35 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       10.09        14.53         1.91        27.19        38.63         2.76 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       49.35        37.35        58.85         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J TCGA-S2-AA1A 
        2.43        10.09        19.13        71.05        59.11        16.87 

$`7P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 TCGA-05-4422 
       50.07        14.01         9.96        24.03        19.00        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       24.00        15.02        15.02         9.04         2.04         0.46 
TCGA-38-4626 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
      120.79        35.28        26.30         4.37        43.53        46.98 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-3917 
       42.08        42.77         3.19        25.02        38.24        38.89 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
       34.06        26.56        33.30        28.01        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 
       27.78        23.15        21.63        63.72        61.28        22.72 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A 
       29.00        29.23        13.74         3.25         8.55        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4487 TCGA-49-4501 TCGA-49-4507 
        9.44        11.54        76.21        28.11        46.72         8.81 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR2 
       29.46        55.89        16.04        53.29        55.33        73.12 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARR TCGA-50-5044 TCGA-50-5051 
       62.24         8.55        37.32       164.12        20.52        15.72 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5939 
       49.28         9.27        14.27        40.60        21.47        15.12 
TCGA-50-5942 TCGA-50-6592 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       29.03        25.55        10.13        36.99         7.59        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
       30.54        13.94        35.21        23.05        38.73        48.62 
TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6983 TCGA-55-6984 
       32.65        42.51        40.73        15.25        60.03        24.99 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 
      107.21         0.59         0.20         0.13         3.12         1.28 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
        0.79         1.78        18.64        17.65         6.15         0.16 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 
       15.19         3.29        19.66         0.13        15.65        17.98 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        2.17        22.16        15.42         0.36         0.26         0.49 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
        0.10         4.80        17.62         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A4DF TCGA-62-8395 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46S 
       20.71        20.19        39.98        49.25        47.80        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 
       67.96        72.30        39.25        40.96        20.65        39.09 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 
       87.98         2.04        42.90        28.47        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 
       14.73         5.72         4.64         6.12        22.68         7.56 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4659 
        4.41        12.56        14.01        13.45        25.91        23.38 
TCGA-73-4666 TCGA-73-4677 TCGA-73-7498 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       26.30         1.25        39.09         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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        26.53         8.02        53.33        26.01 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-86-6851 TCGA-86-7711 
       50.24       232.18        39.75        10.55         5.88        34.39 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 
       20.55        19.89        37.74         4.57        32.65        31.04 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF 
        1.15        30.84        27.58        26.50         3.81        24.23 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 
       26.47        10.62        41.36         1.97        13.71        12.23 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.18        14.27         1.18        19.82        22.45 
TCGA-93-8067 TCGA-93-A4JN TCGA-95-7043 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
        6.12        23.61        16.54        15.65        27.29        21.40 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 TCGA-97-7941 
       19.89        31.69        64.60        63.52         0.59         0.72 
TCGA-97-8172 TCGA-97-8174 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       17.92         5.39        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       17.75        20.84        18.67        24.56        36.76         1.45 
TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
       21.63        32.48        14.30        21.83        18.58        15.65 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.14        58.45        86.04         5.49        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       24.36        14.10        11.15        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        29.13         0.26         0.43        19.82        20.28 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              0.0               0.1 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           238.29            232.18 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            19.00             21.12 
[1] "0.0 - 238.3 (19.0)" "0.1 - 232.2 (21.1)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         4       60       67        1        24        35
  7P GAIN WILD-TYPE       1       75       72        0        28        37
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7P GAIN MUTATED           45          6       16
  7P GAIN WILD-TYPE         27          5       10
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                60                75
  STAGE IB                67                72
  STAGE II                 1                 0
  STAGE IIA               24                28
  STAGE IIB               35                37
  STAGE IIIA              45                27
  STAGE IIIB               6                 5
  STAGE IV                16                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    79 140  29   8
  7P GAIN WILD-TYPE  91 138  17  11
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              79                91
  T2             140               138
  T3              29                17
  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   153  46    53
  7P GAIN WILD-TYPE 179  50    23
D13V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                153               179
  N1                 46                50
  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   166  15
  7P GAIN WILD-TYPE 183  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    166   15
  7P GAIN WILD-TYPE  183   10
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             166               183
  1              15                10
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   140 118
  7P GAIN WILD-TYPE 135 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    140  118
  7P GAIN WILD-TYPE  135  122
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             140               135
  MALE               118               122
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   174  29
  7P GAIN WILD-TYPE 186  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    174   29
  7P GAIN WILD-TYPE  186   25
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              174               186
  YES              29                25
[1] 2 2
[1] FALSE
D13V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7P GAIN MUTATED                            7
  7P GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7P GAIN MUTATED                                  49
  7P GAIN WILD-TYPE                                57
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                  171
  7P GAIN WILD-TYPE                                                149
                   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                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             171
  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)               149
  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   173   6   3  15
  7P GAIN WILD-TYPE 170   6   1  11
D13V13, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             173               170
  R1               6                 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                          28   192
  7P GAIN WILD-TYPE                        23   197
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                     28                23
  WHITE                                        192               197
[1] 4 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     3 194
  7P GAIN WILD-TYPE   4 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3  194
  7P GAIN WILD-TYPE    4  188
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             194               188
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   130  75
  7Q GAIN WILD-TYPE 195  92
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              205               287 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               75                92 
$`7Q GAIN MUTATED`
TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 
        3.98        37.02         0.00        47.05         8.02        20.05 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
        2.99         9.01        29.98         4.96        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-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-3396 
       44.61        14.73        44.42        44.94        38.10        37.15 
TCGA-44-3919 TCGA-44-6144 TCGA-44-6145 TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 
       33.73        23.77        19.56        32.45        61.28        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 TCGA-44-A47F TCGA-44-A4SS 
       12.03         7.17        18.87        12.66        11.08        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-49-4512 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR4 
       29.75        17.16        22.26        22.26       156.66        28.90 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 
       40.41       123.58       221.33         9.86        71.47        70.55 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 
       31.04         8.09         9.27        21.47         9.37        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6597 TCGA-53-7624 
       22.55        42.35         3.91        11.05        41.69        34.29 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 
       35.21        23.05        45.21         0.07         0.79         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7724 
       40.54        70.26         1.15         7.99         1.32        23.18 
TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-8091 TCGA-55-8092 
        1.28         0.53         6.48        19.82        19.73         5.06 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
        1.08         1.51         1.45         0.76         0.95         0.26 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
       17.72         0.30         6.64         1.58         2.17        21.40 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 
        1.58        19.59         0.92        15.81        17.95         4.57 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46R TCGA-62-A46Y TCGA-62-A472 
       42.38        14.60        88.64        56.71        13.61        29.92 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 
       56.81        81.80        37.02        38.37        28.41        51.25 
TCGA-67-3772 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
       18.84         6.64        22.68        13.61         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
        4.41         2.93        17.16         2.01        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
       82.68        26.30         4.31        30.31         9.24        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7160 TCGA-78-7163 TCGA-78-7220 
      163.10        27.16        19.27        22.92       238.29        26.53 
TCGA-78-7540 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 
       39.35        77.59        27.09        12.36        31.13        38.04 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8280 
       32.78        35.24         4.08        24.33        22.82        23.05 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4P7 TCGA-91-6835 
       14.60        13.91         0.62        28.34        13.64         2.60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC TCGA-93-7348 TCGA-93-A4JN 
       27.68         7.36        16.60         1.45        17.46        23.61 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.08        41.82         2.86        18.67        12.39        15.68 
TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 
        2.76        43.79        25.48         5.95        18.67        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 
       15.39        14.30        20.58        34.85        21.57        24.30 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A50W TCGA-MN-A4N1 TCGA-MN-A4N4 
       18.08        19.00        10.09        14.53        27.19        38.63 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 
       86.14        49.35        37.35        58.85         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J 
       31.23         2.43        10.09        19.13        71.05        59.11 
TCGA-S2-AA1A 
       16.87 

$`7Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 
       50.07        19.96        14.01        45.01         9.96        24.03 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       19.00        14.96        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 
        9.04         2.04         0.46       120.79        28.41        35.28 
TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2662 
       11.64        26.30         4.37        43.53        46.98        42.08 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
       42.77         3.19        25.02        38.24        38.89        34.06 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 
       26.56        33.30        28.37        28.01         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 
       23.15        21.63        23.18        63.72        16.44        22.72 
TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 
       36.07        29.00        29.23        13.74         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4487 
       15.98        15.32         9.44        11.54        76.21        28.11 
TCGA-49-4501 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       46.72         8.81        29.46        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6761 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN 
       55.33        11.64        73.12        62.24         8.55        37.32 
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-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6592 
       40.60        78.67         8.45        15.12        29.03        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         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 
       27.25        30.54        13.94        38.73        48.62         2.86 
TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6982 TCGA-55-6983 
       32.65        42.51        40.73        15.25        32.71        60.03 
TCGA-55-6984 TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
       24.99       107.21         0.59         0.20         0.13         3.12 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
        1.28         1.12         0.79         1.78        18.64        17.65 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8207 TCGA-55-8208 
        0.13        23.64        15.65        17.98         2.17        22.16 
TCGA-55-8299 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       15.42         0.36         0.49         0.10         4.80        17.62 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A491 
        0.49         1.61        16.93        22.65        20.71        20.58 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       20.19        19.99        39.98        49.25        47.80        19.53 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 
       54.35        67.96        72.30        39.25        40.96        20.65 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 
       39.09        87.98         2.04        42.90        28.47         1.02 
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-67-6217 TCGA-69-7761 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
       13.87         6.12         7.56        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-73-4668 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS 
        4.24        25.91        15.35         1.25        39.09        11.18 
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-78-7161 
       19.50        38.50        32.09         5.88        64.90         9.57 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      104.19         8.48        88.14        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 
       26.01        10.55        50.24       232.18        39.75        10.55 
TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
      110.50         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 
        1.15        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-91-6836 TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 
       13.71        12.23         1.15        16.18        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
       19.82        22.45         6.12        19.00        17.29        16.54 
TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       15.65        27.29        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 
       64.60        63.52         0.59         0.72        17.92         5.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       16.41        21.60        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
       17.75        20.84        18.67        20.68        24.56        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
        1.45        21.63        23.80        35.47        32.48        14.30 
TCGA-L9-A443 TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 
        6.35         1.91        21.83        18.58        15.65         2.76 
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        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       29.13         0.26         0.43        19.82        20.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              0.0               0.1 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           238.29            232.18 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            19.56             20.19 
[1] "0.0 - 238.3 (19.6)" "0.1 - 232.2 (20.2)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         3       52       49        1        20        27
  7Q GAIN WILD-TYPE       2       83       90        0        32        45
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7Q GAIN MUTATED           39          5       15
  7Q GAIN WILD-TYPE         33          6       11
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                52                83
  STAGE IB                49                90
  STAGE II                 1                 0
  STAGE IIA               20                32
  STAGE IIB               27                45
  STAGE IIIA              39                33
  STAGE IIIB               5                 6
  STAGE IV                15                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    66 117  20   7
  7Q GAIN WILD-TYPE 104 161  26  12
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              66               104
  T2             117               161
  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
  7Q GAIN MUTATED   124  38    44
  7Q GAIN WILD-TYPE 208  58    32
D14V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                124               208
  N1                 38                58
  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   133  14
  7Q GAIN WILD-TYPE 216  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    133   14
  7Q GAIN WILD-TYPE  216   11
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             133               216
  1              14                11
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   112  99
  7Q GAIN WILD-TYPE 163 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    112   99
  7Q GAIN WILD-TYPE  163  141
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             112               163
  MALE                99               141
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   139  28
  7Q GAIN WILD-TYPE 221  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    139   28
  7Q GAIN WILD-TYPE  221   26
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              139               221
  YES              28                26
[1] 2 2
[1] FALSE
D14V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7Q GAIN MUTATED                            8
  7Q GAIN WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7Q GAIN MUTATED                                  43
  7Q GAIN WILD-TYPE                                63
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                  137
  7Q GAIN WILD-TYPE                                                183
                   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                                       8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             137
  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                                 63
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               183
  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   138   4   3  13
  7Q GAIN WILD-TYPE 205   8   1  13
D14V13, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             138               205
  R1               4                 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                          24   162
  7Q GAIN WILD-TYPE                        27   227
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                     24                27
  WHITE                                        162               227
[1] 4 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     2 165
  7Q GAIN WILD-TYPE   5 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  165
  7Q GAIN WILD-TYPE    5  217
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             165               217
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    80  42
  8P GAIN WILD-TYPE 245 125
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              122               370 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               42               125 
$`8P GAIN MUTATED`
TCGA-05-4250 TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4424 TCGA-05-4432 
        3.98        20.05        14.96         9.01        30.02        25.02 
TCGA-05-5428 TCGA-35-5375 TCGA-38-4625 TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 
       22.03         8.68        97.74        28.41        44.61        14.73 
TCGA-44-6147 TCGA-44-6778 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 
       27.78        61.28        36.07        18.87        29.23        13.74 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47B TCGA-44-A47F TCGA-49-4512 TCGA-49-6742 
        3.25         8.55         9.44        11.08        29.75        16.04 
TCGA-49-AARE TCGA-4B-A93V TCGA-50-5051 TCGA-50-5072 TCGA-50-5933 TCGA-50-5944 
       40.41         9.86        15.72         8.09        78.67        25.12 
TCGA-50-5946 TCGA-50-6592 TCGA-50-7109 TCGA-50-8457 TCGA-55-1592 TCGA-55-1596 
       22.55        25.55        10.13        36.99        23.05        45.21 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-7574 
       40.73        15.25         0.82        48.49         5.49         3.12 
TCGA-55-7724 TCGA-55-7907 TCGA-55-8085 TCGA-55-8096 TCGA-55-8203 TCGA-55-8206 
       23.18         0.53        29.72        23.64        17.98         1.51 
TCGA-55-8301 TCGA-55-8507 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z 
        1.45         0.26        17.62         0.49         2.17        21.40 
TCGA-55-A490 TCGA-55-A494 TCGA-62-8398 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
        1.58        15.81        14.60        19.53        56.71        54.35 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5779 
       39.25        40.96        29.92        20.65        37.02        28.41 
TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
        1.02        20.05        22.68        13.61         7.56         6.05 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
        2.01        52.60        23.38         4.31        30.31         9.24 
TCGA-73-4677 TCGA-78-7143 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7158 
        1.25       163.10        20.58       129.53       119.51         5.88 
TCGA-78-7159 TCGA-78-7535 TCGA-78-8662 TCGA-86-7701 TCGA-86-8280 TCGA-86-8585 
       64.90        31.20       110.50        31.13        23.05         1.15 
TCGA-86-8669 TCGA-86-8674 TCGA-91-6828 TCGA-91-6831 TCGA-91-6840 TCGA-91-7771 
       30.84        26.50        10.62        10.19        12.23        16.18 
TCGA-93-7347 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VP 
       22.45         1.08        19.00        18.67        15.65        19.89 
TCGA-97-7547 TCGA-97-7553 TCGA-97-8171 TCGA-97-8172 TCGA-97-8176 TCGA-97-8552 
       64.60        43.79        18.67        17.92        15.39        20.58 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8033 TCGA-L9-A444 TCGA-L9-A743 
       20.19        20.52        34.85        21.57        10.09        21.83 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF 
       49.35        37.35         5.29        31.23        29.46        11.05 
TCGA-MP-A4TH TCGA-NJ-A4YG 
       24.36        62.60 

$`8P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 
        9.96        24.03        47.05         8.02        19.00         2.99 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
       29.98        12.00        21.99        26.01        26.01        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       24.00        15.02        15.02         4.96        29.00         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-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       49.05        35.28        11.64        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
       46.98        44.42        44.94        38.10        42.08        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-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       19.56         9.93        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       32.45        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7670 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS 
       29.00        12.66        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-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 
       46.72        14.07        32.84         8.81        29.46        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       53.29        55.33        17.16        11.64        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN 
      156.66        73.12        62.24        28.90         8.55        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      123.58       221.33       164.12        20.52        71.47        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         9.27        14.27        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-6590 
       21.47         8.45        15.12         9.37        29.03        42.35 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        11.05        12.16         6.21        41.69         0.72 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       38.73        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6975 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       42.51         3.88         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 
        1.15         7.99         0.20         0.13         1.32         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
        1.28         1.12         0.79         1.78        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82         0.16        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 
       19.66        19.73         5.06         0.13        15.65         1.08 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16        15.42         0.76         0.95         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A491 
        1.58         1.61        16.93        22.65        20.71        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       19.59         0.92        20.19        19.99        17.95         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46U 
       39.98        42.38        88.64        49.25        47.80        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
       72.30        13.61        56.81        39.09        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
       87.98         2.04        42.90        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       14.04        12.66        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        6.64         6.12         5.42         4.41         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4662 
       14.01        13.45         4.24        25.91        17.16        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7145 
       26.30        15.35        39.09        50.33        11.18        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
        5.69        19.27        21.90        39.95        19.50        38.50 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       32.09        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
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-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       21.47        14.60        13.91        27.58         0.62        28.34 
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-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        1.97         2.60        13.71        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 
       16.60        14.27         1.18         1.45        19.82        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        6.12        23.61        17.29        41.82        16.54         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.68        27.29         2.76        21.40        18.18 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       31.69        63.52        25.48         5.95         0.59         0.72 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 
        5.39        18.12        16.41        14.30        21.60        21.44 
TCGA-97-A4M1 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       19.76        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.63        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W 
       35.47        32.48        19.00        14.30         6.35        14.53 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
        1.91        18.58        15.65        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       86.14        58.45        86.04        58.85         5.49        41.59 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
        2.43        10.09        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        29.13         0.26         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 
             0.26              0.00 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           163.10            238.29 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            20.55             19.82 
[1] "0.3 - 163.1 (20.5)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         1       31       39        0        12        15
  8P GAIN WILD-TYPE       4      104      100        1        40        57
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8P GAIN MUTATED           19          4        8
  8P GAIN WILD-TYPE         53          7       18
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                31               104
  STAGE IB                39               100
  STAGE II                 0                 1
  STAGE IIA               12                40
  STAGE IIB               15                57
  STAGE IIIA              19                53
  STAGE IIIB               4                 7
  STAGE IV                 8                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
  8P GAIN MUTATED    34  78  12   3
  8P GAIN WILD-TYPE 136 200  34  16
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              34               136
  T2              78               200
  T3              12                34
  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
  8P GAIN MUTATED    83  21    21
  8P GAIN WILD-TYPE 249  75    55
D15V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                 83               249
  N1                 21                75
  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"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    90   8
  8P GAIN WILD-TYPE 259  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     90    8
  8P GAIN WILD-TYPE  259   17
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              90               259
  1               8                17
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    56  73
  8P GAIN WILD-TYPE 219 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     56   73
  8P GAIN WILD-TYPE  219  167
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              56               219
  MALE                73               167
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    92  14
  8P GAIN WILD-TYPE 268  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     92   14
  8P GAIN WILD-TYPE  268   40
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               92               268
  YES              14                40
[1] 2 2
[1] FALSE
D15V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8P GAIN MUTATED                            6
  8P GAIN WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8P GAIN MUTATED                                  30
  8P GAIN WILD-TYPE                                76
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                   78
  8P GAIN WILD-TYPE                                                242
                   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                             9
  8P GAIN WILD-TYPE                            2                            14
                   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                               30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              78
  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                                    9
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   8P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               242
  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                                     14
  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    84   6   1   5
  8P GAIN WILD-TYPE 259   6   3  21
D15V13, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              84               259
  R1               6                 6
  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
  8P GAIN MUTATED                                  0     4
  8P GAIN WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          11    99
  8P GAIN WILD-TYPE                        40   290
D15V14, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4                 3
  BLACK OR AFRICAN AMERICAN                     11                40
  WHITE                                         99               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"
D15V15, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0  99
  8P GAIN WILD-TYPE   7 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   99
  8P GAIN WILD-TYPE    7  283
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              99               283
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   142  89
  8Q GAIN WILD-TYPE 183  78
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              231               261 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               89                78 
$`8Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 
       50.07         3.98        45.01        37.02         0.00        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4424 TCGA-05-4432 
        8.02        20.05        14.96         9.01        30.02        25.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
       15.02         4.96        22.03         7.40         8.68        97.74 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-3919 
       49.05        28.41        11.64        44.61        14.73        33.73 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 
       28.37        23.77        27.78        21.63        32.45        61.28 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       16.44         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU 
       13.74         3.25         8.55         9.44        11.08        13.45 
TCGA-49-4488 TCGA-49-4501 TCGA-49-4510 TCGA-49-4512 TCGA-49-6761 TCGA-49-6767 
       28.57        46.72        29.46        29.75        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARE TCGA-49-AARO TCGA-4B-A93V 
       22.26        73.12        62.24        40.41       123.58         9.86 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
       15.72        31.04         8.09        14.27        78.67         9.37 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6673 
       25.12        22.55         3.91        25.55        11.05         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       10.13        36.99        13.94        35.21        23.05        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       45.21         2.86        32.65         0.79        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 
        0.82        48.49         5.49         7.79        45.34        32.71 
TCGA-55-6985 TCGA-55-7283 TCGA-55-7574 TCGA-55-7724 TCGA-55-7907 TCGA-55-7914 
       40.54         1.15         3.12        23.18         0.53         6.15 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.82        29.72         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8507 
       17.98         1.08         1.51         1.45         0.76         0.26 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
        0.30         6.64        17.62         0.49         1.58         2.17 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40         1.58        20.58         0.92        15.81 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       39.98        14.60        49.25        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
       54.35        39.25        40.96        29.92        20.65        39.09 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-69-7760 
       37.02         2.04        28.41         1.02        20.05         6.64 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 
       22.68        13.61         7.56         6.05         2.93         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 
       17.16         2.01        52.60        23.38         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7148 
        9.24         1.25        50.33       163.10         5.69        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7220 
      129.53        39.95         5.88        64.90         9.57        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8660 TCGA-78-8662 
       31.20         8.02        26.01        10.55        10.55       110.50 
TCGA-86-7701 TCGA-86-7954 TCGA-86-8054 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       31.13        19.89        37.74        23.05        14.60         1.15 
TCGA-86-8669 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
       30.84         0.62        26.50        29.46         3.81        13.64 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 
       10.62        10.19        12.23        27.68        16.18         1.18 
TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
       22.45         6.12         1.08        19.00        17.29        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
        2.86        18.67        15.65        18.18        19.89        64.60 
TCGA-97-7553 TCGA-97-7938 TCGA-97-8171 TCGA-97-8172 TCGA-97-8176 TCGA-97-8179 
       43.79         0.59        18.67        17.92        15.39        14.30 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.58        20.19        20.52        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
       21.57        23.80        18.08         6.35        10.09        14.53 
TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        1.91        21.83        15.65        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.45        49.35        37.35         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       10.09        29.46        11.05        24.36        14.10        11.15 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A7XG 
       71.05        62.60        20.28 

$`8Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 
       19.96        14.01         9.96        24.03        19.00         2.99 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
       29.98        12.00        21.99        26.01        26.01        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       24.00        15.02        29.00         9.04         2.04         0.46 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F 
        5.98       120.79        37.71        35.28        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
       43.53        46.98        44.42        44.94        38.10        42.08 
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-44-5645 TCGA-44-6145 TCGA-44-6146 
       34.06        26.56        33.30        28.01        19.56         9.93 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       23.15        23.18        63.72        22.72        19.46        12.03 
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-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAR0 
       55.89        16.04        53.29        55.33        17.16       156.66 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 
       28.90         8.55        37.32       221.33       164.12        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 
       71.47        70.55        60.16        49.28         9.27        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6594 
       21.47         8.45        15.12        29.03        42.35        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        6.21        41.69         7.59        27.25        34.29        30.54 
TCGA-55-1594 TCGA-55-6543 TCGA-55-6968 TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 
       38.73         0.07        42.51         3.88         2.20        60.03 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
       24.99       107.21        70.26         0.59         7.99         0.20 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        0.13         1.32         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8087 
        1.78        18.64         6.48        17.65         0.16        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
        3.29        19.66        19.73         2.17        22.16        15.42 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.95         0.36         0.49        17.72         0.10         4.80 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-55-A4DG 
        1.61        16.93        22.65        19.59        20.19        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
       17.95         4.57        42.38        88.64        67.96        72.30 
TCGA-62-A46Y TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
       13.61        56.81        81.80        38.37        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-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7765 TCGA-69-7978 
        5.72         4.64        13.87         6.12         5.42         4.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4662 TCGA-73-4666 
       12.56        14.01        13.45        25.91        82.68        26.30 
TCGA-73-4668 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 
       15.35        39.09        11.18        27.16        19.27        21.90 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7162 
      119.51        19.50        38.50        32.09        22.92       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 
      238.29         8.48        88.14        53.33        39.35        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
      232.18        39.75        77.59        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 
       34.39        38.04        20.55        32.78        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-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4JF 
       31.20        21.47        13.91        27.58        28.34        24.23 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6848 
       26.47        41.36         1.97         2.60        13.71         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 
        1.15        16.60        14.27         1.45        19.82        17.46 
TCGA-93-A4JN TCGA-95-7039 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 
       23.61        41.82        12.39        15.68        27.29         2.76 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
       21.40        31.69        63.52        25.48         5.95         0.72 
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-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-AA5R 
       17.75        20.84        18.67        20.68        24.56        21.63 
TCGA-J2-8192 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A7SV 
       24.30        35.47        32.48        19.00        14.30        18.58 
TCGA-MN-A4N1 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TK 
       27.19        86.04        58.85         5.49        41.59        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       73.91         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        59.11        16.87 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.00              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           163.10            238.29 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            18.87             20.84 
[1] "0.0 - 163.1 (18.9)" "0.1 - 238.3 (20.8)"
[1] "hr=" "1.5"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2       58       67        1        23        35
  8Q GAIN WILD-TYPE       3       77       72        0        29        37
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8Q GAIN MUTATED           37          7       13
  8Q GAIN WILD-TYPE         35          4       13
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                58                77
  STAGE IB                67                72
  STAGE II                 1                 0
  STAGE IIA               23                29
  STAGE IIB               35                37
  STAGE IIIA              37                35
  STAGE IIIB               7                 4
  STAGE IV                13                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    71 137  25   8
  8Q GAIN WILD-TYPE  99 141  21  11
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              71                99
  T2             137               141
  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   155  41    41
  8Q GAIN WILD-TYPE 177  55    35
D16V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                155               177
  N1                 41                55
  N2+N3              41                35
[1] 3 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   162  13
  8Q GAIN WILD-TYPE 187  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    162   13
  8Q GAIN WILD-TYPE  187   12
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             162               187
  1              13                12
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   125 118
  8Q GAIN WILD-TYPE 150 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    125  118
  8Q GAIN WILD-TYPE  150  122
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             125               150
  MALE               118               122
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   169  27
  8Q GAIN WILD-TYPE 191  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    169   27
  8Q GAIN WILD-TYPE  191   27
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              169               191
  YES              27                27
[1] 2 2
[1] FALSE
D16V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8Q GAIN MUTATED                           13
  8Q GAIN WILD-TYPE                          6
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8Q GAIN MUTATED                                  51
  8Q GAIN WILD-TYPE                                55
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                  154
  8Q GAIN WILD-TYPE                                                166
                   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                            12
  8Q GAIN WILD-TYPE                            2                            11
                   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                                      13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             154
  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                                   12
  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)               166
  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                                     11
  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   161   8   3  13
  8Q GAIN WILD-TYPE 182   4   1  13
D16V13, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             161               182
  R1               8                 4
  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
  8Q GAIN MUTATED                                  0     7
  8Q GAIN WILD-TYPE                                1     0
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          26   179
  8Q GAIN WILD-TYPE                        25   210
D16V14, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                 0
  BLACK OR AFRICAN AMERICAN                     26                25
  WHITE                                        179               210
[1] 4 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     3 175
  8Q GAIN WILD-TYPE   4 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  175
  8Q GAIN WILD-TYPE    4  207
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             175               207
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    29  13
  9P GAIN WILD-TYPE 296 154
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               42               450 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               154 
$`9P GAIN MUTATED`
TCGA-05-4390 TCGA-05-4427 TCGA-44-6774 TCGA-44-8119 TCGA-44-A47F TCGA-49-AARQ 
       37.02        26.01        21.63         3.25        11.08       221.33 
TCGA-4B-A93V TCGA-50-5051 TCGA-50-6597 TCGA-55-6972 TCGA-55-7903 TCGA-55-7995 
        9.86        15.72        41.69        48.49        18.64         0.16 
TCGA-55-8301 TCGA-55-8514 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A4DF TCGA-62-A46R 
        1.45         6.64         2.17        21.40        20.19        56.71 
TCGA-64-5775 TCGA-69-7973 TCGA-69-7979 TCGA-69-8253 TCGA-69-A59K TCGA-73-4659 
        2.04         7.56         2.93        14.01        17.16        23.38 
TCGA-73-4666 TCGA-73-7499 TCGA-78-7163 TCGA-78-8662 TCGA-86-7953 TCGA-86-8669 
       26.30        50.33       238.29       110.50        32.78        30.84 
TCGA-91-6828 TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN TCGA-97-7553 
       10.62        41.82         2.86        15.68        18.18        43.79 
TCGA-97-7554 TCGA-L9-A444 TCGA-L9-A5IP TCGA-MP-A4TC TCGA-MP-A4TJ TCGA-S2-AA1A 
       25.48        10.09         1.91         2.43        11.15        16.87 

$`9P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         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-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.94        38.10        42.08        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-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       18.87        29.00        29.23        13.74        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-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
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-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26       156.66        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 
       40.41        37.32       123.58       164.12        20.52        71.47 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       70.55        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        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-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
       35.21        23.05        38.73        48.62        45.21         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        0.82         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.78         0.53         6.48        17.65         6.15        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16        15.42         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.62         0.49         1.58         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71         1.58        20.58        19.59         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-A46S TCGA-62-A46U 
       88.64        49.25        47.80        19.53        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-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       20.65        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         1.02        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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         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        12.56        13.45         4.24        25.91 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        2.01        52.60        82.68        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        11.18       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-78-7166 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19         8.48        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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       50.24       232.18        39.75        77.59        10.55        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-86-8054 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-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       21.47        14.60         1.15        13.91        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-91-6836 
       26.47        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
        6.12        23.61         1.08        19.00        17.29        16.54 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       18.67        12.39        15.65        27.29         2.76        21.40 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7938 
       19.89        31.69        64.60        63.52         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
       14.30         6.35        14.53        21.83        18.58        15.65 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        20.28        59.11 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.16              0.00 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           238.29            232.18 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            17.67             20.05 
[1] "0.2 - 238.3 (17.7)" "0.0 - 232.2 (20.1)"
[1] "hr=" "1.1"
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      122      127        1        49        67
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9P GAIN MUTATED            7          1        3
  9P GAIN WILD-TYPE         65         10       23
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                13               122
  STAGE IB                12               127
  STAGE II                 0                 1
  STAGE IIA                3                49
  STAGE IIB                5                67
  STAGE IIIA               7                65
  STAGE IIIB               1                10
  STAGE IV                 3                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
  9P GAIN MUTATED    19  20   5   1
  9P GAIN WILD-TYPE 151 258  41  18
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              19               151
  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    31   6     8
  9P GAIN WILD-TYPE 301  90    68
D17V5, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0                 31               301
  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 246 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     29   16
  9P GAIN WILD-TYPE  246  224
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              29               246
  MALE                16               224
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    33   6
  9P GAIN WILD-TYPE 327  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     33    6
  9P GAIN WILD-TYPE  327   48
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               33               327
  YES               6                48
[1] 2 2
[1] FALSE
D17V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9P GAIN MUTATED                            1
  9P GAIN WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9P GAIN MUTATED                                  11
  9P GAIN WILD-TYPE                                95
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                   26
  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                               11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              26
  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                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 95
  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    31   1   1   3
  9P GAIN WILD-TYPE 312  11   3  23
D17V13, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              31               312
  R1               1                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
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           8    30
  9P GAIN WILD-TYPE                        43   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                      8                43
  WHITE                                         30               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   7 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   37
  9P GAIN WILD-TYPE    7  345
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              37               345
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    20  11
  9Q GAIN WILD-TYPE 305 156
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               31               461 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11               156 
$`9Q GAIN MUTATED`
TCGA-05-4390 TCGA-05-4427 TCGA-44-6778 TCGA-44-8119 TCGA-44-A47F TCGA-4B-A93V 
       37.02        26.01        61.28         3.25        11.08         9.86 
TCGA-50-5051 TCGA-50-6590 TCGA-50-6597 TCGA-55-6972 TCGA-55-7995 TCGA-55-8091 
       15.72        42.35        41.69        48.49         0.16        19.73 
TCGA-55-8620 TCGA-55-A48Z TCGA-69-8253 TCGA-73-4666 TCGA-73-7499 TCGA-78-7160 
        2.17        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-91-6836 
      238.29        10.55       110.50        32.78        30.84        13.71 
TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN TCGA-97-7553 TCGA-L9-A5IP TCGA-MP-A4TC 
        2.86        15.68        18.18        43.79         1.91         2.43 
TCGA-S2-AA1A 
       16.87 

$`9Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         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-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.94        38.10        42.08        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-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       18.87        29.00        29.23        13.74        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-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
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-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26       156.66        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 
       40.41        37.32       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        70.55        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       15.12         9.37        29.03        25.12        22.55         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-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
       35.21        23.05        38.73        48.62        45.21         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        0.82         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.78        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 
       19.82        29.72        15.19         3.29        19.66         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
        0.92        15.81        20.19        19.99        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-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-64-1677 TCGA-64-1678 
       39.25        40.96        29.92        56.81        20.65        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         1.02        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       14.04        12.66        14.73         5.72         4.64        13.87 
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-69-7980 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41         2.93        12.56        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       25.91        17.16         2.01        52.60        23.38        82.68 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       11.18       163.10        27.16         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-78-7161 TCGA-78-7162 TCGA-78-7166 
       32.09         5.88        64.90         9.57       104.19         8.48 
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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        50.24       232.18        39.75        77.59        10.55 
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-86-8278 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-86-8671 
       23.05        21.47        14.60         1.15        13.91        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-91-7771 
        2.60        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 
       41.82        16.54        18.67        12.39        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        19.89        31.69        64.60        63.52 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
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-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
        1.45        21.57        21.63        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
       14.53        21.83        18.58        15.65        27.19        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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD 
       58.85         5.49         5.29        41.59        31.23        10.09 
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        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.26         0.43        19.82        20.28        59.11 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.16              0.00 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           238.29            232.18 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            19.73             19.99 
[1] "0.2 - 238.3 (19.7)" "0.0 - 232.2 (20.0)"
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         0        8       11        0         3         3
  9Q GAIN WILD-TYPE       5      127      128        1        49        69
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9Q GAIN MUTATED            2          1        4
  9Q GAIN WILD-TYPE         70         10       22
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 8               127
  STAGE IB                11               128
  STAGE II                 0                 1
  STAGE IIA                3                49
  STAGE IIB                3                69
  STAGE IIIA               2                70
  STAGE IIIB               1                10
  STAGE IV                 4                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
  9Q GAIN MUTATED    13  16   2   1
  9Q GAIN WILD-TYPE 157 262  44  18
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              13               157
  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
  9Q GAIN MUTATED    21   6     5
  9Q GAIN WILD-TYPE 311  90    71
D18V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                 21               311
  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    22   4
  9Q GAIN WILD-TYPE 327  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     22    4
  9Q GAIN WILD-TYPE  327   21
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              22               327
  1               4                21
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    19  13
  9Q GAIN WILD-TYPE 256 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19   13
  9Q GAIN WILD-TYPE  256  227
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              19               256
  MALE                13               227
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    23   5
  9Q GAIN WILD-TYPE 337  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     23    5
  9Q GAIN WILD-TYPE  337   49
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               23               337
  YES               5                49
[1] 2 2
[1] FALSE
D18V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9Q GAIN MUTATED                            0
  9Q GAIN WILD-TYPE                         19
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9Q GAIN MUTATED                                   8
  9Q GAIN WILD-TYPE                                98
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                   20
  9Q GAIN WILD-TYPE                                                300
                   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)              20
  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                                        19
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               300
  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    22   1   0   2
  9Q GAIN WILD-TYPE 321  11   4  24
D18V13, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              22               321
  R1               1                11
  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    22
  9Q GAIN WILD-TYPE                        45   367
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                45
  WHITE                                         22               367
[1] 4 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  24
  9Q GAIN WILD-TYPE   7 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   24
  9Q GAIN WILD-TYPE    7  358
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              24               358
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    68  37
  10P GAIN WILD-TYPE 257 130
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               105                387 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                37                130 
$`10P GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       45.01        37.02        20.05         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 
       12.00        30.02        25.02        25.02        15.02        29.00 
TCGA-35-4122 TCGA-38-4632 TCGA-44-3396 TCGA-44-6144 TCGA-44-6145 TCGA-44-7667 
        7.40        44.61        37.15        23.77        19.56        36.07 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-49-4487 TCGA-49-AAR2 
       29.23        13.74        12.66         8.55        28.11        73.12 
TCGA-49-AARE TCGA-4B-A93V TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 TCGA-50-5933 
       40.41         9.86        70.55        15.72        49.28        78.67 
TCGA-50-5946 TCGA-50-6592 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-55-1596 
       22.55        25.55        10.13        34.29        13.94        45.21 
TCGA-55-6642 TCGA-55-6970 TCGA-55-6972 TCGA-55-6978 TCGA-55-7283 TCGA-55-7910 
       32.65        15.25        48.49         5.49         1.15         6.48 
TCGA-55-8092 TCGA-55-8302 TCGA-55-8511 TCGA-55-8615 TCGA-55-8620 TCGA-55-A491 
        5.06         0.76         0.30         0.49         2.17        20.58 
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         2.93 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-A9RS 
        2.01        52.60         4.31        30.31         1.25        11.18 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
      129.53        19.50        38.50        64.90        22.92         9.57 
TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8662 TCGA-86-7701 TCGA-86-7711 
       26.01        10.55        50.24       110.50        31.13        34.39 
TCGA-86-7713 TCGA-86-7955 TCGA-86-8358 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 
       38.04        35.24        21.47         0.62        28.34        29.46 
TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-95-7567 
        3.81        41.36        13.71        16.18         6.12        18.67 
TCGA-95-7944 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       12.39        18.18        19.89        43.79        25.48         5.95 
TCGA-97-8179 TCGA-99-8025 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV 
       14.30        34.85        23.80         6.35        10.09        18.58 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TD 
       27.19        38.63         2.76         5.49         5.29        10.09 
TCGA-MP-A4TE TCGA-NJ-A4YF TCGA-NJ-A4YQ 
       29.46        71.05        29.13 

$`10P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        19.96        14.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4418 TCGA-05-4425 
       24.03        47.05         8.02        19.00         9.01        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5428 
       26.01        26.01        24.00        15.02         4.96        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-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.94        38.10        42.08        42.77         3.19        25.02 
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-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       28.37        28.01         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 
       19.46        12.03         7.17        18.87        29.00         3.25 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        76.21        28.57        12.66        35.54        46.72 
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-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       16.04        53.29        55.33        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN 
       22.26       156.66        62.24        28.90         8.55        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 
      123.58       221.33       164.12        20.52        71.47        60.16 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
       31.04         8.09         9.27        14.27        40.60        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
        8.45        15.12         9.37        29.03        25.12        42.35 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        11.05        12.16         6.21        41.69         0.72 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 
       36.99         7.59        27.25        30.54        35.21        23.05 
TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       38.73        48.62         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6975 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       40.73         0.82         3.88         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        0.59         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         0.53        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
       29.72        15.19         3.29        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42         1.45         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.49        17.72         0.10         4.80         6.64        17.62 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1.58        19.59         0.92        15.81        20.19        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 
       17.95         4.57        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-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 
       40.96        29.92        56.81        20.65        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         1.02        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
       13.61         5.42         7.56         6.05         4.41        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 
       14.01        13.45         4.24        25.91        17.16        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
       82.68        26.30        15.35         9.24        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
      163.10        27.16         5.69        19.27        20.58        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 
       39.95       119.51        32.09         5.88       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       39.35       232.18        39.75        77.59        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
       12.36         5.88        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-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.04        31.20        23.05        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       30.84        27.58        26.50        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       10.62         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-A4BC 
        7.36         1.15        16.60        14.27         1.18         1.45 
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-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
       17.29        41.82        16.54         2.86        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        21.40        31.69        64.60        63.52 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       24.56        36.76         1.45        21.57        21.63        24.30 
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-A743 TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        1.91        21.83        15.65        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       37.35        86.04        58.85        41.59        31.23         2.43 
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 
       62.60         0.13         1.64         0.26         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 
               0.3                0.0 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            129.53             238.29 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             22.55              19.82 
[1] "0.3 - 129.5 (22.6)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         0       26       34        0        11        14
  10P GAIN WILD-TYPE       5      109      105        1        41        58
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10P GAIN MUTATED           15          4        7
  10P GAIN WILD-TYPE         57          7       19
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 26                109
  STAGE IB                 34                105
  STAGE II                  0                  1
  STAGE IIA                11                 41
  STAGE IIB                14                 58
  STAGE IIIA               15                 57
  STAGE IIIB                4                  7
  STAGE IV                  7                 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
  10P GAIN MUTATED    25  68  13   5
  10P GAIN WILD-TYPE 145 210  33  14
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               25                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    80  13    17
  10P GAIN WILD-TYPE 252  83    59
D19V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                  80                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  65
  10P GAIN WILD-TYPE 229 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     46   65
  10P GAIN WILD-TYPE  229  175
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               46                229
  MALE                 65                175
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    77  12
  10P GAIN WILD-TYPE 283  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     77   12
  10P GAIN WILD-TYPE  283   42
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                77                283
  YES               12                 42
[1] 2 2
[1] FALSE
D19V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10P GAIN MUTATED                            5
  10P GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10P GAIN MUTATED                                  26
  10P GAIN WILD-TYPE                                80
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                   67
  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)               67
  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                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  80
  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    73   3   0   9
  10P GAIN WILD-TYPE 270   9   4  17
D19V13, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               73                270
  R1                3                  9
  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     4
  10P GAIN WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                          12    74
  10P GAIN WILD-TYPE                        39   315
D19V14, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  3
  BLACK OR AFRICAN AMERICAN                      12                 39
  WHITE                                          74                315
[1] 4 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  73
  10P GAIN WILD-TYPE   5 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   73
  10P GAIN WILD-TYPE    5  309
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               73                309
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    48  26
  10Q GAIN WILD-TYPE 277 141
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                74                418 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                141 
$`10Q GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4430 
       45.01        37.02         2.99        14.96        12.00        25.02 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 TCGA-38-4632 TCGA-44-6144 
       25.02        15.02        29.00         7.40        44.61        23.77 
TCGA-44-6145 TCGA-44-7667 TCGA-44-7671 TCGA-49-4487 TCGA-50-5049 TCGA-50-5051 
       19.56        36.07        29.23        28.11        70.55        15.72 
TCGA-50-5068 TCGA-50-5933 TCGA-50-5946 TCGA-50-6593 TCGA-53-7624 TCGA-55-1596 
       49.28        78.67        22.55        11.05        34.29        45.21 
TCGA-55-6642 TCGA-55-6970 TCGA-55-6972 TCGA-55-6978 TCGA-55-7283 TCGA-55-8205 
       32.65        15.25        48.49         5.49         1.15         1.08 
TCGA-55-8302 TCGA-55-8615 TCGA-55-A491 TCGA-62-8398 TCGA-62-A46S TCGA-62-A470 
        0.76         0.49        20.58        14.60        54.35        39.25 
TCGA-69-7763 TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       22.68         2.01        52.60         4.31        30.31         1.25 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-8662 
      129.53        19.50        64.90        22.92         9.57       110.50 
TCGA-86-7701 TCGA-86-7713 TCGA-86-8279 TCGA-86-8358 TCGA-86-8672 TCGA-86-8673 
       31.13        38.04        31.20        21.47         0.62        28.34 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-7771 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VP 
       29.46         3.81        16.18        18.67         2.76        19.89 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 TCGA-99-8025 TCGA-J2-8194 
       43.79        25.48         5.95        14.30        34.85        23.80 
TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TD 
       18.58        38.63         2.76         5.49         5.29        10.09 
TCGA-MP-A4TE TCGA-MP-A5C7 
       29.46        73.91 

$`10Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        19.96        14.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4418 
       24.03        47.05         8.02        19.00        20.05         9.01 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 
       29.98        30.02        21.99        26.01        26.01        24.00 
TCGA-05-4434 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       15.02         4.96        22.03         9.04         2.04         0.46 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
       43.53        46.98        44.42        44.94        38.10        42.08 
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-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        7.17        18.87        29.00        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        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-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       22.26        22.26       156.66        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
        8.55        40.41        37.32       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        9.86        20.52        71.47        60.16        31.04         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        9.27        14.27        40.60        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
        9.37        29.03        25.12        42.35         3.91        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        30.54        13.94        35.21        23.05 
TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       38.73        48.62         2.86         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6975 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       40.73         0.82         3.88         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        0.59         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 
        5.06         0.13        23.64        15.65        17.98         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16        15.42         1.45         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64        17.62         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
       22.65        20.71        21.40         1.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       15.81        20.19        19.99        17.95         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-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       67.96        72.30        13.61        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       20.65        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         1.02 
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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        4.64        13.87         6.64         6.12        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 
       13.45         4.24        25.91        17.16        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
       26.30        15.35         9.24        39.09        50.33        11.18 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
      163.10        27.16         5.69        19.27        20.58        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 
       39.95       119.51        38.50        32.09         5.88       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        10.55        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         1.15        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-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        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-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.68        15.65        27.29        21.40        18.18 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       31.69        64.60        63.52         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       17.92         5.39        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        24.56        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        21.63        24.30        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       19.00        14.30         6.35        10.09        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       21.83        15.65        27.19        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       37.35        86.04        58.85        41.59        31.23         2.43 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF 
       11.05        24.36        14.10        11.15        19.13        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.49               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            129.53             238.29 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             22.80              19.82 
[1] "0.5 - 129.5 (22.8)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         0       16       19        0         7        11
  10Q GAIN WILD-TYPE       5      119      120        1        45        61
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10Q GAIN MUTATED           15          3        6
  10Q GAIN WILD-TYPE         57          8       20
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 16                119
  STAGE IB                 19                120
  STAGE II                  0                  1
  STAGE IIA                 7                 45
  STAGE IIB                11                 61
  STAGE IIIA               15                 57
  STAGE IIIB                3                  8
  STAGE IV                  6                 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
  10Q GAIN MUTATED    15  48  10   4
  10Q GAIN WILD-TYPE 155 230  36  15
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               15                155
  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    49  10    17
  10Q GAIN WILD-TYPE 283  86    59
D20V5, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                  49                283
  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    29  48
  10Q GAIN WILD-TYPE 246 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     29   48
  10Q GAIN WILD-TYPE  246  192
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               29                246
  MALE                 48                192
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    52   8
  10Q GAIN WILD-TYPE 308  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     52    8
  10Q GAIN WILD-TYPE  308   46
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                52                308
  YES                8                 46
[1] 2 2
[1] FALSE
D20V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10Q GAIN MUTATED                            3
  10Q GAIN WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10Q GAIN MUTATED                                  19
  10Q GAIN WILD-TYPE                                87
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                   45
  10Q GAIN WILD-TYPE                                                275
                    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)               45
  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                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                275
  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    52   2   0   5
  10Q GAIN WILD-TYPE 291  10   4  21
D20V13, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               52                291
  R1                2                 10
  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     3
  10Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           4    55
  10Q GAIN WILD-TYPE                        47   334
D20V14, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  4
  BLACK OR AFRICAN AMERICAN                       4                 47
  WHITE                                          55                334
[1] 4 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  50
  10Q GAIN WILD-TYPE   6 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   50
  10Q GAIN WILD-TYPE    6  332
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               50                332
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    53  38
  11P GAIN WILD-TYPE 272 129
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                91                401 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                38                129 
$`11P GAIN MUTATED`
TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 TCGA-05-4432 
        8.02         2.99        14.96        29.98        21.99        25.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-38-4628 TCGA-38-4629 TCGA-44-2659 
       15.02         4.96         9.04        49.05        28.41        44.94 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7669 TCGA-44-7670 
       61.28        16.44        19.46        12.03        18.87        29.00 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU TCGA-49-4488 
        3.25        15.98        15.32         9.44        13.45        28.57 
TCGA-49-4512 TCGA-49-6743 TCGA-50-5933 TCGA-50-6597 TCGA-53-7813 TCGA-55-1592 
       29.75        53.29        78.67        41.69        13.94        23.05 
TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 TCGA-55-6979 
       38.73         0.07         0.79         0.82         3.88         7.79 
TCGA-55-6981 TCGA-55-7995 TCGA-55-8092 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 
       45.34         0.16         5.06        23.64        17.98         1.08 
TCGA-55-8514 TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 
        6.64         2.17        15.81        20.19        17.95         4.57 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A470 TCGA-64-1677 TCGA-64-1681 TCGA-64-5775 
       88.64        49.25        39.25        20.65        38.37         2.04 
TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-6215 TCGA-69-7764 TCGA-69-7973 
       28.41         1.02        20.05         5.72        13.61         7.56 
TCGA-69-7974 TCGA-71-6725 TCGA-73-4662 TCGA-78-7163 TCGA-78-7167 TCGA-78-7542 
        6.05         2.01        82.68       238.29        88.14        10.55 
TCGA-78-8655 TCGA-86-6851 TCGA-86-7955 TCGA-86-8278 TCGA-86-8280 TCGA-86-A4P7 
       77.59         5.88        35.24        31.04        23.05        13.64 
TCGA-91-6829 TCGA-91-6840 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7043 
       41.36        12.23         7.36        17.46         1.08        16.54 
TCGA-95-7562 TCGA-97-7554 TCGA-97-7937 TCGA-97-8177 TCGA-99-8033 TCGA-L9-A443 
        2.86        25.48         5.95        16.41        21.57         6.35 
TCGA-MN-A4N4 TCGA-MP-A4T6 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TJ TCGA-O1-A52J 
       38.63        58.85        31.23         2.43        11.15        59.11 
TCGA-S2-AA1A 
       16.87 

$`11P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03        47.05        19.00        20.05 
TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
        9.01        12.00        30.02        26.01        26.01        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 
       24.00        15.02        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-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
       43.53        46.98        44.42        38.10        42.08        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-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 
       63.72        32.45        22.72         7.17        36.07        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       13.74        12.66         8.55        11.08        11.54        13.64 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       76.21        28.11        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
       32.84         8.81        29.46        55.89        16.04        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       17.16        11.64        22.26        22.26       156.66        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO 
       62.24        28.90         8.55        40.41        37.32       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        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        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-A4EZ TCGA-55-1595 
        7.59        27.25        34.29        30.54        35.21        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       45.21         2.86        32.65        42.51        40.73        15.25 
TCGA-55-6972 TCGA-55-6978 TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
       48.49         5.49         2.20        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1.28         1.12         0.79         1.78        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 
        3.29        19.66        19.73         0.13        15.65         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
        4.80        17.62         0.49         1.58         1.61        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46O 
        0.92        19.99        39.98        42.38        14.60        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-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-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       87.98        42.90        51.25        28.47        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       22.68         5.42         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 
       13.45         4.24        25.91        17.16        52.60        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-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       39.09        50.33        11.18       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-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        9.57       104.19         8.48        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        50.24       232.18        39.75 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       10.55       110.50        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-86-8279 
        4.57        24.33         0.79        22.82        32.65        31.20 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        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-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62         1.97        10.19         2.60        13.71 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP 
        1.45        19.82        22.45         6.12        23.61        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       17.29        41.82        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        43.79         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 
       17.92         5.39        18.12        15.39        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.63        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       32.48        19.00        14.30        10.09        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
       21.83        18.58        15.65        27.19         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
       58.45        49.35        37.35        86.04         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       41.59        10.09        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       29.13         0.26         0.43        19.82        20.28 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            238.29             232.18 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             16.54              20.55 
[1] "0.1 - 238.3 (16.5)" "0.0 - 232.2 (20.6)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         0       26       23        0         6        12
  11P GAIN WILD-TYPE       5      109      116        1        46        60
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11P GAIN MUTATED           18          4        5
  11P GAIN WILD-TYPE         54          7       21
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 26                109
  STAGE IB                 23                116
  STAGE II                  0                  1
  STAGE IIA                 6                 46
  STAGE IIB                12                 60
  STAGE IIIA               18                 54
  STAGE IIIB                4                  7
  STAGE IV                  5                 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    34  50   4   5
  11P GAIN WILD-TYPE 136 228  42  14
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               34                136
  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
  11P GAIN MUTATED    58  14    20
  11P GAIN WILD-TYPE 274  82    56
D21V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                  58                274
  N1                  14                 82
  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"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    61   5
  11P GAIN WILD-TYPE 288  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     61    5
  11P GAIN WILD-TYPE  288   20
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               61                288
  1                5                 20
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    58  36
  11P GAIN WILD-TYPE 217 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     58   36
  11P GAIN WILD-TYPE  217  204
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               58                217
  MALE                 36                204
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    71   6
  11P GAIN WILD-TYPE 289  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     71    6
  11P GAIN WILD-TYPE  289   48
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                71                289
  YES                6                 48
[1] 2 2
[1] FALSE
D21V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11P GAIN MUTATED                            2
  11P GAIN WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11P GAIN MUTATED                                  19
  11P GAIN WILD-TYPE                                87
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                   61
  11P GAIN WILD-TYPE                                                259
                    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                             4
  11P GAIN WILD-TYPE                            2                            19
                    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                                19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               61
  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                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   11P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                259
  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                                      19
  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   2   1   4
  11P GAIN WILD-TYPE 280  10   3  22
D21V13, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               63                280
  R1                2                 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
  11P GAIN MUTATED                                  0     1
  11P GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           8    71
  11P GAIN WILD-TYPE                        43   318
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                       8                 43
  WHITE                                          71                318
[1] 4 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     1  69
  11P GAIN WILD-TYPE   6 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   69
  11P GAIN WILD-TYPE    6  313
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               69                313
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    65  44
  11Q GAIN WILD-TYPE 260 123
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               109                383 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                44                123 
$`11Q GAIN MUTATED`
TCGA-05-4402 TCGA-05-4415 TCGA-05-4420 TCGA-05-4425 TCGA-05-4432 TCGA-05-5423 
        8.02         2.99        29.98        21.99        25.02         4.96 
TCGA-05-5429 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 TCGA-44-2659 TCGA-44-6774 
        9.04        49.05        28.41        44.61        44.94        21.63 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
       61.28        16.44        19.46        12.03         7.17        18.87 
TCGA-44-7670 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU 
       29.00        12.66        15.98        15.32         9.44        13.45 
TCGA-49-4512 TCGA-49-6743 TCGA-49-AAR3 TCGA-49-AARO TCGA-50-5933 TCGA-50-6597 
       29.75        53.29        62.24       123.58        78.67        41.69 
TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 
       34.29        13.94        23.05        38.73        45.21         0.07 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 TCGA-55-6979 TCGA-55-6981 TCGA-55-7910 
        0.79         0.82         3.88         7.79        45.34         6.48 
TCGA-55-7994 TCGA-55-8092 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8506 
       19.82         5.06        23.64        17.98         1.08         0.36 
TCGA-55-8510 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DF 
       17.72         6.64         1.58         2.17        15.81        20.19 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 
       19.99        17.95         4.57        88.64        49.25        20.65 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-6215 
       38.37         2.04        28.41         1.02        20.05         5.72 
TCGA-69-7973 TCGA-69-7974 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4666 
        7.56         6.05        17.16         2.01        52.60        26.30 
TCGA-73-4668 TCGA-73-4676 TCGA-78-7154 TCGA-78-7155 TCGA-78-7163 TCGA-78-7167 
       15.35         9.24        19.50        38.50       238.29        88.14 
TCGA-78-7535 TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 TCGA-86-7955 TCGA-86-8278 
       31.20        77.59       110.50         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-91-A4BC TCGA-93-7348 TCGA-93-A4JO TCGA-95-7043 TCGA-95-7562 
        7.36         1.45        17.46         1.08        16.54         2.86 
TCGA-97-7553 TCGA-97-7937 TCGA-97-8177 TCGA-97-A4M1 TCGA-99-8033 TCGA-L9-A443 
       43.79         5.95        16.41        19.76        21.57         6.35 
TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MP-A4T6 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-O1-A52J 
        1.91        38.63        58.85        31.23         2.43        59.11 
TCGA-S2-AA1A 
       16.87 

$`11Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03        47.05        19.00        20.05 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 
       14.96         9.01        12.00        30.02        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 
       25.02        24.00        15.02        15.02        29.00        22.03 
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-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
      120.79        37.71        35.28        11.64        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
        4.37        43.53        46.98        44.42        38.10        42.08 
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-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
       23.77        19.56         9.93        27.78        23.15        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 
       63.72        32.45        22.72        36.07        29.23        13.74 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
        3.25         8.55        11.08        11.54        13.64        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
       32.84         8.81        29.46        55.89        16.04        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       17.16        11.64        22.26        22.26       156.66        73.12 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        40.41        37.32       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        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        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         7.59        27.25 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 
       30.54        35.21        48.62         2.86        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6978 TCGA-55-6980 TCGA-55-6982 
       40.73        15.25        48.49         5.49         2.20        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
       18.64         0.53        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 
       15.19         3.29        19.66        19.73         0.13        15.65 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.95         0.26         0.49         0.30         0.10         4.80 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
       17.62         0.49         1.61        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-62-8395 
       21.40         1.58        20.58        19.59         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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        5.42         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 
        4.24        25.91        23.38        82.68         4.31        30.31 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        1.25        39.09        50.33        11.18       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-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
      119.51        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      104.19         8.48        26.53         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 
       39.35        10.55        50.24       232.18        39.75        10.55 
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-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       32.78        19.89        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
        0.79        22.82        32.65        21.47         1.15        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-91-6830 TCGA-91-6831 
        3.81        24.23        26.47        10.62         1.97        10.19 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
        2.60        13.71        27.68         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45         6.12        23.61 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       19.00        17.29        41.82        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 
       31.69        64.60        63.52        25.48         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
       18.67        17.92         5.39        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.58        20.19        21.44        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.63        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 
       32.48        19.00        14.30        10.09        14.53        21.83 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       18.58        15.65        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        86.04         5.49         5.29        41.59 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       10.09        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        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       29.13         0.26         0.43        19.82        20.28 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            238.29             232.18 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             17.98              20.55 
[1] "0.1 - 238.3 (18.0)" "0.0 - 232.2 (20.6)"
[1] "hr=" "1.3"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         0       25       30        0        10        18
  11Q GAIN WILD-TYPE       5      110      109        1        42        54
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11Q GAIN MUTATED           18          4        9
  11Q GAIN WILD-TYPE         54          7       17
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 25                110
  STAGE IB                 30                109
  STAGE II                  0                  1
  STAGE IIA                10                 42
  STAGE IIB                18                 54
  STAGE IIIA               18                 54
  STAGE IIIB                4                  7
  STAGE IV                  9                 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
  11Q GAIN MUTATED    35  64   9   5
  11Q GAIN WILD-TYPE 135 214  37  14
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               35                135
  T2               64                214
  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
  11Q GAIN MUTATED    70  21    21
  11Q GAIN WILD-TYPE 262  75    55
D22V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                  70                262
  N1                  21                 75
  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"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    69   9
  11Q GAIN WILD-TYPE 280  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     69    9
  11Q GAIN WILD-TYPE  280   16
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               69                280
  1                9                 16
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    68  46
  11Q GAIN WILD-TYPE 207 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     68   46
  11Q GAIN WILD-TYPE  207  194
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               68                207
  MALE                 46                194
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    79  11
  11Q GAIN WILD-TYPE 281  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     79   11
  11Q GAIN WILD-TYPE  281   43
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                79                281
  YES               11                 43
[1] 2 2
[1] FALSE
D22V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11Q GAIN MUTATED                            1
  11Q GAIN WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11Q GAIN MUTATED                                  20
  11Q GAIN WILD-TYPE                                86
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                   80
  11Q GAIN WILD-TYPE                                                240
                    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                             4
  11Q GAIN WILD-TYPE                            2                            19
                    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                                20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               80
  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                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   11Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                240
  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                                      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"
D22V11, continuous
D22V12, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    76   3   1   5
  11Q GAIN WILD-TYPE 267   9   3  21
D22V13, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               76                267
  R1                3                  9
  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
  11Q GAIN MUTATED                                  1     2
  11Q GAIN WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                          14    83
  11Q GAIN WILD-TYPE                        37   306
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                 37
  WHITE                                          83                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"
D22V15, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     2  86
  11Q GAIN WILD-TYPE   5 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2   86
  11Q GAIN WILD-TYPE    5  296
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               86                296
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    84  49
  12P GAIN WILD-TYPE 241 118
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               133                359 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                118 
$`12P GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 
       45.01        37.02         0.00         8.02         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4432 TCGA-05-5420 TCGA-05-5428 TCGA-35-4122 
        9.01        29.98        25.02        15.02        22.03         7.40 
TCGA-35-5375 TCGA-38-4631 TCGA-38-4632 TCGA-44-5643 TCGA-44-5644 TCGA-44-7660 
        8.68        11.64        44.61        33.30        28.37        19.46 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
       36.07        18.87        29.00        13.74         3.25        15.98 
TCGA-44-A47A TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6767 TCGA-49-AAR0 
       15.32        29.46        29.75        16.04        22.26       156.66 
TCGA-49-AAR9 TCGA-49-AARO TCGA-50-5045 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 
        8.55       123.58        71.47         8.09        14.27         9.37 
TCGA-50-5944 TCGA-50-6592 TCGA-50-6597 TCGA-50-6673 TCGA-55-1594 TCGA-55-1595 
       25.12        25.55        41.69         0.72        38.73        48.62 
TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 
       45.21        32.65         0.79         5.49         2.20        45.34 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7284 TCGA-55-7576 TCGA-55-7726 TCGA-55-7728 
       40.54        70.26         7.99         1.32         1.28         0.79 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 
        0.53         6.48        17.65         0.16         3.29         0.13 
TCGA-55-8096 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       23.64        22.16         0.76         0.95         0.26         0.49 
TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 
        0.49         1.58         0.92        15.81        20.19        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 
       49.25        47.80        13.61        39.25        40.96        39.09 
TCGA-64-1681 TCGA-64-5775 TCGA-67-3774 TCGA-69-7973 TCGA-69-7980 TCGA-69-A59K 
       38.37         2.04        12.66         7.56        12.56        17.16 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
       26.30         4.31        30.31        27.16         5.69        20.58 
TCGA-78-7154 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 TCGA-78-8655 TCGA-86-6562 
       19.50        64.90        88.14        26.53        77.59        12.36 
TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8278 TCGA-86-8280 
        5.88        38.04        32.78        19.89        31.04        23.05 
TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6836 
        1.15        30.84         3.81        10.62        41.36        13.71 
TCGA-91-6848 TCGA-91-8499 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 
        7.36         1.18         6.12        18.67        12.39         2.76 
TCGA-95-A4VP TCGA-97-8176 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 
       19.89        15.39        20.58        20.68         1.45        21.57 
TCGA-L9-A443 TCGA-L9-A5IP TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY 
        6.35         1.91        27.19        38.63        86.14        49.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TI TCGA-NJ-A55R 
       58.85         5.49        10.09        29.46        14.10        19.82 
TCGA-S2-AA1A 
       16.87 

$`12P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 
       50.07         3.98        19.96        14.01         9.96        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       47.05        19.00        20.05        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 
       26.01        26.01        25.02        24.00        15.02         4.96 
TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 
       29.00         9.04         2.04         0.46         5.98        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 
      120.79        37.71        49.05        28.41        35.28        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       26.30         4.37        43.53        46.98        44.42        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       38.10        42.08        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       38.24        38.89        34.06        33.73        26.56        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47B 
       12.03         7.17        29.23        12.66         8.55         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        8.81        55.89        53.29        55.33        17.16        11.64 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN 
       22.26        73.12        62.24        28.90        40.41        37.32 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 
      221.33       164.12         9.86        20.52        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
       60.16        31.04        49.28         9.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
       21.47         8.45        15.12        29.03        22.55        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 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       23.05         2.86         0.07        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 TCGA-55-6982 TCGA-55-6983 
        0.82        48.49         3.88         7.79        32.71        60.03 
TCGA-55-6984 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 
       24.99       107.21         0.59         1.15         0.20         0.13 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
        3.12        23.18         1.28         1.12         1.78        18.64 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
        6.15        19.82        29.72        15.19        19.66        19.73 
TCGA-55-8092 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        5.06        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
       15.42         1.45         0.36        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64        17.62         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
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-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
       19.53        56.71        54.35        67.96        72.30        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 
       56.81        20.65        81.80        37.02        87.98        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         1.02        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         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 
        2.93        14.01        13.45         4.24        25.91         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 
       52.60        23.38        82.68        15.35         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7147 TCGA-78-7149 
       39.09        50.33        11.18       163.10        19.27       129.53 
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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
       22.92         9.57       104.19       238.29         8.48        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-7701 
      232.18        39.75        10.55       110.50        27.09        31.13 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       34.39        20.55        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8358 
       24.33         0.79        22.82        32.65        31.20        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       14.60        13.91        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 
       29.46        24.23        13.64        26.47         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
        2.60        12.23        27.68         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.45        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 
       15.68        15.65        27.29        21.40        18.18        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        0.72        18.67        17.92         5.39        18.12        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       14.30        21.60        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       17.75        20.84        18.67        24.56        34.85        36.76 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.63        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
       19.00        14.30        10.09        14.53        21.83        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 
       15.65         2.76        58.45        37.35        86.04         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ 
       41.59        31.23         2.43        11.05        24.36        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        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13         0.26         0.43        20.28        59.11 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.00               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            156.66             238.29 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             17.16              20.58 
[1] "0.0 - 156.7 (17.2)" "0.1 - 238.3 (20.6)"
[1] "hr=" "1.4"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         3       31       30        0        20        15
  12P GAIN WILD-TYPE       2      104      109        1        32        57
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12P GAIN MUTATED           26          2       10
  12P GAIN WILD-TYPE         46          9       16
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 31                104
  STAGE IB                 30                109
  STAGE II                  0                  1
  STAGE IIA                20                 32
  STAGE IIB                15                 57
  STAGE IIIA               26                 46
  STAGE IIIB                2                  9
  STAGE IV                 10                 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
  12P GAIN MUTATED    41  78  13   4
  12P GAIN WILD-TYPE 129 200  33  15
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               41                129
  T2               78                200
  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    82  26    26
  12P GAIN WILD-TYPE 250  70    50
D23V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                  82                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"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    88  10
  12P GAIN WILD-TYPE 261  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     88   10
  12P GAIN WILD-TYPE  261   15
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               88                261
  1               10                 15
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    67  70
  12P GAIN WILD-TYPE 208 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     67   70
  12P GAIN WILD-TYPE  208  170
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               67                208
  MALE                 70                170
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    89  12
  12P GAIN WILD-TYPE 271  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     89   12
  12P GAIN WILD-TYPE  271   42
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                89                271
  YES               12                 42
[1] 2 2
[1] FALSE
D23V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12P GAIN MUTATED                            4
  12P GAIN WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12P GAIN MUTATED                                  23
  12P GAIN WILD-TYPE                                83
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                   95
  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)               95
  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                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  83
  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    97   3   2   6
  12P GAIN WILD-TYPE 246   9   2  20
D23V13, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               97                246
  R1                3                  9
  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                          16    99
  12P GAIN WILD-TYPE                        35   290
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                      16                 35
  WHITE                                          99                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"
D23V15, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1  99
  12P GAIN WILD-TYPE   6 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   99
  12P GAIN WILD-TYPE    6  283
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               99                283
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    81  44
  12Q GAIN WILD-TYPE 244 123
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               125                367 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                44                123 
$`12Q GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 
       45.01        37.02         0.00         8.02         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 
        9.01        29.98        25.02        15.02        29.00         7.40 
TCGA-35-5375 TCGA-38-4631 TCGA-44-5644 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 
        8.68        11.64        28.37        61.28        19.46        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
       18.87        29.00        13.74         3.25        15.98        15.32 
TCGA-44-A47B TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6767 TCGA-49-AAR0 
        9.44        29.46        29.75        16.04        22.26       156.66 
TCGA-49-AAR9 TCGA-50-5045 TCGA-50-5051 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 
        8.55        71.47        15.72         8.09        14.27         9.37 
TCGA-50-5944 TCGA-50-6592 TCGA-50-6673 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 
       25.12        25.55         0.72        13.94        38.73        48.62 
TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6978 TCGA-55-6981 
       45.21        32.65         0.79         0.82         5.49        45.34 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 
       70.26         7.99         1.28         0.79         1.78         6.48 
TCGA-55-7911 TCGA-55-8089 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       17.65         3.29        22.16         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
        0.49         0.49         1.58        20.58         0.92        15.81 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V TCGA-62-A470 
       20.19        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 
       12.56         4.24        17.16        26.30         4.31        30.31 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7167 TCGA-78-7220 TCGA-78-8655 
       27.16         5.69        20.58        88.14        26.53        77.59 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
       12.36         5.88        31.13        38.04        32.78        19.89 
TCGA-86-8278 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 
       31.04        21.47         1.15        30.84         3.81        10.62 
TCGA-91-6836 TCGA-91-6840 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 
       13.71        12.23         6.12        18.67        12.39         2.76 
TCGA-95-A4VP TCGA-97-8176 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 
       19.89        15.39        20.58        20.68         1.45        21.57 
TCGA-L9-A443 TCGA-L9-A5IP TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 
        6.35         1.91        86.14        49.35        58.85         5.49 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TI TCGA-NJ-A4YI TCGA-NJ-A55R 
       10.09        29.46        14.10         0.13        19.82 

$`12Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 
       50.07         3.98        19.96        14.01         9.96        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       47.05        19.00        20.05        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 
       26.01        26.01        25.02        24.00        15.02         4.96 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 
       22.03         9.04         2.04         0.46         5.98        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
      120.79        37.71        49.05        28.41        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.94        38.10        42.08        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-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 
       23.15        21.63        23.18        63.72        32.45        16.44 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 
       22.72        12.03         7.17        29.23        12.66         8.55 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        8.81        55.89        53.29        55.33        17.16        11.64 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN 
       22.26        73.12        62.24        28.90        40.41        37.32 
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        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
       60.16        31.04        49.28         9.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
       21.47         8.45        15.12        29.03        22.55        42.35 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-7109 
        3.91        11.05        12.16         6.21        41.69        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       36.99         7.59        27.25        34.29        30.54        35.21 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       23.05         2.86         0.07        42.51        40.73        15.25 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 
       48.49         3.88         7.79         2.20        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
       24.99        40.54       107.21         0.59         1.15         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 
        0.13         3.12         1.32        23.18         1.28         1.12 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       18.64         0.53         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
       15.65        17.98         1.08         1.51         2.17        15.42 
TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        1.45         0.36        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64        17.62         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 TCGA-55-A4DG TCGA-55-A57B 
       22.65        20.71        21.40        19.59        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R 
        4.57        39.98        42.38        88.64        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       54.35        67.96        13.61        29.92        56.81        20.65 
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         1.02        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
       13.61         5.42         6.05         4.41         2.93        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       13.45        25.91         2.01        52.60        23.38        82.68 
TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
       15.35         9.24         1.25        39.09        50.33        11.18 
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-78-7154 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-78-7166 TCGA-78-7535 TCGA-78-7536 
        9.57       104.19       238.29         8.48        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-7711 TCGA-86-7714 
       39.75        10.55       110.50        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-86-8280 TCGA-86-8359 TCGA-86-8668 
       22.82        32.65        31.20        23.05        14.60        13.91 
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-91-6829 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-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
        1.18         1.45        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 
       15.68        15.65        27.29        21.40        18.18        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        0.72        18.67        17.92         5.39        18.12        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       14.30        21.60        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       17.75        20.84        18.67        24.56        34.85        36.76 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.63        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
       19.00        14.30        10.09        14.53        21.83        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
       15.65        27.19        38.63         2.76        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
       86.04         5.29        41.59        31.23         2.43        11.05 
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        62.60 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.00               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            156.66             238.29 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             15.98              20.71 
[1] "0.0 - 156.7 (16.0)" "0.1 - 238.3 (20.7)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         3       28       31        0        16        16
  12Q GAIN WILD-TYPE       2      107      108        1        36        56
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12Q GAIN MUTATED           24          3        9
  12Q GAIN WILD-TYPE         48          8       17
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 28                107
  STAGE IB                 31                108
  STAGE II                  0                  1
  STAGE IIA                16                 36
  STAGE IIB                16                 56
  STAGE IIIA               24                 48
  STAGE IIIB                3                  8
  STAGE IV                  9                 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
  12Q GAIN MUTATED    37  76  12   4
  12Q GAIN WILD-TYPE 133 202  34  15
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               37                133
  T2               76                202
  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    80  23    25
  12Q GAIN WILD-TYPE 252  73    51
D24V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                  80                252
  N1                  23                 73
  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"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    85   9
  12Q GAIN WILD-TYPE 264  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     85    9
  12Q GAIN WILD-TYPE  264   16
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               85                264
  1                9                 16
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    65  65
  12Q GAIN WILD-TYPE 210 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     65   65
  12Q GAIN WILD-TYPE  210  175
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               65                210
  MALE                 65                175
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    88  11
  12Q GAIN WILD-TYPE 272  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     88   11
  12Q GAIN WILD-TYPE  272   43
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                88                272
  YES               11                 43
[1] 2 2
[1] FALSE
D24V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12Q GAIN MUTATED                            5
  12Q GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12Q GAIN MUTATED                                  22
  12Q GAIN WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                   90
  12Q GAIN WILD-TYPE                                                230
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12Q GAIN MUTATED                                            0
  12Q GAIN WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12Q GAIN MUTATED                                               4
  12Q GAIN WILD-TYPE                                            15
                    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)               90
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  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                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                230
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  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    90   3   2   6
  12Q GAIN WILD-TYPE 253   9   2  20
D24V13, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               90                253
  R1                3                  9
  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                          11    95
  12Q GAIN WILD-TYPE                        40   294
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                      11                 40
  WHITE                                          95                294
[1] 4 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  90
  12Q GAIN WILD-TYPE   5 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   90
  12Q GAIN WILD-TYPE    5  292
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               90                292
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    25  17
  13Q GAIN WILD-TYPE 300 150
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                42                450 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                17                150 
$`13Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-5428 TCGA-38-4631 TCGA-44-2655 TCGA-44-2659 
       50.07        19.96        22.03        11.64        43.53        44.94 
TCGA-44-7660 TCGA-44-7671 TCGA-49-6742 TCGA-50-6591 TCGA-50-6673 TCGA-53-7624 
       19.46        29.23        16.04         3.91         0.72        34.29 
TCGA-53-7626 TCGA-55-6968 TCGA-55-7281 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 
       30.54        42.51         0.59         1.28         0.53         6.48 
TCGA-55-8089 TCGA-55-8205 TCGA-55-8620 TCGA-55-A492 TCGA-62-8402 TCGA-64-1678 
        3.29         1.08         2.17        19.59        49.25        39.09 
TCGA-64-1680 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-69-8253 TCGA-73-4677 
       37.02        20.05        18.84         5.72        14.01         1.25 
TCGA-78-7143 TCGA-78-7149 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-86-6562 
      163.10       129.53        88.14        26.53        53.33        12.36 
TCGA-86-8074 TCGA-86-8672 TCGA-97-7547 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-NJ-A4YG 
        0.79         0.62        64.60        58.45         5.49        62.60 

$`13Q GAIN WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
        3.98        14.01        45.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       15.02         4.96        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-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        4.37        46.98        44.42        38.10        42.08        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-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
       63.72        32.45        61.28        16.44        22.72        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
        7.17        36.07        18.87        29.00        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
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-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.46        29.75        55.89        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       11.64        22.26        22.26       156.66        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       28.90         8.55        40.41        37.32       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        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 
       29.03        25.12        22.55        42.35        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21        41.69        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
       27.25        13.94        35.21        23.05        38.73        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       45.21         2.86         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
      107.21        70.26         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        3.12         1.32        23.18         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        1.78        18.64        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19        19.66        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65        17.98         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       17.62         0.49         1.58         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40         1.58        20.58         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       20.19        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-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 
       42.90        28.41        51.25        28.47         1.02        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         4.64        13.87         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 
        2.93        12.56        13.45         4.24        25.91        17.16 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
        4.31        30.31         9.24        39.09        50.33        11.18 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        19.27        20.58        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-78-7166 TCGA-78-7535 
       22.92         9.57       104.19       238.29         8.48        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 
       39.75        77.59        10.55       110.50        27.09         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-86-8075 
       35.24        37.74         4.08         4.57        24.33        22.82 
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-86-8673 TCGA-86-8674 
        1.15        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-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 
        2.76        21.40        18.18        19.89        31.69        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       36.76         1.45        21.57        21.63        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       18.08        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
       10.09        14.53         1.91        21.83        18.58        15.65 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19        38.63         2.76        86.14        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       86.04        58.85         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       10.09        29.46        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        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.26         0.43        19.82        20.28        59.11        16.87 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.53               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            163.10             238.29 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            19.775             20.020 
[1] "0.5 - 163.1 (19.8)" "0.0 - 238.3 (20.0)"
[1] "hr=" "1"  
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         1        7       12        0         9         4
  13Q GAIN WILD-TYPE       4      128      127        1        43        68
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  13Q GAIN MUTATED            3          1        7
  13Q GAIN WILD-TYPE         69         10       19
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  7                128
  STAGE IB                 12                127
  STAGE II                  0                  1
  STAGE IIA                 9                 43
  STAGE IIB                 4                 68
  STAGE IIIA                3                 69
  STAGE IIIB                1                 10
  STAGE IV                  7                 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  28   1   1
  13Q GAIN WILD-TYPE 156 250  45  18
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               14                156
  T2               28                250
  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    30  10     4
  13Q GAIN WILD-TYPE 302  86    72
D25V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                  30                302
  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   7
  13Q GAIN WILD-TYPE 318  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     31    7
  13Q GAIN WILD-TYPE  318   18
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               31                318
  1                7                 18
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    24  20
  13Q GAIN WILD-TYPE 251 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     24   20
  13Q GAIN WILD-TYPE  251  220
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               24                251
  MALE                 20                220
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    28   6
  13Q GAIN WILD-TYPE 332  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     28    6
  13Q GAIN WILD-TYPE  332   48
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                28                332
  YES                6                 48
[1] 2 2
[1] FALSE
D25V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  13Q GAIN MUTATED                            0
  13Q GAIN WILD-TYPE                         19
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  13Q GAIN MUTATED                                   9
  13Q GAIN WILD-TYPE                                97
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                   31
  13Q GAIN WILD-TYPE                                                289
                    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)               31
  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                                         19
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                289
  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 307  12   4  26
D25V13, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               36                307
  R1                0                 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
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           4    33
  13Q GAIN WILD-TYPE                        47   356
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                 47
  WHITE                                          33                356
[1] 4 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  28
  13Q GAIN WILD-TYPE   6 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   28
  13Q GAIN WILD-TYPE    6  354
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               28                354
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    82  41
  14Q GAIN WILD-TYPE 243 126
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               123                369 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                41                126 
$`14Q GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 TCGA-05-4424 
       45.01        37.02         8.02         2.99        14.96        30.02 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4627 TCGA-38-4629 TCGA-44-2659 TCGA-44-3917 
        5.98         8.68        37.71        28.41        44.94        38.89 
TCGA-44-6147 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       27.78        61.28        16.44        19.46         7.17        36.07 
TCGA-44-7670 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU 
       29.00         3.25        15.98        15.32         9.44        13.45 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAQV 
       76.21        28.57        12.66        29.75        22.26        22.26 
TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5941 TCGA-50-5946 
       28.90       123.58       221.33         9.86         9.37        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 TCGA-50-7109 TCGA-53-A4EZ TCGA-55-5899 
       42.35         3.91        12.16        10.13        35.21         2.86 
TCGA-55-6543 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6983 TCGA-55-7724 
        0.07        15.25         0.82         3.88        60.03        23.18 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8091 
        1.78         0.53         6.48         0.16        29.72        19.73 
TCGA-55-8096 TCGA-55-8203 TCGA-55-8206 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
       23.64        17.98         1.51         0.76         0.36         0.26 
TCGA-55-8510 TCGA-55-8614 TCGA-55-A490 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       17.72        17.62         1.58        19.99        17.95         4.57 
TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-67-3770 TCGA-67-3771 
       20.65        39.09        87.98         2.04         1.02        20.05 
TCGA-67-3773 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-71-6725 
       14.04        22.68         7.56         6.05         2.93         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4677 TCGA-73-7499 TCGA-78-7145 
       52.60        23.38        26.30         1.25        50.33        27.16 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-83-5908 
       20.58       129.53        64.90         9.57        88.14        27.09 
TCGA-86-6562 TCGA-86-7955 TCGA-86-8054 TCGA-86-8074 TCGA-86-8278 TCGA-86-8280 
       12.36        35.24        37.74         0.79        31.04        23.05 
TCGA-86-8358 TCGA-86-8585 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       21.47         1.15        10.62         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-8067 TCGA-93-A4JN 
       27.68        16.60        14.27         1.18         6.12        23.61 
TCGA-93-A4JP TCGA-95-7562 TCGA-95-A4VP TCGA-97-7546 TCGA-97-8179 TCGA-97-A4LX 
       19.00         2.86        19.89        31.69        14.30        20.19 
TCGA-J2-8192 TCGA-L9-A443 TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TE 
       24.30         6.35        49.35        58.85        41.59        29.46 
TCGA-MP-A4TF TCGA-NJ-A55R TCGA-O1-A52J 
       11.05        19.82        59.11 

$`14Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        19.96        14.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4418 TCGA-05-4420 
       24.03        47.05        19.00        20.05         9.01        29.98 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       12.00        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         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-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
        4.37        43.53        46.98        44.42        38.10        42.08 
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-44-5643 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-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       19.56         9.93        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 
       32.45        22.72        12.03        18.87        29.23        13.74 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4487 
       12.66         8.55        11.08        11.54        13.64        28.11 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
      156.66        73.12        62.24         8.55        40.41        37.32 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
      164.12        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       78.67        21.47         8.45        15.12        29.03        25.12 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 
       25.55        11.05         6.21        41.69         0.72        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
        7.59        27.25        34.29        30.54        13.94        23.05 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       38.73        48.62        45.21        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       40.73        48.49         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       32.71        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7911 
        1.28         1.28         1.12         0.79        18.64        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 
        6.15        19.82        15.19         3.29        19.66         5.06 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
        0.13        15.65         1.08         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        1.45         0.95         0.49         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       22.65        20.71        21.40        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       15.81        20.19        39.98        42.38        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-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       81.80        37.02        38.37        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        18.84        12.66        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 
       13.87         6.64         6.12        13.61         5.42         4.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K 
       12.56        14.01        13.45         4.24        25.91        17.16 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 
       82.68        15.35         4.31        30.31         9.24        39.09 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 
       11.18       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-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29         8.48        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 TCGA-86-7701 
       39.75        77.59        10.55       110.50         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8055 
       34.39        38.04        20.55        32.78        19.89         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8359 
        4.57        24.33        22.82        32.65        31.20        14.60 
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-91-6829 
       29.46         3.81        24.23        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-A4BC 
        1.97        10.19         7.36         1.15        16.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 
       19.82        22.45        17.46         1.08        17.29        41.82 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
       16.54        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        21.40        18.18        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
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-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.63        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
       14.30        10.09        14.53         1.91        21.83        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       15.65        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       37.35        86.04         5.49         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       10.09        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        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.43        20.28        16.87 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.07               0.00 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            221.33             238.29 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             19.00              20.52 
[1] "0.1 - 221.3 (19.0)" "0.0 - 238.3 (20.5)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         1       37       36        1        15        15
  14Q GAIN WILD-TYPE       4       98      103        0        37        57
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  14Q GAIN MUTATED           15          3        7
  14Q GAIN WILD-TYPE         57          8       19
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 37                 98
  STAGE IB                 36                103
  STAGE II                  1                  0
  STAGE IIA                15                 37
  STAGE IIB                15                 57
  STAGE IIIA               15                 57
  STAGE IIIB                3                  8
  STAGE IV                  7                 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  72   9   5
  14Q GAIN WILD-TYPE 127 206  37  14
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               43                127
  T2               72                206
  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    89  20    16
  14Q GAIN WILD-TYPE 243  76    60
D26V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                  89                243
  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    74   7
  14Q GAIN WILD-TYPE 275  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     74    7
  14Q GAIN WILD-TYPE  275   18
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               74                275
  1                7                 18
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    76  54
  14Q GAIN WILD-TYPE 199 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     76   54
  14Q GAIN WILD-TYPE  199  186
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               76                199
  MALE                 54                186
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    92  11
  14Q GAIN WILD-TYPE 268  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     92   11
  14Q GAIN WILD-TYPE  268   43
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                92                268
  YES               11                 43
[1] 2 2
[1] FALSE
D26V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  14Q GAIN MUTATED                            7
  14Q GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  14Q GAIN MUTATED                                  21
  14Q GAIN WILD-TYPE                                85
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                   89
  14Q GAIN WILD-TYPE                                                231
                    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                             6
  14Q GAIN WILD-TYPE                            2                            17
                    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                                        7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                21
  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                                     6
  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)                231
  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                                      17
  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    82   5   1   9
  14Q GAIN WILD-TYPE 261   7   3  17
D26V13, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               82                261
  R1                5                  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   102
  14Q GAIN WILD-TYPE                        39   287
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                 39
  WHITE                                         102                287
[1] 4 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     2  99
  14Q GAIN WILD-TYPE   5 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   99
  14Q GAIN WILD-TYPE    5  283
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               99                283
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    19  19
  15Q GAIN WILD-TYPE 306 148
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                38                454 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                19                148 
$`15Q GAIN MUTATED`
TCGA-05-4403 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-5420 TCGA-44-2661 
       19.00         2.99         9.01        29.98        15.02        38.10 
TCGA-49-4506 TCGA-49-6742 TCGA-4B-A93V TCGA-50-5072 TCGA-50-5936 TCGA-50-5944 
       32.84        16.04         9.86         8.09         8.45        25.12 
TCGA-55-1594 TCGA-55-7284 TCGA-55-8207 TCGA-55-8505 TCGA-62-8398 TCGA-62-8402 
       38.73         7.99         2.17         0.95        14.60        49.25 
TCGA-64-1678 TCGA-69-7980 TCGA-71-6725 TCGA-73-4670 TCGA-73-A9RS TCGA-78-7148 
       39.09        12.56         2.01         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        43.79         5.39        20.58         1.91         5.49 
TCGA-NJ-A4YP TCGA-S2-AA1A 
        1.64        16.87 

$`15Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 
        0.00         9.96        24.03        47.05         8.02        20.05 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       14.96        12.00        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 
       25.02        25.02        24.00        15.02         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-38-4629 
        8.68        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 
       43.53        46.98        44.42        44.94        42.08        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-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
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-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       17.16        11.64        22.26        22.26       156.66        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO 
       62.24        28.90         8.55        40.41        37.32       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      221.33       164.12        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04        49.28         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
       78.67        21.47        15.12         9.37        29.03        22.55 
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-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       34.29        30.54        13.94        35.21        23.05        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       45.21         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        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         0.59         1.15         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        1.12         0.79         1.78        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.08         1.51        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       20.19        19.99        17.95         4.57        39.98        42.38 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        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-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       20.65        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         1.02        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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         4.41         2.93        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.24        25.91        17.16        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       26.30        15.35        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 
       50.33       163.10        27.16         5.69        19.27        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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 
       31.20         8.02        53.33        26.01        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
      232.18        39.75        77.59        10.55        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-86-8056 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-86-8280 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         1.15        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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
       41.82        16.54         2.86        18.67        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
        1.45        21.57        21.63        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
       14.53        21.83        18.58        15.65        27.19        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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.29        41.59        31.23         2.43        10.09 
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        62.60         0.13        29.13         0.26 
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 
              0.95               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            129.53             238.29 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            14.810             20.235 
[1] "0.9 - 129.5 (14.8)" "0.0 - 238.3 (20.2)"
[1] "hr=" "1.9"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         2        6        7        0         4         4
  15Q GAIN WILD-TYPE       3      129      132        1        48        68
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  15Q GAIN MUTATED           10          2        3
  15Q GAIN WILD-TYPE         62          9       23
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  6                129
  STAGE IB                  7                132
  STAGE II                  0                  1
  STAGE IIA                 4                 48
  STAGE IIB                 4                 68
  STAGE IIIA               10                 62
  STAGE IIIB                2                  9
  STAGE IV                  3                 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
  15Q GAIN MUTATED     9  22   5   2
  15Q GAIN WILD-TYPE 161 256  41  17
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                9                161
  T2               22                256
  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    22   4    12
  15Q GAIN WILD-TYPE 310  92    64
D27V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                  22                310
  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    30   3
  15Q GAIN WILD-TYPE 319  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     30    3
  15Q GAIN WILD-TYPE  319   22
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               30                319
  1                3                 22
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    17  21
  15Q GAIN WILD-TYPE 258 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     17   21
  15Q GAIN WILD-TYPE  258  219
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               17                258
  MALE                 21                219
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    23   4
  15Q GAIN WILD-TYPE 337  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     23    4
  15Q GAIN WILD-TYPE  337   50
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                23                337
  YES                4                 50
[1] 2 2
[1] FALSE
D27V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  15Q GAIN MUTATED                            2
  15Q GAIN WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  15Q GAIN MUTATED                                  10
  15Q GAIN WILD-TYPE                                96
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                   16
  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                                10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               16
  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                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  96
  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    28   2   0   1
  15Q GAIN WILD-TYPE 315  10   4  25
D27V13, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               28                315
  R1                2                 10
  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                           4    26
  15Q GAIN WILD-TYPE                        47   363
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                       4                 47
  WHITE                                          26                363
[1] 4 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  25
  15Q GAIN WILD-TYPE   7 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   25
  15Q GAIN WILD-TYPE    7  357
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               25                357
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    78  45
  16P GAIN WILD-TYPE 247 122
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               123                369 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                45                122 
$`16P GAIN MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4395 TCGA-05-5423 TCGA-38-4627 TCGA-38-4628 
       50.07        37.02         0.00         4.96        37.71        49.05 
TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-2659 TCGA-44-2665 TCGA-44-3919 
       28.41        11.64        14.73        44.94        42.77        33.73 
TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 TCGA-44-A47A 
       28.37        61.28        16.44         7.17        18.87        15.32 
TCGA-44-A47B TCGA-44-A4SU TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 
        9.44        13.45        12.66        14.07         8.81        29.75 
TCGA-49-6744 TCGA-49-AAR0 TCGA-49-AARE TCGA-49-AARO TCGA-4B-A93V TCGA-50-5933 
       55.33       156.66        40.41       123.58         9.86        78.67 
TCGA-50-5935 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8460 TCGA-55-1592 
       21.47        41.69         0.72        36.99        27.25        23.05 
TCGA-55-6712 TCGA-55-6980 TCGA-55-7281 TCGA-55-7284 TCGA-55-7573 TCGA-55-7726 
        0.79         2.20         0.59         7.99         0.13         1.28 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 
        0.53         6.48         0.16        19.73         5.06        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8512 TCGA-55-8615 TCGA-55-8620 TCGA-55-A490 
       15.65         1.51         0.10         0.49         2.17         1.58 
TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8398 TCGA-62-A46S TCGA-64-1676 
        0.92        19.99        17.95        14.60        54.35        56.81 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-67-3772 TCGA-67-6215 TCGA-67-6217 
       81.80        37.02        38.37        18.84         5.72        13.87 
TCGA-69-7760 TCGA-69-7764 TCGA-69-7980 TCGA-71-6725 TCGA-73-4658 TCGA-73-4668 
        6.64        13.61        12.56         2.01        52.60        15.35 
TCGA-73-4675 TCGA-78-7152 TCGA-78-7154 TCGA-78-7156 TCGA-78-7163 TCGA-78-7535 
       30.31        39.95        19.50        32.09       238.29        31.20 
TCGA-78-7542 TCGA-78-8640 TCGA-86-7701 TCGA-86-7955 TCGA-86-8055 TCGA-86-8075 
       10.55       232.18        31.13        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         1.15        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-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
       23.61        19.00        15.68        21.40        31.69        64.60 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M7 TCGA-99-8025 
       16.41        14.30        20.58        19.76        20.68        34.85 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 
       21.57        18.08        32.48         1.91        15.65        38.63 
TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55R 
       58.45        58.85        62.60         0.13         1.64        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

$`16P GAIN WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 
        3.98        19.96        14.01        45.01         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
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-38-4630 TCGA-38-4632 
        5.98         8.68        97.74       120.79        35.28        44.61 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       26.30         4.37        43.53        46.98        44.42        38.10 
TCGA-44-2662 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.08         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       34.06        26.56        33.30        28.01        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7670 
       32.45        22.72        19.46        12.03        36.07        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.23        13.74        12.66         3.25         8.55        15.98 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.08        11.54        13.64        76.21        28.11        28.57 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
       35.54        46.72        32.84        29.46        55.89        16.04 
TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       53.29        17.16        11.64        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90         8.55        37.32       221.33       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5936 
       49.28         8.09         9.27        14.27        40.60         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        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-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
        7.59        34.29        30.54        13.94        35.21        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       48.62        45.21         2.86         0.07        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
      107.21        70.26         1.15         0.20         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       23.18         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8094 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 
       19.66         0.13        17.98         1.08         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.49        17.72         0.30         4.80         6.64        17.62 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61        16.93        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 
       20.58        19.59        15.81        20.19         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-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-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       20.65        39.09        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
       51.25        28.47         1.02        20.05        14.04        12.66 
TCGA-67-4679 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 
       14.73         4.64         6.12        22.68         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         2.93        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
       25.91        17.16        23.38        82.68        26.30         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
        9.24         1.25        39.09        50.33        11.18       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-78-7153 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
      119.51        38.50         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
      104.19         8.48        88.14        26.53         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       26.01        39.35        50.24        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36         5.88        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       20.55        32.78        19.89        37.74         4.57        24.33 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8358 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
        0.79        32.65        21.47        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       28.34        26.50        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 
       41.36         1.97        10.19         2.60        13.71        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        7.36         1.15        16.18         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       22.45         6.12         1.08        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        12.39        15.65        27.29         2.76 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       18.18        19.89        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 
       15.39        21.60        20.19        21.44        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       20.84        18.67        24.56        36.76         1.45        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       24.30        23.80        35.47        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 
       10.09        14.53        21.83        18.58        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
       86.14        49.35        37.35        86.04         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        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-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       29.13         0.26         0.43 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.00               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            238.29             221.33 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             19.00              20.52 
[1] "0.0 - 238.3 (19.0)" "0.1 - 221.3 (20.5)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         3       39       33        0        13        14
  16P GAIN WILD-TYPE       2       96      106        1        39        58
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16P GAIN MUTATED           17          2       10
  16P GAIN WILD-TYPE         55          9       16
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 39                 96
  STAGE IB                 33                106
  STAGE II                  0                  1
  STAGE IIA                13                 39
  STAGE IIB                14                 58
  STAGE IIIA               17                 55
  STAGE IIIB                2                  9
  STAGE IV                 10                 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
  16P GAIN MUTATED    49  63  13   4
  16P GAIN WILD-TYPE 121 215  33  15
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               49                121
  T2               63                215
  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
  16P GAIN MUTATED    84  25    19
  16P GAIN WILD-TYPE 248  71    57
D28V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                  84                248
  N1                  25                 71
  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"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    84  10
  16P GAIN WILD-TYPE 265  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     84   10
  16P GAIN WILD-TYPE  265   15
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               84                265
  1               10                 15
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    70  61
  16P GAIN WILD-TYPE 205 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     70   61
  16P GAIN WILD-TYPE  205  179
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               70                205
  MALE                 61                179
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    91  15
  16P GAIN WILD-TYPE 269  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     91   15
  16P GAIN WILD-TYPE  269   39
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                91                269
  YES               15                 39
[1] 2 2
[1] FALSE
D28V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16P GAIN MUTATED                            4
  16P GAIN WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16P GAIN MUTATED                                  17
  16P GAIN WILD-TYPE                                89
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                   90
  16P GAIN WILD-TYPE                                                230
                    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                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               90
  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                                  89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                230
  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    90   3   1   8
  16P GAIN WILD-TYPE 253   9   3  18
D28V13, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               90                253
  R1                3                  9
  R2                1                  3
  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
  16P GAIN MUTATED                                  1     3
  16P GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          14   100
  16P GAIN WILD-TYPE                        37   289
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                      14                 37
  WHITE                                         100                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"
D28V15, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0 102
  16P GAIN WILD-TYPE   7 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0  102
  16P GAIN WILD-TYPE    7  280
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO              102                280
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    59  34
  16Q GAIN WILD-TYPE 266 133
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                93                399 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                34                133 
$`16Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4395 TCGA-05-5423 TCGA-38-4627 TCGA-38-4629 TCGA-38-4631 
       50.07         0.00         4.96        37.71        28.41        11.64 
TCGA-38-6178 TCGA-44-2659 TCGA-44-2665 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 
       14.73        44.94        42.77        61.28        16.44         7.17 
TCGA-44-A47A TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-AAR0 
       15.32        14.07         8.81        29.75        55.33       156.66 
TCGA-49-AARE TCGA-4B-A93V TCGA-50-5933 TCGA-50-5935 TCGA-50-6597 TCGA-50-6673 
       40.41         9.86        78.67        21.47        41.69         0.72 
TCGA-50-8460 TCGA-55-1592 TCGA-55-1594 TCGA-55-6712 TCGA-55-6980 TCGA-55-7284 
       27.25        23.05        38.73         0.79         2.20         7.99 
TCGA-55-7726 TCGA-55-7910 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 
        1.28         6.48         3.29        19.73         5.06        15.65 
TCGA-55-8206 TCGA-55-8512 TCGA-55-8615 TCGA-55-A490 TCGA-55-A4DG TCGA-62-8398 
        1.51         0.10         0.49         1.58        19.99        14.60 
TCGA-62-8402 TCGA-62-A46S TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-67-6215 
       49.25        54.35        56.81        81.80        38.37         5.72 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7764 TCGA-69-7980 TCGA-71-6725 TCGA-73-4668 
       13.87         6.64        13.61        12.56         2.01        15.35 
TCGA-73-4675 TCGA-78-7145 TCGA-78-7154 TCGA-78-7163 TCGA-78-7535 TCGA-78-7542 
       30.31        27.16        19.50       238.29        31.20        10.55 
TCGA-78-8640 TCGA-86-7701 TCGA-86-7955 TCGA-86-8055 TCGA-86-8278 TCGA-86-8279 
      232.18        31.13        35.24         4.08        31.04        31.20 
TCGA-86-8280 TCGA-86-8585 TCGA-86-8668 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6840 
       23.05         1.15        13.91        29.46         3.81        12.23 
TCGA-91-8497 TCGA-93-A4JN TCGA-97-7547 TCGA-97-7553 TCGA-97-8177 TCGA-97-8179 
       14.27        23.61        64.60        43.79        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD 
       20.58        19.76        20.68        34.85        21.57        18.08 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T6 TCGA-NJ-A4YG TCGA-NJ-A55R 
        1.91        15.65        38.63        58.85        62.60        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

$`16Q GAIN WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        3.98        19.96        14.01        45.01        37.02         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       15.02        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-38-4628 
        7.40         5.98         8.68        97.74       120.79        49.05 
TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       35.28        44.61        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        38.10        42.08         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-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 
       23.15        21.63        23.18        63.72        32.45        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46        12.03        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       13.74        12.66         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 
       28.57        12.66        35.54        46.72        32.84        29.46 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       55.89        16.04        53.29        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN 
       22.26        73.12        62.24        28.90         8.55        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      123.58       221.33       164.12        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       14.27        40.60         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 
       12.16         6.21        10.13        36.99         7.59        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
       30.54        13.94        35.21        48.62        45.21         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
        0.07        32.65        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 
       48.49         3.88         5.49         7.79        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        1.15         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1.28         1.12         0.79         1.78        18.64         0.53 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 
       19.66         0.13        23.64        17.98         1.08         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 
        0.26         0.49        17.72         0.30         4.80         6.64 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
       17.62         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
       20.19        17.95         4.57        39.98        42.38        88.64 
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-64-1677 TCGA-64-1678 TCGA-64-1680 
       39.25        40.96        29.92        20.65        39.09        37.02 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
        1.02        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        4.64         6.12        22.68         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        4.41         2.93        14.01        13.45         4.24        25.91 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
       17.16        52.60        23.38        82.68        26.30         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
        9.24         1.25        39.09        50.33        11.18       163.10 
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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        9.57       104.19         8.48        88.14        26.53         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35        50.24        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 
       10.55       110.50        27.09        12.36         5.88        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 
       38.04        20.55        32.78        19.89        37.74         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8358 TCGA-86-8359 
       24.33         0.79        22.82        32.65        21.47        14.60 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF 
       30.84        27.58         0.62        28.34        26.50        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-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
        2.60        13.71        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60         1.18         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
        6.12         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 
        2.76        21.40        18.18        19.89        31.69        63.52 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 
        5.39        18.12        15.39        21.60        20.19        21.44 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       20.52        17.75        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        21.63        24.30        23.80        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 
       19.00        14.30         6.35        10.09        14.53        21.83 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       18.58        27.19         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.35        86.04         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        2.43        10.09        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 
       29.13         0.26         0.43 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.00               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            238.29             221.33 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             19.76              20.05 
[1] "0.0 - 238.3 (19.8)" "0.1 - 221.3 (20.1)"
[1] "hr=" "1"  
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         3       29       22        0        11        11
  16Q GAIN WILD-TYPE       2      106      117        1        41        61
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16Q GAIN MUTATED           15          2        6
  16Q GAIN WILD-TYPE         57          9       20
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 29                106
  STAGE IB                 22                117
  STAGE II                  0                  1
  STAGE IIA                11                 41
  STAGE IIB                11                 61
  STAGE IIIA               15                 57
  STAGE IIIB                2                  9
  STAGE IV                  6                 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
  16Q GAIN MUTATED    37  46  11   4
  16Q GAIN WILD-TYPE 133 232  35  15
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               37                133
  T2               46                232
  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    64  19    15
  16Q GAIN WILD-TYPE 268  77    61
D29V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                  64                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    66   6
  16Q GAIN WILD-TYPE 283  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     66    6
  16Q GAIN WILD-TYPE  283   19
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               66                283
  1                6                 19
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    50  49
  16Q GAIN WILD-TYPE 225 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     50   49
  16Q GAIN WILD-TYPE  225  191
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               50                225
  MALE                 49                191
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    70  10
  16Q GAIN WILD-TYPE 290  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     70   10
  16Q GAIN WILD-TYPE  290   44
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                70                290
  YES               10                 44
[1] 2 2
[1] FALSE
D29V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16Q GAIN MUTATED                            3
  16Q GAIN WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16Q GAIN MUTATED                                  10
  16Q GAIN WILD-TYPE                                96
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                   70
  16Q GAIN WILD-TYPE                                                250
                    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                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               70
  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)                250
  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   4   1   5
  16Q GAIN WILD-TYPE 274   8   3  21
D29V13, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               69                274
  R1                4                  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    76
  16Q GAIN WILD-TYPE                        41   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                 41
  WHITE                                          76                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  77
  16Q GAIN WILD-TYPE   7 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   77
  16Q GAIN WILD-TYPE    7  305
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               77                305
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    53  28
  17P GAIN WILD-TYPE 272 139
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                81                411 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                28                139 
$`17P GAIN MUTATED`
TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4432 TCGA-35-5375 
       47.05         2.99        14.96         9.01        25.02         8.68 
TCGA-38-4628 TCGA-44-3396 TCGA-44-3918 TCGA-44-6148 TCGA-44-6777 TCGA-44-A479 
       49.05        37.15        34.06        23.15        32.45        15.98 
TCGA-49-6742 TCGA-50-5930 TCGA-50-5935 TCGA-50-6592 TCGA-50-6593 TCGA-55-5899 
       16.04         9.27        21.47        25.55        11.05         2.86 
TCGA-55-6642 TCGA-55-6971 TCGA-55-7815 TCGA-55-7907 TCGA-55-7995 TCGA-55-8094 
       32.65         0.82         1.78         0.53         0.16         0.13 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 TCGA-55-8615 TCGA-55-8620 
        2.17        22.16         0.76         0.26         0.49         2.17 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-A46Y 
       15.81        19.99        17.95         4.57        14.60        13.61 
TCGA-62-A471 TCGA-64-1677 TCGA-64-1680 TCGA-67-3772 TCGA-69-7973 TCGA-69-7980 
       40.96        20.65        37.02        18.84         7.56        12.56 
TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-78-7147 
        2.01        26.30        15.35        30.31         9.24        19.27 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7167 TCGA-78-7220 TCGA-78-8662 TCGA-86-6562 
      129.53        19.50        88.14        26.53       110.50        12.36 
TCGA-86-7713 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8585 TCGA-86-8669 
       38.04        35.24         4.08         0.79         1.15        30.84 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-93-A4JP TCGA-95-7043 
        3.81        10.62         2.60        13.71        19.00        16.54 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-8032 
       16.41        14.30        20.58        19.76        18.67         1.45 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY 
        6.35        21.83        27.19         2.76        86.14        49.35 
TCGA-MP-A4T9 TCGA-NJ-A4YG TCGA-NJ-A7XG 
       41.59        62.60        20.28 

$`17P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       29.98        12.00        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         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-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       97.74       120.79        37.71        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       44.61        14.73        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       44.42        44.94        38.10        42.08        42.77         3.19 
TCGA-44-2668 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       25.02        38.24        38.89        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        63.72        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A 
       29.23        13.74        12.66         3.25         8.55        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        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-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       55.33        17.16        11.64        22.26        22.26       156.66 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
       73.12        62.24        28.90         8.55        40.41        37.32 
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-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        78.67         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 
       29.03        25.12        22.55        42.35         3.91        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 
       38.73        48.62        45.21         0.07         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.12         0.79        18.64         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
       19.82        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        5.06        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
       15.42         1.45         0.95         0.36         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
        0.30         0.10         4.80         6.64        17.62         1.58 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 
       20.58        19.59         0.92        20.19        39.98        42.38 
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-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
       67.96        72.30        39.25        29.92        56.81        39.09 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
       51.25        28.47         1.02        20.05        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         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         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 
       14.01        13.45         4.24        25.91        17.16        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       23.38        82.68         4.31         1.25        39.09        50.33 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 
       11.18       163.10        27.16         5.69        20.58        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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
       22.92         9.57       104.19       238.29         8.48        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 
      232.18        39.75        77.59        10.55        27.09         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
       31.13        34.39        20.55        32.78        19.89        37.74 
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-86-8668 TCGA-86-8671 TCGA-86-8672 
       23.05        21.47        14.60        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       41.36         1.97        10.19        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29        41.82         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 
       15.39        21.60        20.19        21.44        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 
       20.84        20.68        24.56        34.85        36.76        21.57 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.63        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV 
       19.00        14.30        10.09        14.53         1.91        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       15.65        38.63        58.45        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        31.23         2.43        10.09        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-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        59.11        16.87 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.13               0.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            129.53             238.29 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             16.41              20.58 
[1] "0.1 - 129.5 (16.4)" "0.0 - 238.3 (20.6)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         2       19       21        0        10         6
  17P GAIN WILD-TYPE       3      116      118        1        42        66
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17P GAIN MUTATED           14          4        7
  17P GAIN WILD-TYPE         58          7       19
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 19                116
  STAGE IB                 21                118
  STAGE II                  0                  1
  STAGE IIA                10                 42
  STAGE IIB                 6                 66
  STAGE IIIA               14                 58
  STAGE IIIB                4                  7
  STAGE IV                  7                 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
  17P GAIN MUTATED    25  48   4   5
  17P GAIN WILD-TYPE 145 230  42  14
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               25                145
  T2               48                230
  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    46  18    17
  17P GAIN WILD-TYPE 286  78    59
D30V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                  46                286
  N1                  18                 78
  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"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    59   7
  17P GAIN WILD-TYPE 290  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     59    7
  17P GAIN WILD-TYPE  290   18
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               59                290
  1                7                 18
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    37  46
  17P GAIN WILD-TYPE 238 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     37   46
  17P GAIN WILD-TYPE  238  194
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               37                238
  MALE                 46                194
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    50  13
  17P GAIN WILD-TYPE 310  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     50   13
  17P GAIN WILD-TYPE  310   41
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                50                310
  YES               13                 41
[1] 2 2
[1] FALSE
D30V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17P GAIN MUTATED                            2
  17P GAIN WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17P GAIN MUTATED                                  19
  17P GAIN WILD-TYPE                                87
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                   53
  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                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               53
  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    60   0   0   7
  17P GAIN WILD-TYPE 283  12   4  19
D30V13, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               60                283
  R1                0                 12
  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
  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                        46   324
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                 46
  WHITE                                          65                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"
D30V15, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  63
  17P GAIN WILD-TYPE   7 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   63
  17P GAIN WILD-TYPE    7  319
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               63                319
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   119  66
  17Q GAIN WILD-TYPE 206 101
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               185                307 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                66                101 
$`17Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 
       50.07         3.98        19.96        45.01         0.00        47.05 
TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4424 TCGA-05-4425 
        8.02         2.99        14.96         9.01        30.02        21.99 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 
       26.01        25.02        25.02        49.05        28.41        44.61 
TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-6144 TCGA-44-6148 TCGA-44-6775 
       37.15        34.06        33.73        23.77        23.15        23.18 
TCGA-44-6777 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 
       32.45        12.03         7.17        36.07        29.00        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-49-4490 TCGA-49-4501 
        3.25         8.55        15.98         9.44        12.66        46.72 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-AAR4 TCGA-49-AARO TCGA-50-5930 
       16.04        53.29        17.16        28.90       123.58         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 
       14.27        78.67        21.47         9.37        25.12         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-53-7813 TCGA-55-1595 
       25.55        11.05        12.16        41.69        13.94        48.62 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 
        2.86        32.65         0.82         5.49         7.79        45.34 
TCGA-55-6982 TCGA-55-7281 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       32.71         0.59         1.12         1.78        18.64         0.53 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 TCGA-55-8205 
       17.65        19.82         0.16         3.29         0.13         1.08 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 
        2.17        22.16         0.76         0.26        17.72         6.64 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        0.49         1.58         2.17        21.40         1.58        20.58 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-8402 
       15.81        19.99        17.95         4.57        14.60        49.25 
TCGA-62-A46R TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1680 
       56.71        13.61        39.25        40.96        20.65        37.02 
TCGA-64-5774 TCGA-67-3770 TCGA-67-3772 TCGA-67-6215 TCGA-69-7760 TCGA-69-7973 
       87.98         1.02        18.84         5.72         6.64         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 
        6.05         4.41        12.56         2.01        52.60        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 
       26.30        15.35        30.31         9.24        50.33       163.10 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7161 
       27.16        19.27       129.53        19.50        64.90         9.57 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       88.14        26.53        26.01        10.55        50.24       232.18 
TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
       10.55       110.50        12.36         5.88        34.39        38.04 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
       32.78        35.24         4.08         0.79        22.82        31.20 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4P7 
       21.47         1.15        13.91        30.84         3.81        13.64 
TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6848 TCGA-93-7348 TCGA-93-8067 
       10.62         2.60        13.71         7.36        17.46         6.12 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
        1.08        19.00        17.29        41.82        16.54        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 TCGA-97-8175 
       12.39        27.29         2.76        43.79        25.48        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-8025 
       16.41        14.30        20.58        19.76        18.67        34.85 
TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N4 
        1.45        21.57         6.35        21.83        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
        2.76        86.14        49.35        86.04         5.29        41.59 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-NJ-A4YG TCGA-NJ-A7XG TCGA-O1-A52J 
       10.09        29.46        62.60        20.28        59.11 

$`17Q GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 TCGA-05-4405 
       14.01        37.02         9.96        24.03        19.00        20.05 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4426 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       29.98        12.00        26.01        24.00        15.02        15.02 
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-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       35.28        11.64        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
       46.98        44.42        44.94        38.10        42.08        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-3917 TCGA-44-4112 TCGA-44-5643 
        3.19        25.02        38.24        38.89        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 
       28.37        28.01        19.56         9.93        27.78        21.63 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7669 
       63.72        61.28        16.44        22.72        19.46        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       29.23        13.74        15.32        11.08        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-49-6744 
       32.84         8.81        29.46        29.75        55.89        55.33 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       11.64        22.26        22.26       156.66        73.12        62.24 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41        37.32       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        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       49.28         8.09        40.60         8.45        15.12        29.03 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       22.55        42.35         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 
        7.59        27.25        34.29        30.54        35.21        23.05 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       38.73        45.21         0.07         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 
       15.25        48.49         3.88         2.20        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
       40.54       107.21        70.26         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7728 TCGA-55-7910 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        0.79         6.48         6.15        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 
       19.73         5.06        23.64        15.65        17.98         1.51 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 
       15.42         1.45         0.95         0.36         0.49         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
        0.10         4.80        17.62         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 
       20.71        19.59         0.92        20.19        39.98        42.38 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       88.64        47.80        19.53        54.35        67.96        72.30 
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-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 
       42.90        28.41        51.25        28.47        20.05        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 
       12.66        14.73         4.64        13.87         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
       13.61         5.42         2.93        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 
       25.91        17.16        23.38         4.31         1.25        39.09 
TCGA-73-A9RS TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       11.18         5.69        20.58        21.90        39.95       119.51 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
       38.50        32.09         5.88        22.92       104.19       238.29 
TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 
        8.48        31.20         8.02        53.33        39.35        39.75 
TCGA-78-8655 TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
       77.59        27.09        31.13        20.55        19.89        37.74 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 
        4.57        24.33        32.65        31.04        23.05        14.60 
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-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-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
       19.82        22.45        23.61         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8176 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 
       15.39        21.60        20.19        21.44        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-8192 
       20.84        20.68        24.56        36.76        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SW 
       10.09        14.53         1.91        18.58        15.65        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
       37.35        58.85         5.49        31.23         2.43        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 TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-S2-AA1A 
       16.87 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.00               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            232.18             238.29 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             18.67              20.58 
[1] "0.0 - 232.2 (18.7)" "0.1 - 238.3 (20.6)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         2       43       52        0        20        23
  17Q GAIN WILD-TYPE       3       92       87        1        32        49
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17Q GAIN MUTATED           30          8       13
  17Q GAIN WILD-TYPE         42          3       13
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 43                 92
  STAGE IB                 52                 87
  STAGE II                  0                  1
  STAGE IIA                20                 32
  STAGE IIB                23                 49
  STAGE IIIA               30                 42
  STAGE IIIB                8                  3
  STAGE IV                 13                 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
  17Q GAIN MUTATED    56 108  16   9
  17Q GAIN WILD-TYPE 114 170  30  10
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               56                114
  T2              108                170
  T3               16                 30
  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
  17Q GAIN MUTATED   116  35    35
  17Q GAIN WILD-TYPE 216  61    41
D31V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                 116                216
  N1                  35                 61
  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 175 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    100   91
  17Q GAIN WILD-TYPE  175  149
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE              100                175
  MALE                 91                149
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   128  23
  17Q GAIN WILD-TYPE 232  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    128   23
  17Q GAIN WILD-TYPE  232   31
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO               128                232
  YES               23                 31
[1] 2 2
[1] FALSE
D31V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17Q GAIN MUTATED                            7
  17Q GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17Q GAIN MUTATED                                  41
  17Q GAIN WILD-TYPE                                65
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                  125
  17Q GAIN WILD-TYPE                                                195
                    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                                        7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                41
  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                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                195
  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   122   4   2  17
  17Q GAIN WILD-TYPE 221   8   2   9
D31V13, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0              122                221
  R1                4                  8
  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                          12   147
  17Q GAIN WILD-TYPE                        39   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                      12                 39
  WHITE                                         147                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     3 135
  17Q GAIN WILD-TYPE   4 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3  135
  17Q GAIN WILD-TYPE    4  247
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              135                247
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    55  33
  18P GAIN WILD-TYPE 270 134
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                88                404 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                33                134 
$`18P GAIN MUTATED`
TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-5428 TCGA-35-4122 
        2.99        29.98        30.02        25.02        22.03         7.40 
TCGA-44-2657 TCGA-44-2659 TCGA-44-6144 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       44.42        44.94        23.77        13.74        12.66         3.25 
TCGA-44-A47A TCGA-49-4487 TCGA-49-6761 TCGA-50-5068 TCGA-50-5931 TCGA-50-6591 
       15.32        28.11        11.64        49.28        14.27         3.91 
TCGA-50-6593 TCGA-50-6673 TCGA-50-7109 TCGA-53-7813 TCGA-55-6970 TCGA-55-6980 
       11.05         0.72        10.13        13.94        15.25         2.20 
TCGA-55-7907 TCGA-55-7994 TCGA-55-8089 TCGA-55-8096 TCGA-55-8508 TCGA-55-8511 
        0.53        19.82         3.29        23.64         0.49         0.30 
TCGA-55-8615 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 
        0.49        15.81        20.19        19.99        14.60        88.64 
TCGA-62-8402 TCGA-64-1676 TCGA-64-1677 TCGA-64-5775 TCGA-64-5779 TCGA-69-7764 
       49.25        56.81        20.65         2.04        28.41        13.61 
TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 
        7.56        12.56        14.01        82.68        15.35        30.31 
TCGA-73-4676 TCGA-78-7143 TCGA-78-7147 TCGA-78-7148 TCGA-78-7155 TCGA-78-7536 
        9.24       163.10        19.27        20.58        38.50         8.02 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8662 TCGA-86-7701 TCGA-86-7713 TCGA-86-7955 
       26.01        10.55       110.50        31.13        38.04        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8359 TCGA-86-8585 
       37.74         4.08         0.79        22.82        14.60         1.15 
TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 TCGA-93-A4JN 
        3.81        41.36        10.19        12.23         1.18        23.61 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-97-7546 TCGA-97-7554 TCGA-97-8175 
        2.86        12.39        15.68        31.69        25.48        18.12 
TCGA-97-8179 TCGA-97-8552 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4TD 
       14.30        20.58         6.35        10.09        38.63        10.09 
TCGA-MP-A4TK TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       19.13        19.82        20.28        16.87 

$`18P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       20.05        14.96         9.01        12.00        21.99        26.01 
TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 
       29.00         9.04         2.04         0.46         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       11.64        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        38.10        42.08        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-44-6146 TCGA-44-6147 
       33.30        28.37        28.01        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       18.87        29.00        29.23         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 
       11.08        11.54        13.64        13.45        76.21        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       17.16        22.26        22.26       156.66        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       28.90         8.55        40.41        37.32       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        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
       60.16        31.04         8.09         9.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
       22.55        42.35        25.55        12.16         6.21        41.69 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       36.99         7.59        27.25        34.29        30.54        35.21 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
       23.05        38.73        48.62        45.21         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
       32.65         0.79        42.51        40.73         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        3.88         5.49         7.79        45.34        32.71        60.03 
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         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1.28         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         5.06         0.13        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 
        0.76         0.95         0.36         0.26        17.72         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64        17.62         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       19.59         0.92        17.95         4.57        39.98        42.38 
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-64-1678 TCGA-64-1679 
       13.61        39.25        40.96        29.92        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
       37.02        38.37        87.98        42.90        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
        1.02        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 
        5.42         6.05         4.41         2.93        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
       25.91        17.16         2.01        52.60        23.38        26.30 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7145 
        4.31         1.25        39.09        50.33        11.18        27.16 
TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        5.69       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-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 
      238.29         8.48        88.14        26.53        31.20        53.33 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        50.24       232.18        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
       27.09        12.36         5.88        34.39        20.55        32.78 
TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       19.89         4.57        24.33        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       23.05        21.47        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
       10.62         1.97         2.60        13.71        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.18        16.60        14.27         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       22.45        17.46         6.12         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       41.82        16.54        18.67        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        18.18        19.89        64.60        63.52        43.79 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        16.41        21.60        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       34.85        36.76         1.45        21.57        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
       14.53         1.91        21.83        18.58        15.65        27.19 
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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
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-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-O1-A52J 
        0.43        59.11 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               0.3                0.0 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            163.10             238.29 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            15.515             20.695 
[1] "0.3 - 163.1 (15.5)" "0.0 - 238.3 (20.7)"
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         3       23       23        0        11        10
  18P GAIN WILD-TYPE       2      112      116        1        41        62
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18P GAIN MUTATED           16          2        3
  18P GAIN WILD-TYPE         56          9       23
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 23                112
  STAGE IB                 23                116
  STAGE II                  0                  1
  STAGE IIA                11                 41
  STAGE IIB                10                 62
  STAGE IIIA               16                 56
  STAGE IIIB                2                  9
  STAGE IV                  3                 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
  18P GAIN MUTATED    32  49   6   4
  18P GAIN WILD-TYPE 138 229  40  15
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               32                138
  T2               49                229
  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
  18P GAIN MUTATED    59  17    14
  18P GAIN WILD-TYPE 273  79    62
D32V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                  59                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    65   3
  18P GAIN WILD-TYPE 284  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     65    3
  18P GAIN WILD-TYPE  284   22
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               65                284
  1                3                 22
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    44  47
  18P GAIN WILD-TYPE 231 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     44   47
  18P GAIN WILD-TYPE  231  193
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               44                231
  MALE                 47                193
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    65   9
  18P GAIN WILD-TYPE 295  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     65    9
  18P GAIN WILD-TYPE  295   45
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                65                295
  YES                9                 45
[1] 2 2
[1] FALSE
D32V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18P GAIN MUTATED                            5
  18P GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18P GAIN MUTATED                                  15
  18P GAIN WILD-TYPE                                91
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                   58
  18P GAIN WILD-TYPE                                                262
                    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                              0                             3
  18P GAIN WILD-TYPE                            2                            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                                      0
  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                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  91
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                262
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  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                                        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 280  10   4  19
D32V13, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               63                280
  R1                2                 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
  18P GAIN MUTATED                                  1     0
  18P GAIN WILD-TYPE                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           5    75
  18P GAIN WILD-TYPE                        46   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                 46
  WHITE                                          75                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  70
  18P GAIN WILD-TYPE   7 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   70
  18P GAIN WILD-TYPE    7  312
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               70                312
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    46  21
  18Q GAIN WILD-TYPE 279 146
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                67                425 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                146 
$`18Q GAIN MUTATED`
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-44-8119 TCGA-44-A47A 
       61.28        19.46        36.07        13.74         3.25        15.32 
TCGA-49-4510 TCGA-49-AAR2 TCGA-4B-A93V TCGA-50-5931 TCGA-50-6591 TCGA-53-7813 
       29.46        73.12         9.86        14.27         3.91        13.94 
TCGA-55-6970 TCGA-55-7907 TCGA-55-8089 TCGA-55-8096 TCGA-55-8508 TCGA-55-8511 
       15.25         0.53         3.29        23.64         0.49         0.30 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 
        0.49         2.17        15.81        20.19        19.99        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-5779 
       88.64        49.25        56.81        20.65        39.09        28.41 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-71-6725 TCGA-73-4668 
       13.61         7.56        12.56        14.01         2.01        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-78-7148 TCGA-78-7167 TCGA-78-7542 TCGA-86-7713 
       30.31         9.24        20.58        88.14        10.55        38.04 
TCGA-86-7955 TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-A4D0 
       35.24        22.82        21.47        14.60         1.15         3.81 
TCGA-91-6831 TCGA-91-8499 TCGA-93-A4JN TCGA-95-7562 TCGA-97-7546 TCGA-97-7554 
       10.19         1.18        23.61         2.86        31.69        25.48 
TCGA-97-8175 TCGA-97-8552 TCGA-L9-A7SV TCGA-MP-A4TD TCGA-NJ-A55R TCGA-NJ-A7XG 
       18.12        20.58        18.58        10.09        19.82        20.28 
TCGA-S2-AA1A 
       16.87 

$`18Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
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-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
        4.37        43.53        46.98        44.42        38.10        42.08 
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-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
       63.72        32.45        16.44        22.72        12.03         7.17 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       18.87        29.00        29.23        12.66         8.55        15.98 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       32.84         8.81        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       55.33        17.16        11.64        22.26        22.26       156.66 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO 
       62.24        28.90         8.55        40.41        37.32       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      221.33       164.12        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
       60.16        31.04        49.28         8.09         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       25.12        22.55        42.35        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       27.25        34.29        30.54        35.21        23.05        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       48.62        45.21         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       42.51        40.73         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
        1.28         1.12         0.79         1.78        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         5.06         0.13        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 
        0.76         0.95         0.36         0.26        17.72         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
        4.80         6.64        17.62         1.58         1.61        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46O 
        0.92        17.95         4.57        39.98        42.38        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-64-1679 TCGA-64-1680 TCGA-64-1681 
       39.25        40.96        29.92        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         1.02 
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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 
        4.64        13.87         6.64         6.12        22.68         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        6.05         4.41         2.93        13.45         4.24        25.91 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
       17.16        52.60        23.38        82.68        26.30         4.31 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        1.25        39.09        50.33        11.18       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27       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-78-7166 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29         8.48        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 
        8.02        53.33        26.01        39.35        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        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-86-8054 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-86-8668 TCGA-86-8669 TCGA-86-8671 
       31.04        31.20        23.05        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-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62        41.36         1.97         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       14.27         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
        1.08        19.00        17.29        41.82        16.54        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       18.18        19.89        64.60        63.52        43.79         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 
        0.59         0.72        18.67        17.92         5.39        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       34.85        36.76         1.45        21.57        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 
        6.35        10.09        14.53         1.91        21.83        15.65 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       37.35        86.04        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23         2.43        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        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        1.64        29.13         0.26         0.43        59.11 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               0.3                0.0 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             88.64             238.29 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             16.87              20.52 
[1] "0.3 - 88.6 (16.9)"  "0.0 - 238.3 (20.5)"
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         2       14       20        0         9         6
  18Q GAIN WILD-TYPE       3      121      119        1        43        66
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18Q GAIN MUTATED           12          2        4
  18Q GAIN WILD-TYPE         60          9       22
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 14                121
  STAGE IB                 20                119
  STAGE II                  0                  1
  STAGE IIA                 9                 43
  STAGE IIB                 6                 66
  STAGE IIIA               12                 60
  STAGE IIIB                2                  9
  STAGE IV                  4                 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
  18Q GAIN MUTATED    19  42   5   3
  18Q GAIN WILD-TYPE 151 236  41  16
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               19                151
  T2               42                236
  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 287  83    65
D33V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                  45                287
  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    45   4
  18Q GAIN WILD-TYPE 304  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     45    4
  18Q GAIN WILD-TYPE  304   21
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               45                304
  1                4                 21
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    31  38
  18Q GAIN WILD-TYPE 244 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     31   38
  18Q GAIN WILD-TYPE  244  202
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               31                244
  MALE                 38                202
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    49   6
  18Q GAIN WILD-TYPE 311  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     49    6
  18Q GAIN WILD-TYPE  311   48
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                49                311
  YES                6                 48
[1] 2 2
[1] FALSE
D33V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18Q GAIN MUTATED                            4
  18Q GAIN WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18Q GAIN MUTATED                                  11
  18Q GAIN WILD-TYPE                                95
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                   42
  18Q GAIN WILD-TYPE                                                278
                    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                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                278
  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 301  11   4  18
D33V13, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               42                301
  R1                1                 11
  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                          10    52
  18Q GAIN WILD-TYPE                        41   337
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                      10                 41
  WHITE                                          52                337
[1] 4 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  58
  18Q GAIN WILD-TYPE   7 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   58
  18Q GAIN WILD-TYPE    7  324
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               58                324
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    22   7
  19P GAIN WILD-TYPE 303 160
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                29                463 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                160 
$`19P GAIN MUTATED`
TCGA-05-4390 TCGA-05-4424 TCGA-44-A47A TCGA-44-A47F TCGA-50-5049 TCGA-50-5935 
       37.02        30.02        15.32        11.08        70.55        21.47 
TCGA-50-6594 TCGA-53-7624 TCGA-55-7907 TCGA-55-8615 TCGA-55-8620 TCGA-62-8399 
       12.16        34.29         0.53         0.49         2.17        88.64 
TCGA-69-7973 TCGA-69-8253 TCGA-73-4675 TCGA-78-7154 TCGA-86-8359 TCGA-86-8585 
        7.56        14.01        30.31        19.50        14.60         1.15 
TCGA-93-A4JN TCGA-95-7944 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 
       23.61        12.39         2.76        25.48         5.95        18.12 
TCGA-97-8179 TCGA-MN-A4N4 TCGA-MP-A4TJ TCGA-NJ-A55O TCGA-S2-AA1A 
       14.30        38.63        11.15         0.43        16.87 

$`19P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        2.99        14.96         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         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-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.94        38.10        42.08        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-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        22.72        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        3.25         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-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       55.89        16.04        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       22.26        22.26       156.66        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
        8.55        40.41        37.32       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        9.86        20.52        71.47        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12         9.37        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 
       42.35         3.91        25.55        11.05         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        0.72        10.13        36.99         7.59        27.25        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
       13.94        35.21        23.05        38.73        48.62        45.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        1.12         0.79         1.78        18.64         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61        16.93        22.65        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        1.58        20.58        19.59         0.92        15.81        20.19 
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-62-8402 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-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       20.65        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         1.02 
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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
        5.42         6.05         4.41         2.93        12.56        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
        4.24        25.91        17.16         2.01        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
       82.68        26.30        15.35         4.31         9.24         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       39.09        50.33        11.18       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-78-7155 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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        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-86-8278 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-86-8669 TCGA-86-8671 TCGA-86-8672 
       23.05        21.47        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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
       17.46         6.12         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
       16.54         2.86        18.67        15.68        15.65        27.29 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       43.79         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       14.30         6.35        10.09        14.53         1.91        21.83 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       18.58        15.65        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        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        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.13         1.64        29.13         0.26        19.82        20.28 
TCGA-O1-A52J 
       59.11 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.43               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             88.64             238.29 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             14.60              20.19 
[1] "0.4 - 88.6 (14.6)"  "0.0 - 238.3 (20.2)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         0        7        7        0         4         2
  19P GAIN WILD-TYPE       5      128      132        1        48        70
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19P GAIN MUTATED            7          0        3
  19P GAIN WILD-TYPE         65         11       23
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  7                128
  STAGE IB                  7                132
  STAGE II                  0                  1
  STAGE IIA                 4                 48
  STAGE IIB                 2                 70
  STAGE IIIA                7                 65
  STAGE IIIB                0                 11
  STAGE IV                  3                 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
  19P GAIN MUTATED     9  15   6   0
  19P GAIN WILD-TYPE 161 263  40  19
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                9                161
  T2               15                263
  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    17   7     6
  19P GAIN WILD-TYPE 315  89    70
D34V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                  17                315
  N1                   7                 89
  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    22   3
  19P GAIN WILD-TYPE 327  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     22    3
  19P GAIN WILD-TYPE  327   22
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               22                327
  1                3                 22
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    13  17
  19P GAIN WILD-TYPE 262 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     13   17
  19P GAIN WILD-TYPE  262  223
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               13                262
  MALE                 17                223
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    20   4
  19P GAIN WILD-TYPE 340  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     20    4
  19P GAIN WILD-TYPE  340   50
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                20                340
  YES                4                 50
[1] 2 2
[1] FALSE
D34V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19P GAIN MUTATED                            2
  19P GAIN WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19P GAIN MUTATED                                   4
  19P GAIN WILD-TYPE                               102
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                   16
  19P GAIN WILD-TYPE                                                304
                    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                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               16
  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                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                304
  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    16   1   0   2
  19P GAIN WILD-TYPE 327  11   4  24
D34V13, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               16                327
  R1                1                 11
  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    23
  19P GAIN WILD-TYPE                        48   366
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                 48
  WHITE                                          23                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"
D34V15, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  24
  19P GAIN WILD-TYPE   6 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   24
  19P GAIN WILD-TYPE    6  358
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               24                358
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    48  24
  19Q GAIN WILD-TYPE 277 143
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                72                420 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                24                143 
$`19Q GAIN MUTATED`
TCGA-05-4390 TCGA-05-4418 TCGA-05-4424 TCGA-35-4122 TCGA-35-5375 TCGA-38-4631 
       37.02         9.01        30.02         7.40         8.68        11.64 
TCGA-44-6144 TCGA-44-6776 TCGA-44-7660 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B 
       23.77        63.72        19.46        18.87        15.32         9.44 
TCGA-44-A47F TCGA-44-A4SS TCGA-49-4510 TCGA-49-6743 TCGA-49-AAR4 TCGA-50-5049 
       11.08        13.64        29.46        53.29        28.90        70.55 
TCGA-50-5935 TCGA-50-5936 TCGA-50-6594 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
       21.47         8.45        12.16        34.29        13.94        35.21 
TCGA-55-6971 TCGA-55-7907 TCGA-55-8092 TCGA-55-8302 TCGA-55-8614 TCGA-55-8615 
        0.82         0.53         5.06         0.76        17.62         0.49 
TCGA-55-8620 TCGA-62-8399 TCGA-62-A46S TCGA-64-5778 TCGA-64-5781 TCGA-69-7763 
        2.17        88.64        54.35        42.90        51.25        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8453 TCGA-73-4675 
       13.61         7.56        12.56        14.01        25.91        30.31 
TCGA-78-7150 TCGA-78-7154 TCGA-86-7713 TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 
       21.90        19.50        38.04         4.08        22.82        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8673 TCGA-91-6830 TCGA-93-A4JN TCGA-95-7043 
       14.60         1.15        28.34         1.97        23.61        16.54 
TCGA-95-7944 TCGA-95-A4VP TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 
       12.39        19.89        25.48         5.95        17.92         5.39 
TCGA-97-8179 TCGA-99-8025 TCGA-L9-A443 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.30        34.85         6.35         1.91        15.65        38.63 
TCGA-MP-A4T7 TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-NJ-A55O TCGA-S2-AA1A 
        5.49         2.43        24.36        11.15         0.43        16.87 

$`19Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
        2.99        14.96        29.98        12.00        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
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-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        5.98        97.74       120.79        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       35.28        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
       46.98        44.42        44.94        38.10        42.08        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-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
        9.93        27.78        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        12.03         7.17        36.07 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       15.98        11.54        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        16.04        55.33        17.16        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 
       22.26        22.26       156.66        73.12        62.24         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       40.41        37.32       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        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5939 
        8.09         9.27        14.27        40.60        78.67        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 
       36.99         7.59        27.25        30.54        23.05        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       48.62        45.21         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       42.51        40.73        15.25        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
        1.28         1.12         0.79         1.78        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
        3.29        19.66        19.73         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 
        0.30         0.10         4.80         6.64         1.58         1.61 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B 
       19.59         0.92        15.81        20.19        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-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
       40.96        29.92        56.81        20.65        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 
       37.02        38.37        87.98         2.04        28.41        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
        1.02        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 
        5.72         4.64        13.87         6.64         6.12         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        6.05         4.41         2.93        13.45         4.24        17.16 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
        4.31         9.24         1.25        39.09        50.33        11.18 
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-78-7152 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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        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-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        32.65        31.04        31.20        23.05 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58         0.62        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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46         6.12         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
       17.29        41.82         2.86        18.67        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 
       27.29         2.76        21.40        18.18        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       63.52        43.79         0.59         0.72        18.67        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        16.41        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       24.56        36.76         1.45        21.57        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 
       10.09        14.53        21.83        18.58        27.19         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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59        31.23        10.09        29.46        11.05 
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        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        1.64        29.13         0.26        19.82        20.28        59.11 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.43               0.00 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             88.64             238.29 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            16.095             20.535 
[1] "0.4 - 88.6 (16.1)"  "0.0 - 238.3 (20.5)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         1       16       22        0         9         6
  19Q GAIN WILD-TYPE       4      119      117        1        43        66
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19Q GAIN MUTATED           15          1        5
  19Q GAIN WILD-TYPE         57         10       21
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 16                119
  STAGE IB                 22                117
  STAGE II                  0                  1
  STAGE IIA                 9                 43
  STAGE IIB                 6                 66
  STAGE IIIA               15                 57
  STAGE IIIB                1                 10
  STAGE IV                  5                 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
  19Q GAIN MUTATED    23  40  11   1
  19Q GAIN WILD-TYPE 147 238  35  18
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               23                147
  T2               40                238
  T3               11                 35
  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    48  12    15
  19Q GAIN WILD-TYPE 284  84    61
D35V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                  48                284
  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    50   5
  19Q GAIN WILD-TYPE 299  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     50    5
  19Q GAIN WILD-TYPE  299   20
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               50                299
  1                5                 20
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    32  43
  19Q GAIN WILD-TYPE 243 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     32   43
  19Q GAIN WILD-TYPE  243  197
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               32                243
  MALE                 43                197
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    55   8
  19Q GAIN WILD-TYPE 305  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     55    8
  19Q GAIN WILD-TYPE  305   46
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                55                305
  YES                8                 46
[1] 2 2
[1] FALSE
D35V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19Q GAIN MUTATED                            5
  19Q GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19Q GAIN MUTATED                                   9
  19Q GAIN WILD-TYPE                                97
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                   46
  19Q GAIN WILD-TYPE                                                274
                    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)               46
  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                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                274
  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    44   2   0   4
  19Q GAIN WILD-TYPE 299  10   4  22
D35V13, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               44                299
  R1                2                 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
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           9    58
  19Q GAIN WILD-TYPE                        42   331
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                       9                 42
  WHITE                                          58                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"
D35V15, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  58
  19Q GAIN WILD-TYPE   5 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   58
  19Q GAIN WILD-TYPE    5  324
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               58                324
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   108  60
  20P GAIN WILD-TYPE 217 107
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               168                324 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                60                107 
$`20P GAIN MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4402 TCGA-05-4417 TCGA-05-4424 
       50.07         3.98        45.01         8.02        14.96        30.02 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-35-5375 TCGA-38-4625 
       25.02        25.02        15.02        29.00         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-2657 
       37.71        49.05        28.41        11.64        14.73        44.42 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6774 TCGA-44-6778 TCGA-44-7660 
       28.37        28.01        23.77        21.63        61.28        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
        7.17        36.07        18.87        29.23        13.74         3.25 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 
       15.98         9.44        11.08        13.64        13.45        35.54 
TCGA-49-4506 TCGA-49-4510 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR9 TCGA-49-AARN 
       32.84        29.46        22.26       156.66         8.55        37.32 
TCGA-49-AARO TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 
      123.58         9.86        71.47        70.55        31.04        49.28 
TCGA-50-5931 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       14.27        21.47         9.37        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 
       25.55         6.21         0.72        10.13        13.94        23.05 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 
       45.21         2.86         0.07        32.65        40.73        15.25 
TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7574 TCGA-55-7724 
       48.49         5.49         7.79         7.99         3.12        23.18 
TCGA-55-7726 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8097 
        1.28         0.16        29.72        15.19        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 
        1.08         1.51        22.16         0.76         0.26         0.49 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 
        6.64        17.62         0.49        21.40        20.58         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8399 TCGA-62-8402 
       15.81        20.19        19.99         4.57        88.64        49.25 
TCGA-64-1677 TCGA-64-5775 TCGA-67-3771 TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 
       20.65         2.04        20.05        18.84        22.68        13.61 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-71-6725 TCGA-73-4658 
        4.41         2.93        12.56        14.01         2.01        52.60 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4677 TCGA-73-A9RS TCGA-78-7153 TCGA-78-7154 
       82.68        15.35         1.25        11.18       119.51        19.50 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       38.50        64.90       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-83-5908 TCGA-86-6562 TCGA-86-7713 
        8.02        10.55       232.18        27.09        12.36        38.04 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8585 TCGA-86-8669 
       37.74         4.08        24.33        22.82         1.15        30.84 
TCGA-91-6829 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 TCGA-91-A4BC 
       41.36        13.71        12.23        27.68         1.18         1.45 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7043 TCGA-95-7567 
        6.12        23.61         1.08        19.00        16.54        18.67 
TCGA-95-8494 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8174 TCGA-97-8175 
        2.76        31.69        43.79         5.95         5.39        18.12 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-99-8025 TCGA-L9-A5IP TCGA-L9-A8F4 
       14.30        20.58        19.76        34.85         1.91        15.65 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
       27.19         2.76        49.35        37.35        58.85         5.49 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK TCGA-NJ-A4YP TCGA-NJ-A55R TCGA-S2-AA1A 
       29.46        11.05        19.13         1.64        19.82        16.87 

$`20P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       19.96        14.01        37.02         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 
       47.05        19.00        20.05         2.99         9.01        29.98 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 
       12.00        21.99        26.01        26.01        24.00        15.02 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
        4.96        22.03         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
        5.98       120.79        35.28        44.61        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
       43.53        46.98        44.94        38.10        42.08        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-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.73        26.56        33.30        19.56         9.93        27.78 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       23.15        23.18        63.72        32.45        16.44        22.72 
TCGA-44-7661 TCGA-44-7670 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47G 
       12.03        29.00        12.66         8.55        15.32        11.54 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 
       76.21        28.11        28.57        12.66        46.72        14.07 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
        8.81        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       17.16        11.64        22.26        73.12        62.24        28.90 
TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 
       40.41       221.33       164.12        20.52        15.72        60.16 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.09         9.27        40.60        78.67         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-8457 
       29.03        25.12        11.05        12.16        41.69        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 
        7.59        27.25        34.29        30.54        35.21        38.73 
TCGA-55-1595 TCGA-55-6712 TCGA-55-6968 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 
       48.62         0.79        42.51         0.82         3.88         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
       70.26         0.59         1.15         0.20         0.13         1.32 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1.28         1.12         0.79         1.78        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 
        6.48        17.65         6.15        19.82         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 TCGA-55-8207 TCGA-55-8299 
       19.73         5.06         0.13        17.98         2.17        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        1.45         0.95         0.36        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        4.80         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
       20.71         1.58        19.59        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-64-1681 TCGA-64-5774 TCGA-64-5778 
       39.09        81.80        37.02        38.37        87.98        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 
       28.41        51.25        28.47         1.02        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        5.42         7.56         6.05        13.45         4.24        25.91 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       17.16        23.38        26.30         4.31        30.31         9.24 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       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-78-7166 TCGA-78-7537 TCGA-78-7539 
       22.92         9.57       104.19         8.48        53.33        26.01 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       39.35        50.24        39.75        77.59        10.55       110.50 
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-86-7955 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       35.24         4.57         0.79        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       23.05        21.47        14.60        13.91        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-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6848 
       26.47        10.62         1.97        10.19         2.60         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.18        16.60        14.27        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       17.46        17.29        41.82         2.86        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
       15.65        27.29        21.40        18.18        19.89        64.60 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       63.52        25.48         0.59         0.72        18.67        17.92 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 
       15.39        16.41        21.60        20.19        21.44        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
       17.75        20.84        18.67        20.68        24.56        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
        1.45        21.57        21.63        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
       14.53        21.83        18.58        38.63        86.14        58.45 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       86.04         5.29        41.59        31.23         2.43        10.09 
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        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
        0.13        29.13         0.26         0.43        20.28        59.11 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.00 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            238.29             221.33 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            19.065             20.535 
[1] "0.1 - 238.3 (19.1)" "0.0 - 221.3 (20.5)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         3       49       52        0        15        24
  20P GAIN WILD-TYPE       2       86       87        1        37        48
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20P GAIN MUTATED           19          3        7
  20P GAIN WILD-TYPE         53          8       19
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 49                 86
  STAGE IB                 52                 87
  STAGE II                  0                  1
  STAGE IIA                15                 37
  STAGE IIB                24                 48
  STAGE IIIA               19                 53
  STAGE IIIB                3                  8
  STAGE IV                  7                 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 GAIN MUTATED    55  99  14   3
  20P GAIN WILD-TYPE 115 179  32  16
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               55                115
  T2               99                179
  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   120  27    20
  20P GAIN WILD-TYPE 212  69    56
D36V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                 120                212
  N1                  27                 69
  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   107   7
  20P GAIN WILD-TYPE 242  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    107    7
  20P GAIN WILD-TYPE  242   18
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              107                242
  1                7                 18
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    88  84
  20P GAIN WILD-TYPE 187 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     88   84
  20P GAIN WILD-TYPE  187  156
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               88                187
  MALE                 84                156
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   114  19
  20P GAIN WILD-TYPE 246  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    114   19
  20P GAIN WILD-TYPE  246   35
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               114                246
  YES               19                 35
[1] 2 2
[1] FALSE
D36V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20P GAIN MUTATED                            5
  20P GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20P GAIN MUTATED                                  25
  20P GAIN WILD-TYPE                                81
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                  119
  20P GAIN WILD-TYPE                                                201
                    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                            10
  20P GAIN WILD-TYPE                            2                            13
                    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)              119
  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                                    10
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   20P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                201
  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                                      13
  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   7
  20P GAIN WILD-TYPE 239   6   2  19
D36V13, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              104                239
  R1                6                  6
  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
  20P GAIN MUTATED                                  1     4
  20P GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          23   127
  20P GAIN WILD-TYPE                        28   262
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                 28
  WHITE                                         127                262
[1] 4 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     0 134
  20P GAIN WILD-TYPE   7 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0  134
  20P GAIN WILD-TYPE    7  248
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO              134                248
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   121  63
  20Q GAIN WILD-TYPE 204 104
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               184                308 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                63                104 
$`20Q GAIN MUTATED`
TCGA-05-4250 TCGA-05-4389 TCGA-05-4397 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
        3.98        45.01        24.03        14.96        29.98        30.02 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-35-5375 
       25.02        25.02        15.02         4.96        29.00         8.68 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 
       97.74        37.71        49.05        28.41        11.64        14.73 
TCGA-44-2657 TCGA-44-6144 TCGA-44-6774 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 
       44.42        23.77        21.63        61.28        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SU TCGA-49-4487 
        3.25        15.98        15.32        11.08        13.45        28.11 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR9 
       35.54        32.84        29.46        22.26       156.66         8.55 
TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5066 TCGA-50-5068 
       37.32       123.58       221.33         9.86        31.04        49.28 
TCGA-50-5931 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
       14.27        21.47         9.37        22.55        42.35        25.55 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
        6.21         0.72        10.13        13.94        23.05        38.73 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       45.21         0.07        32.65         0.79        40.73        15.25 
TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 
       48.49         5.49         7.79         7.99        23.18         1.28 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8092 TCGA-55-8096 
        0.53         6.48         0.16        29.72         5.06        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8208 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
       15.65         1.08        22.16         0.76         0.36         0.26 
TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z 
        0.49         6.64        17.62         0.49         2.17        21.40 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8399 
       20.58         0.92        20.19        19.99         4.57        88.64 
TCGA-62-8402 TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 
       49.25        20.65        38.37        87.98         2.04        51.25 
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         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4666 
       12.56        14.01         4.24         2.01        52.60        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-73-A9RS TCGA-78-7153 TCGA-78-7154 
       15.35         4.31         1.25        11.18       119.51        19.50 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       38.50        64.90       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
        8.02        10.55       232.18        10.55        27.09        12.36 
TCGA-86-7713 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 
       38.04        37.74         4.08        24.33        22.82        31.20 
TCGA-86-8585 TCGA-86-8669 TCGA-91-6829 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
        1.15        30.84        41.36         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JN 
       27.68        16.18         1.18         1.45         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        41.82        16.54         2.86        18.67 
TCGA-95-7947 TCGA-95-8494 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8175 
       15.68         2.76        31.69        43.79         5.95        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-99-8025 TCGA-L9-A444 
       16.41        14.30        20.58        19.76        34.85        10.09 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY 
       15.65        27.19        38.63         2.76        86.14        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK 
       37.35        58.85         5.49        29.46        11.05        19.13 
TCGA-NJ-A4YP TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        1.64        19.82        59.11        16.87 

$`20Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07        19.96        14.01        37.02         0.00         9.96 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 
       47.05         8.02        19.00        20.05         2.99         9.01 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 
       12.00        21.99        26.01        26.01        24.00        15.02 
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-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
      120.79        35.28        44.61        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       46.98        44.94        38.10        42.08        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-44-6145 TCGA-44-6146 
       26.56        33.30        28.37        28.01        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 
       27.78        23.15        23.18        63.72        32.45        16.44 
TCGA-44-7659 TCGA-44-7661 TCGA-44-8120 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       22.72        12.03         8.55         9.44        11.54        13.64 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 
       76.21        28.57        12.66        46.72        14.07         8.81 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        16.04        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE 
       11.64        22.26        73.12        62.24        28.90        40.41 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
      164.12        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.09         9.27        40.60        78.67         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 
       29.03        25.12         3.91        11.05        12.16        41.69 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       36.99         7.59        27.25        34.29        30.54        35.21 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 
       48.62         2.86        42.51         0.82         3.88         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
       70.26         0.59         1.15         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1.32         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       17.65         6.15        19.82        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
       19.73         0.13        17.98         1.51         2.17        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        1.45         0.95        17.72         0.30         0.10         4.80 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
        1.58         1.61        16.93        22.65        20.71         1.58 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       19.59        15.81        17.95        39.98        42.38        14.60 
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-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 
       81.80        37.02        42.90        28.41        28.47         1.02 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       14.04        12.66        14.73         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8254 
        6.64         6.12         5.42         7.56         6.05        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 
       25.91        17.16        23.38        82.68        30.31         9.24 
TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       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-78-7166 TCGA-78-7537 TCGA-78-7539 
       22.92         9.57       104.19         8.48        53.33        26.01 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 
       39.35        50.24        39.75        77.59       110.50         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        20.55        32.78        19.89        35.24 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
        4.57         0.79        32.65        31.04        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       14.60        13.91        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-91-6830 TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
        1.97        10.19         7.36         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JQ TCGA-95-7944 TCGA-95-7948 
       19.82        22.45        17.46        17.29        12.39        15.65 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       27.29        21.40        18.18        19.89        64.60        63.52 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       25.48         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8176 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 
       15.39        21.60        20.19        21.44        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        24.56        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       21.57        21.63        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP 
       32.48        19.00        14.30         6.35        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
       21.83        18.58        58.45        86.04         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       31.23         2.43        10.09        24.36        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        62.60         0.13        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A7XG 
        0.43        20.28 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.00 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            238.29             164.12 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            19.295             20.520 
[1] "0.1 - 238.3 (19.3)" "0.0 - 164.1 (20.5)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         4       50       53        0        20        32
  20Q GAIN WILD-TYPE       1       85       86        1        32        40
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20Q GAIN MUTATED           22          3        7
  20Q GAIN WILD-TYPE         50          8       19
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   4                  1
  STAGE IA                 50                 85
  STAGE IB                 53                 86
  STAGE II                  0                  1
  STAGE IIA                20                 32
  STAGE IIB                32                 40
  STAGE IIIA               22                 50
  STAGE IIIB                3                  8
  STAGE IV                  7                 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
  20Q GAIN MUTATED    61 108  18   3
  20Q GAIN WILD-TYPE 109 170  28  16
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               61                109
  T2              108                170
  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   131  35    22
  20Q GAIN WILD-TYPE 201  61    54
D37V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                 131                201
  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   120   7
  20Q GAIN WILD-TYPE 229  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    120    7
  20Q GAIN WILD-TYPE  229   18
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              120                229
  1                7                 18
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    96  95
  20Q GAIN WILD-TYPE 179 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     96   95
  20Q GAIN WILD-TYPE  179  145
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               96                179
  MALE                 95                145
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   126  22
  20Q GAIN WILD-TYPE 234  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    126   22
  20Q GAIN WILD-TYPE  234   32
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               126                234
  YES               22                 32
[1] 2 2
[1] FALSE
D37V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20Q GAIN MUTATED                            5
  20Q GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20Q GAIN MUTATED                                  30
  20Q GAIN WILD-TYPE                                76
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                  132
  20Q GAIN WILD-TYPE                                                188
                    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                            10
  20Q GAIN WILD-TYPE                            2                            13
                    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                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              132
  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                                    10
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   20Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                188
  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                                      13
  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   123   4   2   8
  20Q GAIN WILD-TYPE 220   8   2  18
D37V13, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              123                220
  R1                4                  8
  R2                2                  2
  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
  20Q GAIN MUTATED                                  1     4
  20Q GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          23   140
  20Q GAIN WILD-TYPE                        28   249
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                      23                 28
  WHITE                                         140                249
[1] 4 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     2 144
  20Q GAIN WILD-TYPE   5 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2  144
  20Q GAIN WILD-TYPE    5  238
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              144                238
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    53  38
  21Q GAIN WILD-TYPE 272 129
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                91                401 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                38                129 
$`21Q GAIN MUTATED`
TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-5423 TCGA-05-5428 TCGA-38-4628 
       20.05         2.99         9.01         4.96        22.03        49.05 
TCGA-38-4629 TCGA-38-6178 TCGA-44-2657 TCGA-44-6147 TCGA-44-6774 TCGA-44-6777 
       28.41        14.73        44.42        27.78        21.63        32.45 
TCGA-44-A47A TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 
       15.32        28.11        28.57        12.66        46.72        14.07 
TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-AAQV TCGA-50-5049 TCGA-50-5931 
       29.75        16.04        53.29        22.26        70.55        14.27 
TCGA-50-5941 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-53-7626 
        9.37        12.16        41.69         0.72        36.99        30.54 
TCGA-55-1595 TCGA-55-6642 TCGA-55-6980 TCGA-55-6981 TCGA-55-7727 TCGA-55-7914 
       48.62        32.65         2.20        45.34         1.12         6.15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8511 TCGA-55-8615 TCGA-55-A48Z 
        1.51         2.17        22.16         0.30         0.49        21.40 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46R TCGA-64-1678 
       17.95         4.57        14.60        88.64        56.71        39.09 
TCGA-64-1680 TCGA-67-3771 TCGA-67-6217 TCGA-69-8253 TCGA-69-A59K TCGA-71-6725 
       37.02        20.05        13.87        14.01        17.16         2.01 
TCGA-73-4677 TCGA-73-7499 TCGA-78-7147 TCGA-78-7155 TCGA-78-7163 TCGA-78-7535 
        1.25        50.33        19.27        38.50       238.29        31.20 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8662 TCGA-86-6562 TCGA-86-8075 TCGA-86-8279 
       26.01        10.55       110.50        12.36        22.82        31.20 
TCGA-86-8358 TCGA-91-8496 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7944 
       21.47        16.60         1.18        23.61        19.00        12.39 
TCGA-97-7546 TCGA-97-7553 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX 
       31.69        43.79        16.41        14.30        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-J2-A4AD TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
       21.44        19.76        18.08        10.09        27.19         2.76 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-NJ-A4YG TCGA-O1-A52J 
       58.85         5.49        31.23         2.43        62.60        59.11 
TCGA-S2-AA1A 
       16.87 

$`21Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
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-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
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-38-4630 TCGA-38-4631 
        8.68        97.74       120.79        37.71        35.28        11.64 
TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 
       44.61        26.30         4.37        43.53        46.98        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       38.10        42.08        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-44-6146 TCGA-44-6148 
       28.37        28.01        23.77        19.56         9.93        23.15 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        63.72        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       13.74        12.66         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
       11.08        11.54        13.64        13.45        76.21        35.54 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 
       32.84         8.81        29.46        55.89        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       11.64        22.26       156.66        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
        8.55        40.41        37.32       123.58       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        9.86        20.52        71.47        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.09         9.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
        8.45        15.12        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-7109 TCGA-50-8459 
        3.91        25.55        11.05         6.21        10.13         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       27.25        34.29        13.94        35.21        23.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       45.21         2.86         0.07         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
        1.32        23.18         1.28         1.28         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
       18.64         0.53         6.48        17.65        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8299 
        0.13        23.64        15.65        17.98         1.08        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
       17.72         0.10         4.80         6.64        17.62         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
        1.61         2.17        16.93        22.65        20.71         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S 
       39.98        42.38        49.25        47.80        19.53        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-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 
       42.90        28.41        51.25        28.47         1.02        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         2.93        12.56        13.45         4.24        25.91 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        82.68        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
       30.31         9.24        39.09        11.18       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-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
      104.19         8.48        88.14        26.53         8.02        53.33 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        50.24       232.18        39.75        77.59        10.55 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09         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-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 
       24.33         0.79        32.65        31.04        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        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-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.18        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO 
        1.45        19.82        22.45        17.46         6.12         1.08 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 
       17.29        41.82        16.54         2.86        18.67        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8547 
       18.67        17.92         5.39        18.12        15.39        21.60 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       34.85        36.76         1.45        21.57        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       23.80        35.47        32.48        19.00        14.30         6.35 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.53         1.91        21.83        18.58        15.65        38.63 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 
       86.14        58.45        49.35        37.35        86.04         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       41.59        10.09        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 
       29.13         0.26         0.43        19.82        20.28 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               0.3                0.0 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            238.29             232.18 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             20.19              19.89 
[1] "0.3 - 238.3 (20.2)" "0.0 - 232.2 (19.9)"
[1] "hr=" "1.3"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         2       24       27        1        12         6
  21Q GAIN WILD-TYPE       3      111      112        0        40        66
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  21Q GAIN MUTATED           16          3        5
  21Q GAIN WILD-TYPE         56          8       21
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 24                111
  STAGE IB                 27                112
  STAGE II                  1                  0
  STAGE IIA                12                 40
  STAGE IIB                 6                 66
  STAGE IIIA               16                 56
  STAGE IIIB                3                  8
  STAGE IV                  5                 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
  21Q GAIN MUTATED    36  51   6   2
  21Q GAIN WILD-TYPE 134 227  40  17
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               36                134
  T2               51                227
  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    55  15    21
  21Q GAIN WILD-TYPE 277  81    55
D38V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                  55                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"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    67   5
  21Q GAIN WILD-TYPE 282  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     67    5
  21Q GAIN WILD-TYPE  282   20
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               67                282
  1                5                 20
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    61  35
  21Q GAIN WILD-TYPE 214 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     61   35
  21Q GAIN WILD-TYPE  214  205
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               61                214
  MALE                 35                205
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    69  10
  21Q GAIN WILD-TYPE 291  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     69   10
  21Q GAIN WILD-TYPE  291   44
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                69                291
  YES               10                 44
[1] 2 2
[1] FALSE
D38V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  21Q GAIN MUTATED                            4
  21Q GAIN WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  21Q GAIN MUTATED                                  21
  21Q GAIN WILD-TYPE                                85
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                   58
  21Q GAIN WILD-TYPE                                                262
                    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)               58
  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                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                262
  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    66   2   0   5
  21Q GAIN WILD-TYPE 277  10   4  21
D38V13, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               66                277
  R1                2                 10
  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
  21Q GAIN MUTATED                                  0     3
  21Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           9    72
  21Q GAIN WILD-TYPE                        42   317
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                 42
  WHITE                                          72                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"
D38V15, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  71
  21Q GAIN WILD-TYPE   7 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   71
  21Q GAIN WILD-TYPE    7  311
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               71                311
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    32  25
  22Q GAIN WILD-TYPE 293 142
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                57                435 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                25                142 
$`22Q GAIN MUTATED`
TCGA-05-4420 TCGA-05-4434 TCGA-38-4625 TCGA-38-A44F TCGA-44-3398 TCGA-44-6777 
       29.98        15.02        97.74         4.37        38.24        32.45 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47F TCGA-49-4488 
       16.44         7.17        29.00        15.32        11.08        28.57 
TCGA-49-4490 TCGA-49-6742 TCGA-49-6743 TCGA-50-5931 TCGA-50-5944 TCGA-50-6594 
       12.66        16.04        53.29        14.27        25.12        12.16 
TCGA-55-1592 TCGA-55-1596 TCGA-55-6712 TCGA-55-6981 TCGA-55-6982 TCGA-55-7724 
       23.05        45.21         0.79        45.34        32.71        23.18 
TCGA-55-7726 TCGA-55-7907 TCGA-55-8091 TCGA-55-8096 TCGA-55-8208 TCGA-55-8506 
        1.28         0.53        19.73        23.64        22.16         0.36 
TCGA-55-8514 TCGA-55-8614 TCGA-55-A491 TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 
        6.64        17.62        20.58        17.95        42.38        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-67-3770 TCGA-67-3771 TCGA-73-4675 TCGA-78-7150 
       49.25        47.80         1.02        20.05        30.31        21.90 
TCGA-78-7154 TCGA-78-8662 TCGA-86-6562 TCGA-86-7713 TCGA-86-8055 TCGA-86-8073 
       19.50       110.50        12.36        38.04         4.08        24.33 
TCGA-86-8280 TCGA-91-6847 TCGA-95-7944 TCGA-97-8174 TCGA-97-8552 TCGA-99-8033 
       23.05        27.68        12.39         5.39        20.58        21.57 
TCGA-J2-A4AE TCGA-MP-A4SW TCGA-MP-A4T7 
       35.47        58.45         5.49 

$`22Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        0.46         7.40         5.98         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
       26.30        43.53        46.98        44.42        44.94        38.10 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 
       42.08        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-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       23.18        63.72        61.28        22.72        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        29.23        13.74        12.66         3.25 
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-49-4501 TCGA-49-4505 TCGA-49-4506 
       76.21        28.11        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 
        8.81        29.46        29.75        55.89        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       11.64        22.26        22.26       156.66        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       28.90         8.55        40.41        37.32       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        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
       60.16        31.04        49.28         8.09         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       22.55        42.35         3.91        25.55        11.05         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
       34.29        30.54        13.94        35.21        38.73        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        2.86         0.07        32.65        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
        1.28         1.12         0.79         1.78        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 
        3.29        19.66         5.06         0.13        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.08         1.51         2.17        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        4.80         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
       22.65        20.71        21.40         1.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8399 
       15.81        20.19        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-64-1677 TCGA-64-1678 
       39.25        40.96        29.92        56.81        20.65        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-67-3772 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-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         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 
        2.93        12.56        14.01        13.45         4.24        25.91 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
       17.16         2.01        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31         9.24         1.25        39.09        50.33 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       11.18       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
      129.53        39.95       119.51        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
       10.55        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 
        1.15        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-91-6836 
       10.62        41.36         1.97        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        2.86        18.67        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       17.92        18.12        15.39        16.41        14.30        21.60 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
       21.63        24.30        23.80        18.08        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       14.30         6.35        10.09        14.53         1.91        21.83 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       18.58        15.65        27.19        38.63         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        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        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        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 
             20.58              19.89 
[1] "0.4 - 110.5 (20.6)" "0.0 - 238.3 (19.9)"
[1] "hr=" "1.4"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         1       12       19        0        10         8
  22Q GAIN WILD-TYPE       4      123      120        1        42        64
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  22Q GAIN MUTATED            9          0        3
  22Q GAIN WILD-TYPE         63         11       23
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 12                123
  STAGE IB                 19                120
  STAGE II                  0                  1
  STAGE IIA                10                 42
  STAGE IIB                 8                 64
  STAGE IIIA                9                 63
  STAGE IIIB                0                 11
  STAGE IV                  3                 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
  22Q GAIN MUTATED    15  39   6   1
  22Q GAIN WILD-TYPE 155 239  40  18
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               15                155
  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 295  81    68
D39V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                  37                295
  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 236 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     39   23
  22Q GAIN WILD-TYPE  236  217
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               39                236
  MALE                 23                217
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    45   4
  22Q GAIN WILD-TYPE 315  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     45    4
  22Q GAIN WILD-TYPE  315   50
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                45                315
  YES                4                 50
[1] 2 2
[1] FALSE
D39V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  22Q GAIN MUTATED                            1
  22Q GAIN WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  22Q GAIN MUTATED                                   8
  22Q GAIN WILD-TYPE                                98
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                   46
  22Q GAIN WILD-TYPE                                                274
                    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                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                274
  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   0   1   2
  22Q GAIN WILD-TYPE 298  12   3  24
D39V13, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               45                298
  R1                0                 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                        47   340
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                 47
  WHITE                                          49                340
[1] 4 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   6 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   44
  22Q GAIN WILD-TYPE    6  338
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               44                338
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    31  17
  XP GAIN WILD-TYPE 294 150
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               48               444 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               17               150 
$`XP GAIN MUTATED`
TCGA-05-4397 TCGA-05-4434 TCGA-05-5423 TCGA-35-5375 TCGA-44-2655 TCGA-44-8117 
       24.03        15.02         4.96         8.68        43.53        12.66 
TCGA-44-A47A TCGA-44-A4SU TCGA-49-6761 TCGA-49-AAR9 TCGA-4B-A93V TCGA-50-5933 
       15.32        13.45        11.64         8.55         9.86        78.67 
TCGA-50-6591 TCGA-55-6543 TCGA-55-6712 TCGA-55-6970 TCGA-55-6987 TCGA-55-7576 
        3.91         0.07         0.79        15.25        70.26         1.32 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8094 TCGA-55-8096 TCGA-55-8615 
        0.53         6.48         0.16         0.13        23.64         0.49 
TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-64-1680 TCGA-64-5775 
       20.58        15.81        19.99         4.57        37.02         2.04 
TCGA-67-6215 TCGA-69-7973 TCGA-69-7980 TCGA-73-4676 TCGA-73-4677 TCGA-78-7149 
        5.72         7.56        12.56         9.24         1.25       129.53 
TCGA-78-7155 TCGA-78-7163 TCGA-78-7220 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 
       38.50       238.29        26.53         8.02        26.01       232.18 
TCGA-91-8499 TCGA-93-A4JN TCGA-97-7554 TCGA-97-8179 TCGA-L9-A5IP TCGA-L9-A7SV 
        1.18        23.61        25.48        14.30         1.91        18.58 

$`XP GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       15.02        29.00        22.03         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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        4.37        46.98        44.42        44.94        38.10        42.08 
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-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       29.23        13.74         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.08        11.54        13.64        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       12.66        35.54        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       29.46        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       17.16        22.26        22.26       156.66        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90        40.41        37.32       123.58       221.33       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
       49.28         8.09         9.27        14.27        40.60        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12         9.37        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
       42.35        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
       30.54        13.94        35.21        23.05        38.73        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 
       45.21         2.86        32.65        42.51        40.73         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 
       32.71        60.03        24.99        40.54       107.21         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 
        1.15         7.99         0.20         0.13         3.12        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1.28         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.66        19.73         5.06        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80         6.64        17.62         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
       19.59         0.92        20.19        17.95        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-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
       29.92        56.81        20.65        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         1.02 
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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41         2.93        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       25.91        17.16         2.01        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 
       26.30        15.35         4.31        30.31        39.09        50.33 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       11.18       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95       119.51        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
       64.90        22.92         9.57       104.19         8.48        88.14 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       31.20        53.33        39.35        10.55        50.24        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        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         1.15        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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
        6.12         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       17.92         5.39        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
        1.45        21.57        21.63        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53        21.83        15.65        27.19        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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
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        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.26         0.43        19.82        20.28        59.11        16.87 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.07              0.00 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           238.29            221.33 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           12.610            20.565 
[1] "0.1 - 238.3 (12.6)" "0.0 - 221.3 (20.6)"
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED         1       11       10        0         7         3
  XP GAIN WILD-TYPE       4      124      129        1        45        69
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XP GAIN MUTATED            9          3        7
  XP GAIN WILD-TYPE         63          8       19
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                11               124
  STAGE IB                10               129
  STAGE II                 0                 1
  STAGE IIA                7                45
  STAGE IIB                3                69
  STAGE IIIA               9                63
  STAGE IIIB               3                 8
  STAGE IV                 7                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
  XP GAIN MUTATED    13  30   3   5
  XP GAIN WILD-TYPE 157 248  43  14
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              13               157
  T2              30               248
  T3               3                43
  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
  XP GAIN MUTATED    30   8    13
  XP GAIN WILD-TYPE 302  88    63
D40V5, multiclass
       clus
vv      XP GAIN MUTATED XP GAIN WILD-TYPE
  N0                 30               302
  N1                  8                88
  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    30   7
  XP GAIN WILD-TYPE 319  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     30    7
  XP GAIN WILD-TYPE  319   18
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              30               319
  1               7                18
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    24  27
  XP GAIN WILD-TYPE 251 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     24   27
  XP GAIN WILD-TYPE  251  213
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              24               251
  MALE                27               213
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    29   6
  XP GAIN WILD-TYPE 331  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     29    6
  XP GAIN WILD-TYPE  331   48
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               29               331
  YES               6                48
[1] 2 2
[1] FALSE
D40V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XP GAIN MUTATED                            2
  XP GAIN WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XP GAIN MUTATED                                  10
  XP GAIN WILD-TYPE                                96
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XP GAIN MUTATED                                                   36
  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                               10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              36
  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                                        17
  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   2   1   2
  XP GAIN WILD-TYPE 308  10   3  24
D40V13, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              35               308
  R1               2                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                           6    38
  XP GAIN WILD-TYPE                        45   351
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                      6                45
  WHITE                                         38               351
[1] 4 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  35
  XP GAIN WILD-TYPE   7 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   35
  XP GAIN WILD-TYPE    7  347
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              35               347
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    53  24
  XQ GAIN WILD-TYPE 272 143
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               77               415 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               24               143 
$`XQ GAIN MUTATED`
TCGA-05-4397 TCGA-05-4405 TCGA-05-4426 TCGA-05-4434 TCGA-05-5423 TCGA-35-5375 
       24.03        20.05        26.01        15.02         4.96         8.68 
TCGA-44-2655 TCGA-44-2659 TCGA-44-6778 TCGA-44-8117 TCGA-44-A47A TCGA-44-A4SU 
       43.53        44.94        61.28        12.66        15.32        13.45 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5933 TCGA-50-5941 
       11.64        22.26       221.33         9.86        78.67         9.37 
TCGA-50-5946 TCGA-50-6591 TCGA-53-7626 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
       22.55         3.91        30.54         2.86         0.07         0.79 
TCGA-55-6970 TCGA-55-6987 TCGA-55-7281 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 
       15.25        70.26         0.59         1.28         0.53         6.48 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8094 TCGA-55-8096 TCGA-55-A494 TCGA-55-A4DG 
       19.82         0.16         0.13        23.64        15.81        19.99 
TCGA-55-A57B TCGA-62-8399 TCGA-64-1676 TCGA-64-1680 TCGA-64-5775 TCGA-67-4679 
       17.95        88.64        56.81        37.02         2.04        14.73 
TCGA-67-6215 TCGA-69-7980 TCGA-71-6725 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
        5.72        12.56         2.01         4.31         9.24         1.25 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 TCGA-78-7163 TCGA-78-7535 TCGA-78-7539 
      129.53        19.50        38.50       238.29        31.20        26.01 
TCGA-78-7542 TCGA-78-8640 TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 TCGA-86-A4P7 
       10.55       232.18         4.08        22.82        21.47        13.64 
TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7043 TCGA-97-7554 TCGA-97-7937 
        1.18        23.61         1.08        16.54        25.48         5.95 
TCGA-97-8172 TCGA-97-8179 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4T4 
       17.92        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         0.26        20.28        16.87 

$`XQ GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 
        0.00         9.96        47.05         8.02        19.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 
       26.01        25.02        25.02        24.00        15.02        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-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 
       11.64        44.61        14.73        26.30         4.37        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.42        38.10        42.08        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-44-6146 
       33.30        28.37        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       16.44        22.72        19.46        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        29.23        13.74         3.25         8.55 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       15.98         9.44        11.08        11.54        13.64        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        16.04 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       53.29        55.33        17.16        22.26       156.66        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO 
       62.24        28.90         8.55        40.41        37.32       123.58 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
      164.12        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       21.47         8.45        15.12        29.03        25.12        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
       10.13        36.99         7.59        27.25        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 
       35.21        23.05        38.73        48.62        45.21        32.65 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       42.51        40.73         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
       40.54       107.21         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        3.12         1.32        23.18         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 
        1.78        18.64        17.65         6.15        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 TCGA-55-8203 
        3.29        19.66        19.73         5.06        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
       21.40         1.58        20.58        19.59         0.92        20.19 
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-64-1677 TCGA-64-1678 TCGA-64-1679 
       39.25        40.96        29.92        20.65        39.09        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98        42.90        28.41        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
        1.02        20.05        18.84        14.04        12.66         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         4.41         2.93        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.24        25.91        17.16        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
       26.30        15.35        30.31        39.09        50.33        11.18 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
      163.10        27.16         5.69        19.27        20.58        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       39.95       119.51        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        9.57       104.19         8.48        88.14        26.53         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       53.33        39.35        50.24        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        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         1.15        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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.45        19.82        22.45        17.46 
TCGA-93-8067 TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        6.12        19.00        17.29        41.82         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       18.18        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       34.85        36.76         1.45        21.57        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 
        6.35        10.09        14.53        21.83        15.65        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
        2.76        86.14        58.45        49.35        37.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
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 
       62.60         0.13         1.64        29.13         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.00 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           238.29            164.12 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            15.81             20.58 
[1] "0.1 - 238.3 (15.8)" "0.0 - 164.1 (20.6)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         2       21       21        0        10         8
  XQ GAIN WILD-TYPE       3      114      118        1        42        64
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XQ GAIN MUTATED           10          2        8
  XQ GAIN WILD-TYPE         62          9       18
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                21               114
  STAGE IB                21               118
  STAGE II                 0                 1
  STAGE IIA               10                42
  STAGE IIB                8                64
  STAGE IIIA              10                62
  STAGE IIIB               2                 9
  STAGE IV                 8                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
  XQ GAIN MUTATED    25  48   5   5
  XQ GAIN WILD-TYPE 145 230  41  14
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              25               145
  T2              48               230
  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
  XQ GAIN MUTATED    54  17    12
  XQ GAIN WILD-TYPE 278  79    64
D41V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                 54               278
  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    54   8
  XQ GAIN WILD-TYPE 295  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     54    8
  XQ GAIN WILD-TYPE  295   17
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              54               295
  1               8                17
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    40  43
  XQ GAIN WILD-TYPE 235 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     40   43
  XQ GAIN WILD-TYPE  235  197
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              40               235
  MALE                43               197
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    52   4
  XQ GAIN WILD-TYPE 308  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     52    4
  XQ GAIN WILD-TYPE  308   50
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               52               308
  YES               4                50
[1] 2 2
[1] FALSE
D41V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XQ GAIN MUTATED                            3
  XQ GAIN WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XQ GAIN MUTATED                                  13
  XQ GAIN WILD-TYPE                                93
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                   60
  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                               13
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              60
  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                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 93
  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    58   2   1   4
  XQ GAIN WILD-TYPE 285  10   3  22
D41V13, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              58               285
  R1               2                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                           9    60
  XQ GAIN WILD-TYPE                        42   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                      9                42
  WHITE                                         60               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  54
  XQ GAIN WILD-TYPE   7 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   54
  XQ GAIN WILD-TYPE    7  328
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              54               328
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    48  32
  1P LOSS WILD-TYPE 277 135
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               80               412 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               32               135 
$`1P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4415 
       50.07         3.98        37.02         9.96        47.05         2.99 
TCGA-05-4417 TCGA-05-4422 TCGA-05-5420 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       14.96        12.00        15.02        42.77         3.19        25.02 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6147 TCGA-44-6775 
       33.30        28.01        23.77         9.93        27.78        23.18 
TCGA-44-A47F TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6745 TCGA-49-6761 
       11.08        35.54        32.84         8.81        17.16        11.64 
TCGA-49-AARE TCGA-50-5051 TCGA-50-5935 TCGA-50-5936 TCGA-50-6594 TCGA-50-6595 
       40.41        15.72        21.47         8.45        12.16         6.21 
TCGA-50-7109 TCGA-53-7626 TCGA-55-1596 TCGA-55-6972 TCGA-55-6986 TCGA-55-7283 
       10.13        30.54        45.21        48.49       107.21         1.15 
TCGA-55-8090 TCGA-55-8203 TCGA-55-8205 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 
       19.66        17.98         1.08         0.26         0.49         0.49 
TCGA-55-A48Y TCGA-55-A492 TCGA-62-8402 TCGA-62-A46S TCGA-62-A46U TCGA-64-5774 
       20.71        19.59        49.25        54.35        67.96        87.98 
TCGA-64-5778 TCGA-69-7761 TCGA-69-7973 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 
       42.90         6.12         7.56        23.38        26.30        30.31 
TCGA-73-4677 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7159 
        1.25         5.69        20.58       129.53       119.51        64.90 
TCGA-78-7160 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-8054 TCGA-86-8278 
       22.92        12.36         5.88        31.13        37.74        31.04 
TCGA-86-8669 TCGA-86-A4JF TCGA-91-8499 TCGA-95-7567 TCGA-95-A4VP TCGA-97-7554 
       30.84        24.23         1.18        18.67        19.89        25.48 
TCGA-97-8172 TCGA-97-8174 TCGA-MP-A4T7 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TJ 
       17.92         5.39         5.49        10.09        29.46        11.15 
TCGA-NJ-A4YQ TCGA-NJ-A7XG 
       29.13        20.28 

$`1P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4402 
       19.96        14.01        45.01         0.00        24.03         8.02 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 
       19.00        20.05         9.01        29.98        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       26.30         4.37        43.53        46.98        44.42        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
       38.10        42.08        37.15        38.24        38.89        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       33.73        26.56        28.37        19.56        23.15        21.63 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
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-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
       28.57        12.66        46.72        14.07        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV 
       55.89        16.04        53.29        55.33        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN 
      156.66        73.12        62.24        28.90         8.55        37.32 
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-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       70.55        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       14.27        40.60        78.67        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       25.12        22.55        42.35         3.91        25.55        11.05 
TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       41.69         0.72        36.99         7.59        27.25        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 
       13.94        35.21        23.05        38.73        48.62         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        0.82         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
       32.71        60.03        24.99        40.54        70.26         0.59 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1.28         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19         3.29        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       23.64        15.65         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 
        1.45         0.76         0.95         0.36        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80         6.64        17.62         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        2.17        16.93        22.65        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
        0.92        15.81        20.19        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-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-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       56.81        20.65        39.09        81.80        37.02        38.37 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        2.04        28.41        51.25        28.47         1.02        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-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
       13.87         6.64        22.68        13.61         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41         2.93        12.56        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 
       25.91        17.16         2.01        52.60        82.68        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
        4.31         9.24        39.09        50.33        11.18       163.10 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
       27.16        19.27        21.90        39.95        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       32.09         5.88         9.57       104.19       238.29         8.48 
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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       10.55       110.50        27.09        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       32.78        19.89        35.24         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        0.79        22.82        32.65        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60         1.15        13.91        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       26.50        29.46         3.81        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       18.18        31.69        64.60        63.52        43.79         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.59         0.72        18.67        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       34.85        36.76         1.45        21.57        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
        6.35        10.09        14.53         1.91        21.83        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       15.65        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       31.23         2.43        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        62.60         0.13         1.64         0.26 
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 
             0.26              0.00 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           129.53            238.29 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           20.430            19.925 
[1] "0.3 - 129.5 (20.4)" "0.0 - 238.3 (19.9)"
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         0       17       17        0         7        12
  1P LOSS WILD-TYPE       5      118      122        1        45        60
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1P LOSS MUTATED           21          4        4
  1P LOSS WILD-TYPE         51          7       22
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                17               118
  STAGE IB                17               122
  STAGE II                 0                 1
  STAGE IIA                7                45
  STAGE IIB               12                60
  STAGE IIIA              21                51
  STAGE IIIB               4                 7
  STAGE IV                 4                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
  1P LOSS MUTATED    20  47   9   6
  1P LOSS WILD-TYPE 150 231  37  13
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              20               150
  T2              47               231
  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  18    20
  1P LOSS WILD-TYPE 291  78    56
D42V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                 41               291
  N1                 18                78
  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"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    66   4
  1P LOSS WILD-TYPE 283  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     66    4
  1P LOSS WILD-TYPE  283   21
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              66               283
  1               4                21
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    40  42
  1P LOSS WILD-TYPE 235 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     40   42
  1P LOSS WILD-TYPE  235  198
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              40               235
  MALE                42               198
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    63   7
  1P LOSS WILD-TYPE 297  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     63    7
  1P LOSS WILD-TYPE  297   47
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               63               297
  YES               7                47
[1] 2 2
[1] FALSE
D42V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1P LOSS MUTATED                            4
  1P LOSS WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1P LOSS MUTATED                                  17
  1P LOSS WILD-TYPE                                89
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                   50
  1P LOSS WILD-TYPE                                                270
                   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                              1                             4
  1P LOSS WILD-TYPE                            1                            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                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              50
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  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                                 89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               270
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  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    52   1   1   6
  1P LOSS WILD-TYPE 291  11   3  20
D42V13, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              52               291
  R1               1                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
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           6    62
  1P LOSS WILD-TYPE                        45   327
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                      6                45
  WHITE                                         62               327
[1] 4 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     2  57
  1P LOSS WILD-TYPE   5 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   57
  1P LOSS WILD-TYPE    5  325
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              57               325
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    20  12
  1Q LOSS WILD-TYPE 305 155
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               32               460 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               12               155 
$`1Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4422 TCGA-05-4427 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        9.96        12.00        26.01        42.77         3.19        25.02 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6775 TCGA-49-4507 
       33.30        28.01         9.93        27.78        23.18         8.81 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5936 TCGA-50-6594 TCGA-50-7109 TCGA-55-6986 
       17.16        11.64         8.45        12.16        10.13       107.21 
TCGA-55-8090 TCGA-55-8205 TCGA-55-8507 TCGA-55-8620 TCGA-62-8402 TCGA-64-5774 
       19.66         1.08         0.26         2.17        49.25        87.98 
TCGA-64-5778 TCGA-73-4666 TCGA-78-7146 TCGA-86-6851 TCGA-86-8278 TCGA-91-8499 
       42.90        26.30         5.69         5.88        31.04         1.18 
TCGA-97-8174 TCGA-MP-A4TF 
        5.39        11.05 

$`1Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96         9.01        29.98        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       26.30         4.37        43.53        46.98        44.42        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
       38.10        42.08        37.15        38.24        38.89        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.73        26.56        28.37        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.23        13.74        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       14.07        32.84        29.46        29.75        55.89        16.04 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       53.29        55.33        22.26        22.26       156.66        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO 
       62.24        28.90         8.55        40.41        37.32       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        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        78.67        21.47        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 
       11.05         6.21        41.69         0.72        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94        35.21        23.05 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       38.73        48.62        45.21         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        3.88         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
       60.03        24.99        40.54        70.26         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1.28         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19         3.29        19.73         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65        17.98         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       20.19        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-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       56.81        20.65        39.09        81.80        37.02        38.37 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        2.04        28.41        51.25        28.47         1.02        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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
       13.45         4.24        25.91        17.16         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        82.68        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        1.25        39.09        50.33        11.18       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-78-7166 TCGA-78-7167 TCGA-78-7220 
        9.57       104.19       238.29         8.48        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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
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         1.15        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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        18.67        17.92        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       14.30         6.35        10.09        14.53         1.91        21.83 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       18.58        15.65        27.19        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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
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 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.26              0.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           107.21            238.29 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            12.08             20.12 
[1] "0.3 - 107.2 (12.1)" "0.0 - 238.3 (20.1)"
[1] "hr=" "1.3"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        6        8        0         3         5
  1Q LOSS WILD-TYPE       5      129      131        1        49        67
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1Q LOSS MUTATED            8          1        2
  1Q LOSS WILD-TYPE         64         10       24
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 6               129
  STAGE IB                 8               131
  STAGE II                 0                 1
  STAGE IIA                3                49
  STAGE IIB                5                67
  STAGE IIIA               8                64
  STAGE IIIB               1                10
  STAGE IV                 2                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
  1Q LOSS MUTATED    10  19   3   1
  1Q LOSS WILD-TYPE 160 259  43  18
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              10               160
  T2              19               259
  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
  1Q LOSS MUTATED    17   7     7
  1Q LOSS WILD-TYPE 315  89    69
D43V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0                 17               315
  N1                  7                89
  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    26   2
  1Q LOSS WILD-TYPE 323  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     26    2
  1Q LOSS WILD-TYPE  323   23
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              26               323
  1               2                23
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    17  16
  1Q LOSS WILD-TYPE 258 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     17   16
  1Q LOSS WILD-TYPE  258  224
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              17               258
  MALE                16               224
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    25   4
  1Q LOSS WILD-TYPE 335  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     25    4
  1Q LOSS WILD-TYPE  335   50
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               25               335
  YES               4                50
[1] 2 2
[1] FALSE
D43V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1Q LOSS MUTATED                            0
  1Q LOSS WILD-TYPE                         19
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1Q LOSS MUTATED                                   6
  1Q LOSS WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                   22
  1Q LOSS WILD-TYPE                                                298
                   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                              1                             1
  1Q LOSS WILD-TYPE                            1                            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                                6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              22
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  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                                        19
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               298
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  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    20   0   0   1
  1Q LOSS WILD-TYPE 323  12   4  25
D43V13, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              20               323
  R1               0                12
  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
  1Q LOSS MUTATED                                  0     0
  1Q LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           3    26
  1Q LOSS WILD-TYPE                        48   363
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                      3                48
  WHITE                                         26               363
[1] 4 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     2  24
  1Q LOSS WILD-TYPE   5 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   24
  1Q LOSS WILD-TYPE    5  358
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              24               358
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    16   9
  2P LOSS WILD-TYPE 309 158
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               25               467 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                9               158 
$`2P LOSS MUTATED`
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3918 TCGA-44-5645 TCGA-44-6778 
       42.77         3.19        25.02        34.06        28.01        61.28 
TCGA-50-5936 TCGA-50-6591 TCGA-50-7109 TCGA-55-6986 TCGA-55-7726 TCGA-55-8097 
        8.45         3.91        10.13       107.21         1.28        15.65 
TCGA-62-8397 TCGA-62-A471 TCGA-67-3772 TCGA-71-6725 TCGA-73-7499 TCGA-78-7153 
       42.38        40.96        18.84         2.01        50.33       119.51 
TCGA-78-7220 TCGA-86-8074 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-L4-A4E5 
       26.53         0.79         5.95        17.92         5.39        19.00 
TCGA-MP-A4T8 
        5.29 

$`2P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         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-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       11.64        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-3396 
       46.98        44.42        44.94        38.10        42.08        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-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        63.72        32.45        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        16.04 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       53.29        55.33        17.16        11.64        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
      156.66        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       37.32       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        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.09         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
       35.21        23.05        38.73        48.62        45.21         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 
       45.34        32.71        60.03        24.99        40.54        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1.32        23.18         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        5.06         0.13        23.64        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        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-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-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
       13.61        39.25        29.92        56.81        20.65        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-67-3773 
       28.41        51.25        28.47         1.02        20.05        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       12.66        14.73         5.72         4.64        13.87         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         2.93        12.56        14.01        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
       25.91        17.16        52.60        23.38        82.68        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       11.18       163.10        27.16         5.69        19.27        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-78-7158 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-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         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-86-8075 TCGA-86-8076 
       37.74         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         1.15 
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-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79        25.48         0.59         0.72        18.67 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       21.57        21.63        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       32.48        14.30         6.35        10.09        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       21.83        18.58        15.65        27.19        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-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49        41.59        31.23         2.43        10.09        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        62.60         0.13         1.64        29.13         0.26 
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 

  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 
            18.84             20.05 
[1] "0.8 - 119.5 (18.8)" "0.0 - 238.3 (20.1)"
[1] "hr=" "1"  
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         1        6       12        0         2         3
  2P LOSS WILD-TYPE       4      129      127        1        50        69
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2P LOSS MUTATED            3          0        1
  2P LOSS WILD-TYPE         69         11       25
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 6               129
  STAGE IB                12               127
  STAGE II                 0                 1
  STAGE IIA                2                50
  STAGE IIB                3                69
  STAGE IIIA               3                69
  STAGE IIIB               0                11
  STAGE IV                 1                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
  2P LOSS MUTATED     8  19   1   0
  2P LOSS WILD-TYPE 162 259  45  19
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               8               162
  T2              19               259
  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    21   3     3
  2P LOSS WILD-TYPE 311  93    73
D44V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0                 21               311
  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    22   1
  2P LOSS WILD-TYPE 327  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     22    1
  2P LOSS WILD-TYPE  327   24
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              22               327
  1               1                24
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    18  10
  2P LOSS WILD-TYPE 257 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     18   10
  2P LOSS WILD-TYPE  257  230
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              18               257
  MALE                10               230
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    21   1
  2P LOSS WILD-TYPE 339  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     21    1
  2P LOSS WILD-TYPE  339   53
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               21               339
  YES               1                53
[1] 2 2
[1] FALSE
D44V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2P LOSS MUTATED                            1
  2P LOSS WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2P LOSS MUTATED                                   5
  2P LOSS WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                   17
  2P LOSS WILD-TYPE                                                303
                   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)              17
  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                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               303
  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    16   0   0   2
  2P LOSS WILD-TYPE 327  12   4  24
D44V13, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              16               327
  R1               0                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
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           2    21
  2P LOSS WILD-TYPE                        49   368
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                      2                49
  WHITE                                         21               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"
D44V15, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  19
  2P LOSS WILD-TYPE   6 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   19
  2P LOSS WILD-TYPE    6  363
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              19               363
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    20   6
  2Q LOSS WILD-TYPE 305 161
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               26               466 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               161 
$`2Q LOSS MUTATED`
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3918 TCGA-44-5645 TCGA-44-6778 
       42.77         3.19        25.02        34.06        28.01        61.28 
TCGA-49-AARO TCGA-50-5936 TCGA-50-5946 TCGA-50-6591 TCGA-55-6986 TCGA-55-8097 
      123.58         8.45        22.55         3.91       107.21        15.65 
TCGA-62-8397 TCGA-64-1676 TCGA-67-3772 TCGA-69-7760 TCGA-71-6725 TCGA-73-7499 
       42.38        56.81        18.84         6.64         2.01        50.33 
TCGA-78-7153 TCGA-86-8054 TCGA-86-8074 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 
      119.51        37.74         0.79        25.48         5.95        17.92 
TCGA-L4-A4E5 TCGA-MP-A4T8 
       19.00         5.29 

$`2Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         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-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       11.64        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-3396 
       46.98        44.42        44.94        38.10        42.08        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-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        63.72        32.45        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        16.04 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       53.29        55.33        17.16        11.64        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
      156.66        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
       37.32       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 
       70.55        15.72        60.16        31.04        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 
        9.27        14.27        40.60        78.67        21.47        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 
        9.37        29.03        25.12        42.35        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       12.16         6.21        41.69         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        27.25        34.29        30.54        13.94        35.21 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
       23.05        38.73        48.62        45.21         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
       32.71        60.03        24.99        40.54        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        5.06         0.13        23.64        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        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-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-64-1677 TCGA-64-1678 
       13.61        39.25        40.96        29.92        20.65        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-67-3773 
       28.41        51.25        28.47         1.02        20.05        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 
       12.66        14.73         5.72         4.64        13.87         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 
        2.93        12.56        14.01        13.45         4.24        25.91 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
       17.16        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS 
        4.31        30.31         9.24         1.25        39.09        11.18 
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-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         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-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57        24.33        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         1.15        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-91-6828 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-91-6836 TCGA-91-6840 TCGA-91-6847 
        1.97        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29        41.82        16.54         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       18.67        12.39        15.68        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       21.40        18.18        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       43.79         0.59         0.72        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.63        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       14.30         6.35        10.09        14.53         1.91        21.83 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       18.58        15.65        27.19        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-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        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 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       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 
           23.785            19.925 
[1] "0.8 - 123.6 (23.8)" "0.0 - 238.3 (19.9)"
[1] "hr=" "2"  
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         1        7       11        0         1         5
  2Q LOSS WILD-TYPE       4      128      128        1        51        67
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2Q LOSS MUTATED            3          0        1
  2Q LOSS WILD-TYPE         69         11       25
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 7               128
  STAGE IB                11               128
  STAGE II                 0                 1
  STAGE IIA                1                51
  STAGE IIB                5                67
  STAGE IIIA               3                69
  STAGE IIIB               0                11
  STAGE IV                 1                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
  2Q LOSS MUTATED     9  18   2   0
  2Q LOSS WILD-TYPE 161 260  44  19
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               9               161
  T2              18               260
  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    21   4     3
  2Q LOSS WILD-TYPE 311  92    73
D45V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                 21               311
  N1                  4                92
  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    22   1
  2Q LOSS WILD-TYPE 327  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     22    1
  2Q LOSS WILD-TYPE  327   24
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              22               327
  1               1                24
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    18  11
  2Q LOSS WILD-TYPE 257 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     18   11
  2Q LOSS WILD-TYPE  257  229
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              18               257
  MALE                11               229
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    23   1
  2Q LOSS WILD-TYPE 337  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     23    1
  2Q LOSS WILD-TYPE  337   53
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               23               337
  YES               1                53
[1] 2 2
[1] FALSE
D45V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2Q LOSS MUTATED                            3
  2Q LOSS WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2Q LOSS MUTATED                                   4
  2Q LOSS WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                   16
  2Q LOSS WILD-TYPE                                                304
                   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                                0
  2Q LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  2Q LOSS MUTATED                                    1
  2Q LOSS WILD-TYPE                                  2
                   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                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              16
  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                                    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)               304
  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                                     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    18   0   0   1
  2Q LOSS WILD-TYPE 325  12   4  25
D45V13, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              18               325
  R1               0                12
  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     1
  2Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           3    21
  2Q LOSS WILD-TYPE                        48   368
D45V14, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 6
  BLACK OR AFRICAN AMERICAN                      3                48
  WHITE                                         21               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"
D45V15, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  20
  2Q LOSS WILD-TYPE   6 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   20
  2Q LOSS WILD-TYPE    6  362
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              20               362
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   135  68
  3P LOSS WILD-TYPE 190  99
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              203               289 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               68                99 
$`3P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4402 
       50.07        19.96        45.01        37.02        24.03         8.02 
TCGA-05-4415 TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-05-5715 TCGA-35-4122 
        2.99        25.02        15.02        29.00         2.04         7.40 
TCGA-38-4627 TCGA-38-4628 TCGA-38-6178 TCGA-44-2657 TCGA-44-2668 TCGA-44-3917 
       37.71        49.05        14.73        44.42        25.02        38.89 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6774 
       33.30        28.01        23.77        19.56        27.78        21.63 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7670 TCGA-44-7671 
       63.72        61.28        16.44        19.46        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F 
       13.74        12.66         3.25         8.55        15.98        11.08 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
       46.72        14.07        32.84        29.46        55.89        16.04 
TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-50-5049 
       53.29        55.33        22.26       156.66        73.12        70.55 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 
       49.28         8.09        14.27        40.60        21.47         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       15.12         9.37         3.91        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-1595 
       41.69         0.72        34.29        30.54        38.73        48.62 
TCGA-55-1596 TCGA-55-6968 TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 
       45.21        42.51         3.88        32.71        60.03        40.54 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 
        0.20         0.13         1.32        23.18         1.28         1.12 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-8090 TCGA-55-8094 TCGA-55-8206 
        0.53         6.48         6.15        19.66         0.13         1.51 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.36         0.26         6.64        17.62         0.49         1.58 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-55-A4DG 
        2.17        21.40        20.58        19.59        20.19        19.99 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
        4.57        42.38        14.60        88.64        47.80        19.53 
TCGA-62-A46R TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 
       56.71        13.61        39.25        40.96        56.81        39.09 
TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       87.98        28.41        51.25        28.47         1.02        20.05 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       18.84        13.87        22.68        13.61         5.42         7.56 
TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
        2.93        14.01         2.01        23.38        82.68        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 
        4.31        30.31        39.09        50.33        11.18         5.69 
TCGA-78-7148 TCGA-78-7159 TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       20.58        64.90        22.92        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 
        8.02        26.01        10.55       232.18        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7954 TCGA-86-8054 
       12.36         5.88        31.13        38.04        19.89        37.74 
TCGA-86-8073 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 
       24.33        31.04        23.05        21.47         1.15        30.84 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
        3.81        24.23        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-A4BC TCGA-93-7348 TCGA-95-7039 
       12.23        27.68        16.18         1.45        17.46        41.82 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VP 
       16.54        18.67        15.68        15.65        27.29        19.89 
TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4LX 
       31.69        25.48         5.95         5.39        16.41        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-J2-8192 
       21.44        19.76        20.84        18.67        20.68        24.30 
TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MP-A4T6 
       23.80        32.48        19.00        14.53        18.58        58.85 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ 
        5.29         2.43        10.09        11.05        14.10        11.15 
TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       71.05        29.13         0.43        20.28        59.11 

$`3P LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        3.98        14.01         0.00         9.96        47.05        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       20.05        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 
        4.96        22.03         9.04         0.46         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       97.74       120.79        28.41        35.28        11.64        44.61 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 
       26.30         4.37        43.53        46.98        44.94        38.10 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       42.08        42.77         3.19        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 
       33.73        26.56        28.37         9.93        23.15        23.18 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       32.45        22.72        12.03         7.17        36.07        18.87 
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-49-4507 TCGA-49-4512 
       28.11        28.57        12.66        35.54         8.81        29.75 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       17.16        11.64        22.26        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       40.41        37.32       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        31.04         9.27 
TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
       78.67        29.03        25.12        22.55        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         7.59        27.25        13.94        35.21 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       23.05         2.86         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
       15.25         0.82        48.49         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
       45.34        24.99       107.21        70.26         0.59         1.15 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        7.99         3.12         1.28         0.79         1.78        18.64 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06        23.64        15.65        17.98         1.08 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 
        0.49        17.72         0.30         0.10         4.80         1.61 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       16.93        22.65        20.71         1.58         0.92        15.81 
TCGA-55-A57B TCGA-62-8395 TCGA-62-8402 TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       17.95        39.98        49.25        54.35        67.96        72.30 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
       29.92        20.65        81.80        37.02        38.37         2.04 
TCGA-64-5778 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       42.90        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 
        6.64         6.12         6.05         4.41        12.56        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4668 TCGA-73-4676 
        4.24        25.91        17.16        52.60        15.35         9.24 
TCGA-73-4677 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
        1.25       163.10        27.16        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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7540 
        9.57       104.19       238.29         8.48        53.33        39.35 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-7711 TCGA-86-7714 
       50.24        39.75        77.59       110.50        34.39        20.55 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
       32.78        35.24         4.08         4.57         0.79        22.82 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       32.65        31.20        14.60        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       28.34        26.50        29.46        13.64        26.47        10.62 
TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       13.71         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7944 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       17.29         2.86        12.39         2.76        21.40        18.18 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        43.79         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       17.92        18.12        15.39        14.30        21.60        20.58 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.52        17.75        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-A443 
       21.57        21.63        18.08        35.47        14.30         6.35 
TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
       10.09         1.91        21.83        15.65        27.19        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-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK 
        5.49        41.59        31.23        29.46        24.36        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R 
       73.91        62.60         0.13         1.64         0.26        19.82 
TCGA-S2-AA1A 
       16.87 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.13              0.00 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           232.18            238.29 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            20.19             19.82 
[1] "0.1 - 232.2 (20.2)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         2       51       54        1        27        30
  3P LOSS WILD-TYPE       3       84       85        0        25        42
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3P LOSS MUTATED           32          3       12
  3P LOSS WILD-TYPE         40          8       14
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                51                84
  STAGE IB                54                85
  STAGE II                 1                 0
  STAGE IIA               27                25
  STAGE IIB               30                42
  STAGE IIIA              32                40
  STAGE IIIB               3                 8
  STAGE IV                12                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    73 123  11   5
  3P LOSS WILD-TYPE  97 155  35  14
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              73                97
  T2             123               155
  T3              11                35
  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  44    34
  3P LOSS WILD-TYPE 203  52    42
D46V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                129               203
  N1                 44                52
  N2+N3              34                42
[1] 3 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   148  11
  3P LOSS WILD-TYPE 201  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    148   11
  3P LOSS WILD-TYPE  201   14
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             148               201
  1              11                14
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   113  99
  3P LOSS WILD-TYPE 162 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    113   99
  3P LOSS WILD-TYPE  162  141
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             113               162
  MALE                99               141
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   152  22
  3P LOSS WILD-TYPE 208  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    152   22
  3P LOSS WILD-TYPE  208   32
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO              152               208
  YES              22                32
[1] 2 2
[1] FALSE
D46V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3P LOSS MUTATED                            8
  3P LOSS WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3P LOSS MUTATED                                  51
  3P LOSS WILD-TYPE                                55
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                  133
  3P LOSS WILD-TYPE                                                187
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3P LOSS MUTATED                                            0
  3P LOSS WILD-TYPE                                          5
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  3P LOSS MUTATED                                               5
  3P LOSS WILD-TYPE                                            14
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  3P LOSS MUTATED                                2
  3P LOSS WILD-TYPE                              0
                   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                              4
  3P LOSS WILD-TYPE                            6
D46V10, multiclass
                                                    clus
vv                                                   3P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             133
  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                                    6
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     4
                                                    clus
vv                                                   3P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               187
  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                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  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"
D46V11, continuous
D46V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED   139   2   1   6
  3P LOSS WILD-TYPE 204  10   3  20
D46V13, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0             139               204
  R1               2                10
  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   163
  3P LOSS WILD-TYPE                        28   226
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                28
  WHITE                                        163               226
[1] 4 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   5 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2  165
  3P LOSS WILD-TYPE    5  217
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             165               217
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    92  48
  3Q LOSS WILD-TYPE 233 119
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              140               352 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               48               119 
$`3Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4397 TCGA-05-4415 TCGA-05-4432 TCGA-05-5420 
       50.07        37.02        24.03         2.99        25.02        15.02 
TCGA-05-5715 TCGA-35-4122 TCGA-38-4628 TCGA-44-2668 TCGA-44-3917 TCGA-44-5645 
        2.04         7.40        49.05        25.02        38.89        28.01 
TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
       23.77        27.78        21.63        63.72        61.28        16.44 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       29.23        13.74        12.66         3.25         8.55        15.98 
TCGA-44-A47F TCGA-49-4506 TCGA-49-4510 TCGA-49-6742 TCGA-49-AAQV TCGA-50-5068 
       11.08        32.84        29.46        16.04        22.26        49.28 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 
       40.60        21.47         8.45         3.91        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
        6.21        41.69         0.72        48.62        45.21         2.86 
TCGA-55-6712 TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 TCGA-55-7283 TCGA-55-7573 
        0.79         3.88        32.71        60.03         1.15         0.13 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-8090 TCGA-55-8094 TCGA-55-8203 
        1.12         0.53         6.48        19.66         0.13        17.98 
TCGA-55-8206 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
        1.51         6.64         0.49         1.58         2.17        21.40 
TCGA-55-A492 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
       19.59        20.19        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         1.02        20.05 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
       18.84        13.87        22.68        13.61         5.42         6.05 
TCGA-69-8253 TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4675 
       14.01         2.01        23.38        82.68        26.30        30.31 
TCGA-73-7498 TCGA-73-A9RS TCGA-78-7148 TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 
       39.09        11.18        20.58        22.92        88.14        26.53 
TCGA-78-7535 TCGA-78-7539 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       31.20        26.01        10.55        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         1.15         3.81 
TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 
       12.23        27.68        16.18        17.46        41.82        18.67 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 
       15.65        21.40        19.89        31.69        25.48         5.95 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       17.92         5.39        16.41        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A50W 
       18.67        24.30        23.80        32.48        19.00        14.53 
TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TI TCGA-MP-A4TJ 
       58.85         5.29         2.43        10.09        14.10        11.15 
TCGA-NJ-A55O TCGA-NJ-A7XG 
        0.43        20.28 

$`3Q LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
        3.98        19.96        14.01        45.01         0.00         9.96 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 
       47.05         8.02        19.00        20.05        14.96         9.01 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       29.98        12.00        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        24.00        15.02         4.96        29.00        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-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       37.71        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       26.30         4.37        43.53        46.98        44.42        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       38.10        42.08        42.77         3.19        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-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 
        9.93        23.15        23.18        32.45        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-A47A 
       12.03         7.17        36.07        18.87        29.00        15.32 
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-49-4501 TCGA-49-4505 TCGA-49-4507 
       28.57        12.66        35.54        46.72        14.07         8.81 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26       156.66        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       40.41        37.32       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        70.55        15.72        60.16        31.04 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 
        8.09         9.27        14.27        78.67        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-7109 
       29.03        25.12        22.55        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         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       35.21        23.05        38.73         0.07        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82        48.49         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        2.20        45.34        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        0.59         7.99         0.20         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
        1.28         1.28         0.79         1.78        18.64        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 
       19.73         5.06        23.64        15.65         1.08         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
       17.62         1.61        16.93        22.65        20.71         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8402 
       20.58         0.92        15.81        17.95        39.98        49.25 
TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
       47.80        54.35        67.96        72.30        40.96        29.92 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       20.65        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         2.93        12.56 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4668 
       13.45         4.24        25.91        17.16        52.60        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        4.31         9.24         1.25        50.33       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
       19.50        38.50        32.09         5.88        64.90         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
      104.19       238.29         8.48         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       10.55        50.24       232.18        39.75        77.59       110.50 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 
       31.13        34.39        20.55        32.78        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-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       31.20        21.47        14.60        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-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       13.71         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82        22.45         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       19.00        17.29        16.54         2.86        12.39        15.68 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       27.29         2.76        18.18        64.60        63.52        43.79 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
        0.59         0.72        18.67        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       21.60        20.58        20.19        20.52        17.75        20.68 
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-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP 
       18.08        35.47        14.30         6.35        10.09         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       21.83        18.58        15.65        27.19        38.63         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-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
       41.59        31.23        29.46        11.05        24.36        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        0.26        19.82        59.11        16.87 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.13              0.00 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            88.64            238.29 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           19.625            20.535 
[1] "0.1 - 88.6 (19.6)"  "0.0 - 238.3 (20.5)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2       34       32        1        18        23
  3Q LOSS WILD-TYPE       3      101      107        0        34        49
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3Q LOSS MUTATED           26          3        7
  3Q LOSS WILD-TYPE         46          8       19
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                34               101
  STAGE IB                32               107
  STAGE II                 1                 0
  STAGE IIA               18                34
  STAGE IIB               23                49
  STAGE IIIA              26                46
  STAGE IIIB               3                 8
  STAGE IV                 7                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    49  82  10   5
  3Q LOSS WILD-TYPE 121 196  36  14
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              49               121
  T2              82               196
  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
  3Q LOSS MUTATED    83  33    28
  3Q LOSS WILD-TYPE 249  63    48
D47V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0                 83               249
  N1                 33                63
  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   108   6
  3Q LOSS WILD-TYPE 241  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED    108    6
  3Q LOSS WILD-TYPE  241   19
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0             108               241
  1               6                19
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    80  66
  3Q LOSS WILD-TYPE 195 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     80   66
  3Q LOSS WILD-TYPE  195  174
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              80               195
  MALE                66               174
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED   100  19
  3Q LOSS WILD-TYPE 260  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED    100   19
  3Q LOSS WILD-TYPE  260   35
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO              100               260
  YES              19                35
[1] 2 2
[1] FALSE
D47V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3Q LOSS MUTATED                            6
  3Q LOSS WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3Q LOSS MUTATED                                  37
  3Q LOSS WILD-TYPE                                69
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                   86
  3Q LOSS WILD-TYPE                                                234
                   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                              4
  3Q LOSS WILD-TYPE                            6
D47V10, multiclass
                                                    clus
vv                                                   3Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              86
  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                                     4
                                                    clus
vv                                                   3Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               234
  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                                       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"
D47V11, continuous
D47V12, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    91   1   0   5
  3Q LOSS WILD-TYPE 252  11   4  21
D47V13, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              91               252
  R1               1                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                          16   111
  3Q LOSS WILD-TYPE                        35   278
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                     16                35
  WHITE                                        111               278
[1] 4 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     0 116
  3Q LOSS WILD-TYPE   7 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0  116
  3Q LOSS WILD-TYPE    7  266
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO             116               266
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    82  36
  4P LOSS WILD-TYPE 243 131
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              118               374 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               36               131 
$`4P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
       50.07        37.02         0.00        24.03        47.05         8.02 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-5420 TCGA-35-4123 
       20.05         2.99        29.98        30.02        15.02         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-44-2659 TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 
        8.68        97.74        44.94        25.02        38.89        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-8117 TCGA-44-A479 TCGA-49-4487 
       61.28        19.46        36.07        12.66        15.98        28.11 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 TCGA-49-AAR0 
       46.72        32.84         8.81        16.04        53.29       156.66 
TCGA-49-AARE TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5936 TCGA-50-5946 
       40.41        70.55        15.72        31.04         8.45        22.55 
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        45.21        42.51 
TCGA-55-6971 TCGA-55-6985 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
        0.82        40.54         3.12         1.32        23.18         1.28 
TCGA-55-7815 TCGA-55-7910 TCGA-55-8203 TCGA-55-8505 TCGA-55-8507 TCGA-55-8514 
        1.78         6.48        17.98         0.95         0.26         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DF 
       17.62         0.49         1.58        21.40        20.58        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8398 TCGA-62-A46U TCGA-62-A472 TCGA-64-1677 
       19.99         4.57        14.60        67.96        29.92        20.65 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-69-7763 TCGA-69-7973 
       42.90        28.41        28.47        20.05        22.68         7.56 
TCGA-69-7979 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4670 
        2.93        25.91        17.16         2.01        23.38         4.31 
TCGA-73-4675 TCGA-78-7159 TCGA-78-7536 TCGA-78-8640 TCGA-86-7713 TCGA-86-7954 
       30.31        64.90         8.02       232.18        38.04        19.89 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 TCGA-86-8669 TCGA-86-A4JF TCGA-91-6829 
        4.08        22.82        21.47        30.84        24.23        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JO TCGA-95-7043 
        1.97        10.19        12.23        27.68         1.08        16.54 
TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VN TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-8025 
       18.67        12.39        18.18        21.44        19.76        34.85 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       21.57        18.08        19.00        18.58        15.65        38.63 
TCGA-MP-A4TD TCGA-MP-A4TJ TCGA-NJ-A4YI TCGA-O1-A52J 
       10.09        11.15         0.13        59.11 

$`4P LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4403 
        3.98        19.96        14.01        45.01         9.96        19.00 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       14.96         9.01        12.00        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 
       25.02        25.02        24.00        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-38-4626 
       22.03         9.04         2.04         0.46         7.40       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       38.10        42.08        42.77         3.19        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       34.06        33.73        26.56        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
       63.72        32.45        16.44        22.72        12.03         7.17 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        29.23        13.74         3.25         8.55 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.32         9.44        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4510 
       76.21        28.57        12.66        35.54        14.07        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       29.75        55.89        55.33        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN 
       22.26        73.12        62.24        28.90         8.55        37.32 
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-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        49.28         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67        21.47        15.12         9.37        29.03        25.12 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
       10.13        36.99         7.59        27.25        34.29        13.94 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       23.05        38.73        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
        0.79        40.73        15.25        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 
        0.13         1.28         1.12         0.79        18.64         0.53 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        1.45         0.76         0.36         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.10         4.80         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B 
       20.71         1.58        19.59         0.92        15.81        17.95 
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-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-64-1679 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-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        2.04        51.25         1.02        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
       13.61         5.42         6.05         4.41        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
       13.45         4.24        52.60        82.68        26.30        15.35 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
        9.24         1.25        39.09        50.33        11.18       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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
       50.24        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        31.13        34.39        20.55        32.78 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
       35.24        37.74         4.57        24.33         0.79        32.65 
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         1.15        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-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6848 
       13.64        26.47        10.62         2.60        13.71         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP 
       19.82        22.45        17.46         6.12        23.61        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
       17.29        41.82         2.86        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       21.60        20.58        20.19        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       18.67        20.68        24.56        36.76         1.45        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
       24.30        23.80        35.47        32.48        14.30         6.35 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N5 
       10.09        14.53         1.91        21.83        27.19         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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        5.49         5.29        41.59        31.23         2.43        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         1.64        29.13         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-S2-AA1A 
       20.28        16.87 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.00              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           232.18            238.29 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           20.385            19.820 
[1] "0.0 - 232.2 (20.4)" "0.1 - 238.3 (19.8)"
[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       39        0        10        14
  4P LOSS WILD-TYPE       3      105      100        1        42        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4P LOSS MUTATED           18          5        5
  4P LOSS WILD-TYPE         54          6       21
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                30               105
  STAGE IB                39               100
  STAGE II                 0                 1
  STAGE IIA               10                42
  STAGE IIB               14                58
  STAGE IIIA              18                54
  STAGE IIIB               5                 6
  STAGE IV                 5                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
  4P LOSS MUTATED    39  68  11   4
  4P LOSS WILD-TYPE 131 210  35  15
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              39               131
  T2              68               210
  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    79  17    22
  4P LOSS WILD-TYPE 253  79    54
D48V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                 79               253
  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    81   5
  4P LOSS WILD-TYPE 268  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     81    5
  4P LOSS WILD-TYPE  268   20
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              81               268
  1               5                20
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    64  59
  4P LOSS WILD-TYPE 211 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     64   59
  4P LOSS WILD-TYPE  211  181
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              64               211
  MALE                59               181
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    84  16
  4P LOSS WILD-TYPE 276  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     84   16
  4P LOSS WILD-TYPE  276   38
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               84               276
  YES              16                38
[1] 2 2
[1] FALSE
D48V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4P LOSS MUTATED                            3
  4P LOSS WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4P LOSS MUTATED                                  26
  4P LOSS WILD-TYPE                                80
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                   81
  4P LOSS WILD-TYPE                                                239
                   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                                               2
  4P LOSS WILD-TYPE                                             3
                   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                               26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              81
  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                    2
  MUCINOUS (COLLOID) CARCINOMA                                     3
                                                    clus
vv                                                   4P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               239
  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                      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"
D48V11, continuous
D48V12, continuous
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    80   3   1   9
  4P LOSS WILD-TYPE 263   9   3  17
D48V13, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              80               263
  R1               3                 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
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          15    88
  4P LOSS WILD-TYPE                        36   301
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                36
  WHITE                                         88               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"
D48V15, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  94
  4P LOSS WILD-TYPE   6 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   94
  4P LOSS WILD-TYPE    6  288
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              94               288
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    90  45
  4Q LOSS WILD-TYPE 235 122
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              135               357 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               45               122 
$`4Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 
       50.07        19.96        37.02         0.00        47.05         8.02 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4434 TCGA-05-5420 
       20.05         2.99        29.98        30.02        15.02        15.02 
TCGA-35-4123 TCGA-35-5375 TCGA-38-6178 TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 
        5.98         8.68        14.73        25.02        38.89        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        28.01        23.77        19.56         9.93        27.78 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-A479 TCGA-49-4487 TCGA-49-4501 
       61.28        19.46        36.07        15.98        28.11        46.72 
TCGA-49-4506 TCGA-49-4507 TCGA-49-6743 TCGA-49-AAR0 TCGA-49-AARE TCGA-50-5049 
       32.84         8.81        53.29       156.66        40.41        70.55 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5936 TCGA-50-5946 TCGA-50-6590 TCGA-50-6595 
       15.72        31.04         8.45        22.55        42.35         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
        0.72        10.13        35.21        23.05        38.73        45.21 
TCGA-55-6968 TCGA-55-6971 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
       42.51         0.82         0.13         3.12         1.32        23.18 
TCGA-55-7726 TCGA-55-7815 TCGA-55-7910 TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 
        1.28         1.78         6.48         5.06         0.13        17.98 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8616 TCGA-55-A48Y 
        0.95         0.26         0.49         6.64         1.58        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8398 
       21.40        20.58        19.59        20.19         4.57        14.60 
TCGA-62-A46O TCGA-62-A46U TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       47.80        67.96        29.92        20.65        81.80        38.37 
TCGA-64-5778 TCGA-64-5779 TCGA-67-3771 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       42.90        28.41        20.05        22.68        13.61         7.56 
TCGA-69-7979 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 
        2.93         4.24        25.91         2.01        23.38        82.68 
TCGA-73-4670 TCGA-73-4675 TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        4.31        30.31        64.90        88.14        31.20         8.02 
TCGA-78-8640 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8075 
      232.18        38.04        19.89        35.24         4.08        22.82 
TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 TCGA-86-A4JF TCGA-91-6829 TCGA-91-6830 
       31.20        30.84         0.62        24.23        41.36         1.97 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JO TCGA-95-7043 TCGA-95-7567 
       10.19        12.23        27.68         1.08        16.54        18.67 
TCGA-95-7944 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7937 TCGA-97-A4M0 TCGA-97-A4M1 
       12.39        18.18        19.89         5.95        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-A4TA TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TJ 
       15.65        38.63        31.23        10.09        11.05        11.15 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-O1-A52J 
       71.05         0.13        59.11 

$`4Q LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 
        3.98        14.01        45.01         9.96        24.03        19.00 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       14.96         9.01        12.00        21.99        26.01        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-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       26.30         4.37        43.53        46.98        44.42        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       38.10        42.08        42.77         3.19        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       34.06        33.73        26.56        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
       63.72        32.45        16.44        22.72        12.03         7.17 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       18.87        29.00        29.23        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.32         9.44        11.08        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-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
       29.46        29.75        55.89        16.04        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       11.64        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        37.32       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       20.52        71.47        60.16        49.28         8.09         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        78.67        21.47        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       29.03        25.12         3.91        25.55        11.05        12.16 
TCGA-50-6597 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       41.69        36.99         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        48.62         2.86         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
        1.28         1.12         0.79        18.64         0.53        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
       19.66        19.73        23.64        15.65         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
        2.17        22.16        15.42         1.45         0.76         0.36 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 
       17.72         0.30         0.10         4.80        17.62         0.49 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A490 TCGA-55-A493 
        1.61         2.17        16.93        22.65         1.58         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
       15.81        19.99        17.95        39.98        42.38        88.64 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y 
       49.25        19.53        56.71        54.35        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
       39.25        40.96        56.81        39.09        37.02        87.98 
TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
        2.04        51.25        28.47         1.02        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       12.66        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        6.12         5.42         6.05         4.41        12.56        14.01 
TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
       13.45        17.16        52.60        26.30        15.35         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        1.25        39.09        50.33        11.18       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-78-7160 
      119.51        19.50        38.50        32.09         5.88        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 
        9.57       104.19       238.29         8.48        26.53        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55        50.24        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        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 
        1.15        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-91-6836 
        3.81        13.64        26.47        10.62         2.60        13.71 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
       19.00        17.29        41.82         2.86        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        21.40        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       43.79        25.48         0.59         0.72        18.67        17.92 
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-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       20.58        20.19        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       20.68        24.56        36.76        21.63        24.30        23.80 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
       35.47        32.48        14.30         6.35        10.09        14.53 
TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
        1.91        21.83        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59         2.43        29.46        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       73.91        62.60         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       19.82        20.28        16.87 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.00              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           232.18            238.29 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            20.05             19.82 
[1] "0.0 - 232.2 (20.1)" "0.1 - 238.3 (19.8)"
[1] "hr=" "1"  
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         2       40       38        0        12        12
  4Q LOSS WILD-TYPE       3       95      101        1        40        60
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4Q LOSS MUTATED           23          5        8
  4Q LOSS WILD-TYPE         49          6       18
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                40                95
  STAGE IB                38               101
  STAGE II                 0                 1
  STAGE IIA               12                40
  STAGE IIB               12                60
  STAGE IIIA              23                49
  STAGE IIIB               5                 6
  STAGE IV                 8                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
  4Q LOSS MUTATED    47  76  11   5
  4Q LOSS WILD-TYPE 123 202  35  14
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              47               123
  T2              76               202
  T3              11                35
  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    93  15    27
  4Q LOSS WILD-TYPE 239  81    49
D49V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                 93               239
  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    93   8
  4Q LOSS WILD-TYPE 256  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     93    8
  4Q LOSS WILD-TYPE  256   17
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              93               256
  1               8                17
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    74  66
  4Q LOSS WILD-TYPE 201 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     74   66
  4Q LOSS WILD-TYPE  201  174
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              74               201
  MALE                66               174
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    95  19
  4Q LOSS WILD-TYPE 265  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     95   19
  4Q LOSS WILD-TYPE  265   35
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               95               265
  YES              19                35
[1] 2 2
[1] FALSE
D49V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4Q LOSS MUTATED                            4
  4Q LOSS WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4Q LOSS MUTATED                                  26
  4Q LOSS WILD-TYPE                                80
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                   95
  4Q LOSS WILD-TYPE                                                225
                   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                              1                             3
  4Q LOSS WILD-TYPE                            1                            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                               26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              95
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  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                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               225
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  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    89   4   2   9
  4Q LOSS WILD-TYPE 254   8   2  17
D49V13, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              89               254
  R1               4                 8
  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   103
  4Q LOSS WILD-TYPE                        35   286
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                35
  WHITE                                        103               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"
D49V15, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2 107
  4Q LOSS WILD-TYPE   5 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2  107
  4Q LOSS WILD-TYPE    5  275
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             107               275
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    36  14
  5P LOSS WILD-TYPE 289 153
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               50               442 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14               153 
$`5P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4420 TCGA-05-4432 TCGA-35-4122 
       50.07        19.96        45.01        29.98        25.02         7.40 
TCGA-35-4123 TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
        5.98        46.98        44.42        42.08        42.77         3.19 
TCGA-44-2668 TCGA-44-3917 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       25.02        38.89        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-49-6742 TCGA-49-AAR2 TCGA-49-AARE TCGA-49-AARO TCGA-50-6590 
       27.78        16.04        73.12        40.41       123.58        42.35 
TCGA-55-1596 TCGA-55-6968 TCGA-55-6975 TCGA-55-7281 TCGA-55-7914 TCGA-55-8203 
       45.21        42.51         3.88         0.59         6.15        17.98 
TCGA-55-8505 TCGA-55-A492 TCGA-55-A57B TCGA-62-8398 TCGA-64-5779 TCGA-67-3771 
        0.95        19.59        17.95        14.60        28.41        20.05 
TCGA-67-3772 TCGA-69-7979 TCGA-69-8255 TCGA-73-A9RS TCGA-78-7160 TCGA-78-7161 
       18.84         2.93         4.24        11.18        22.92         9.57 
TCGA-86-7713 TCGA-86-7955 TCGA-86-8074 TCGA-91-6829 TCGA-95-7043 TCGA-97-8175 
       38.04        35.24         0.79        41.36        16.54        18.12 
TCGA-MN-A4N1 TCGA-MN-A4N4 
       27.19        38.63 

$`5P LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
        3.98        14.01        37.02         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        9.01        12.00        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         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-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 
       44.61        14.73        26.30         4.37        43.53        44.94 
TCGA-44-2661 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       38.10        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       33.30        28.37        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        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-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 
       17.16        11.64        22.26        22.26       156.66        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       28.90         8.55        37.32       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        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.09         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       21.47         8.45        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       22.55         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       34.29        30.54        13.94        35.21        23.05        38.73 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       48.62         2.86         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
       15.25         0.82        48.49         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
       70.26         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
        1.78        18.64         0.53         6.48        17.65        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        0.16        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
        5.06         0.13        23.64        15.65         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
        2.17        22.16        15.42         1.45         0.76         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        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-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
       29.92        56.81        20.65        39.09        81.80        37.02 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98         2.04        42.90        51.25        28.47 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
        1.02        14.04        12.66        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         4.41        12.56        14.01        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       25.91        17.16         2.01        52.60        23.38        82.68 
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-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       39.09        50.33       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-78-7159 TCGA-78-7162 TCGA-78-7163 
       38.50        32.09         5.88        64.90       104.19       238.29 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
       31.13        34.39        20.55        32.78        19.89        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57        24.33        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         1.15        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-91-6828 TCGA-91-6830 
        3.81        24.23        13.64        26.47        10.62         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82        22.45        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29        41.82         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.63        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       19.00        14.30         6.35        10.09        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       21.83        18.58        15.65         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        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 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.59              0.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           123.58            238.29 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           23.345            19.855 
[1] "0.6 - 123.6 (23.3)" "0.0 - 238.3 (19.9)"
[1] "hr=" "1.3"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         0       17       17        0         5         8
  5P LOSS WILD-TYPE       5      118      122        1        47        64
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5P LOSS MUTATED            3          0        2
  5P LOSS WILD-TYPE         69         11       24
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                17               118
  STAGE IB                17               122
  STAGE II                 0                 1
  STAGE IIA                5                47
  STAGE IIB                8                64
  STAGE IIIA               3                69
  STAGE IIIB               0                11
  STAGE IV                 2                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
  5P LOSS MUTATED    21  27   3   1
  5P LOSS WILD-TYPE 149 251  43  18
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              21               149
  T2              27               251
  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    36   9     4
  5P LOSS WILD-TYPE 296  87    72
D50V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                 36               296
  N1                  9                87
  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    40   2
  5P LOSS WILD-TYPE 309  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     40    2
  5P LOSS WILD-TYPE  309   23
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              40               309
  1               2                23
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    21  31
  5P LOSS WILD-TYPE 254 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     21   31
  5P LOSS WILD-TYPE  254  209
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              21               254
  MALE                31               209
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    37   5
  5P LOSS WILD-TYPE 323  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     37    5
  5P LOSS WILD-TYPE  323   49
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               37               323
  YES               5                49
[1] 2 2
[1] FALSE
D50V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5P LOSS MUTATED                            3
  5P LOSS WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5P LOSS MUTATED                                  10
  5P LOSS WILD-TYPE                                96
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                   33
  5P LOSS WILD-TYPE                                                287
                   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                              1                             1
  5P LOSS WILD-TYPE                            1                            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                               10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              33
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  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                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 96
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  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    36   1   0   2
  5P LOSS WILD-TYPE 307  11   4  24
D50V13, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              36               307
  R1               1                11
  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                           8    36
  5P LOSS WILD-TYPE                        43   353
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                      8                43
  WHITE                                         36               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"
D50V15, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     2  40
  5P LOSS WILD-TYPE   5 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   40
  5P LOSS WILD-TYPE    5  342
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              40               342
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   106  41
  5Q LOSS WILD-TYPE 219 126
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              147               345 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               41               126 
$`5Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4396 TCGA-05-4405 TCGA-05-4417 
       50.07        19.96        45.01         9.96        20.05        14.96 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 
       29.98        30.02        26.01        25.02        29.00        22.03 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 TCGA-38-4630 
        2.04         7.40         5.98        97.74        49.05        35.28 
TCGA-38-4631 TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       11.64        46.98        44.42        42.08        42.77         3.19 
TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       25.02        38.89        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 
       19.56         9.93        27.78        61.28        19.46         7.17 
TCGA-44-7667 TCGA-44-7670 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4488 TCGA-49-4505 
       36.07        29.00         8.55        13.64        28.57        14.07 
TCGA-49-6742 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-50-5045 
       16.04        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 
       70.55        31.04        49.28         9.37        22.55        42.35 
TCGA-50-6593 TCGA-50-7109 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       11.05        10.13        34.29        35.21        23.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6969 TCGA-55-6975 TCGA-55-6979 
       45.21         2.86        42.51        40.73         3.88         7.79 
TCGA-55-6985 TCGA-55-7281 TCGA-55-7570 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 
       40.54         0.59         0.20        23.18         1.28         1.12 
TCGA-55-7907 TCGA-55-7914 TCGA-55-8094 TCGA-55-8203 TCGA-55-8302 TCGA-55-8505 
        0.53         6.15         0.13        17.98         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8615 TCGA-55-8616 
        0.36         0.26        17.72         0.30         0.49         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A491 TCGA-55-A492 TCGA-55-A57B TCGA-62-8394 
        2.17        20.71        20.58        19.59        17.95         4.57 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A470 TCGA-62-A471 
       39.98        14.60        88.64        49.25        39.25        40.96 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-67-3771 
       56.81        81.80        38.37        42.90        28.41        20.05 
TCGA-67-3772 TCGA-69-7765 TCGA-69-7979 TCGA-69-8255 TCGA-71-6725 TCGA-73-4668 
       18.84         5.42         2.93         4.24         2.01        15.35 
TCGA-73-A9RS TCGA-78-7149 TCGA-78-7150 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       11.18       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         1.15         0.62        41.36 
TCGA-91-6840 TCGA-91-8499 TCGA-93-8067 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7043 
       12.23         1.18         6.12         1.08        41.82        16.54 
TCGA-95-7567 TCGA-95-7948 TCGA-97-7937 TCGA-97-8175 TCGA-99-8025 TCGA-J2-A4AD 
       18.67        15.65         5.95        18.12        34.85        18.08 
TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4T6 TCGA-MP-A4TC 
       10.09        18.58        27.19        38.63        58.85         2.43 
TCGA-MP-A4TE TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        73.91        71.05 

$`5Q LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
        3.98        14.01        37.02         0.00        24.03        47.05 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 
        8.02        19.00         2.99         9.01        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
        9.04         0.46         8.68       120.79        37.71        28.41 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 
       44.61        14.73        26.30         4.37        43.53        44.94 
TCGA-44-2661 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       38.10        37.15        38.24        34.06        33.73        26.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 
       23.15        21.63        23.18        63.72        32.45        16.44 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       22.72        12.03        18.87        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        76.21        28.11        12.66        35.54        46.72 
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-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       55.33        17.16        11.64        22.26        22.26       156.66 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       62.24         8.55        37.32       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       20.52        15.72        60.16         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       40.60        78.67        21.47         8.45        15.12        29.03 
TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
       25.12         3.91        25.55        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
        0.72        36.99         7.59        27.25        30.54        13.94 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6970 TCGA-55-6971 
       48.62         0.07        32.65         0.79        15.25         0.82 
TCGA-55-6972 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       48.49         5.49         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
       24.99       107.21        70.26         1.15         7.99         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        3.12         1.32         1.28         0.79         1.78        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
        3.29        19.66        19.73         5.06        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        1.08         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8619 
        0.49         0.10         4.80         6.64        17.62         1.61 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       16.93        22.65        21.40         1.58         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       20.19        19.99        42.38        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 
       54.35        67.96        72.30        13.61        29.92        20.65 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
       39.09        37.02        87.98         2.04        51.25        28.47 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
        1.02        14.04        12.66        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       13.87         6.64         6.12        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        6.05         4.41        12.56        14.01        13.45        25.91 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
       17.16        52.60        23.38        82.68        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
       30.31         9.24         1.25        39.09        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 
       27.16         5.69        19.27        20.58        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 
       19.50        38.50        32.09         5.88       104.19       238.29 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
       10.55       110.50        27.09        31.13        34.39        20.55 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8075 TCGA-86-8076 
       19.89        37.74         4.08         4.57        22.82        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 
       31.04        23.05        21.47        14.60        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-91-6831 TCGA-91-6835 
       13.64        26.47        10.62         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       13.71        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.45        19.82        22.45        17.46        23.61 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
       19.00        17.29         2.86        12.39        15.68        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79        25.48         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       17.92         5.39        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        24.56        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
       21.57        21.63        24.30        23.80        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       19.00        14.30         6.35        14.53         1.91        21.83 
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-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD 
       86.04         5.49         5.29        41.59        31.23        10.09 
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        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         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 
             0.13              0.00 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           129.53            238.29 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            21.90             19.82 
[1] "0.1 - 129.5 (21.9)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.4"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         0       40       47        0        15        24
  5Q LOSS WILD-TYPE       5       95       92        1        37        48
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5Q LOSS MUTATED           16          3        7
  5Q LOSS WILD-TYPE         56          8       19
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                40                95
  STAGE IB                47                92
  STAGE II                 0                 1
  STAGE IIA               15                37
  STAGE IIB               24                48
  STAGE IIIA              16                56
  STAGE IIIB               3                 8
  STAGE IV                 7                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
  5Q LOSS MUTATED    50  86  11   5
  5Q LOSS WILD-TYPE 120 192  35  14
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              50               120
  T2              86               192
  T3              11                35
  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    99  31    18
  5Q LOSS WILD-TYPE 233  65    58
D51V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                 99               233
  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"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   103   6
  5Q LOSS WILD-TYPE 246  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    103    6
  5Q LOSS WILD-TYPE  246   19
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0             103               246
  1               6                19
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    69  83
  5Q LOSS WILD-TYPE 206 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     69   83
  5Q LOSS WILD-TYPE  206  157
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              69               206
  MALE                83               157
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   102  17
  5Q LOSS WILD-TYPE 258  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    102   17
  5Q LOSS WILD-TYPE  258   37
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO              102               258
  YES              17                37
[1] 2 2
[1] FALSE
D51V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5Q LOSS MUTATED                            5
  5Q LOSS WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5Q LOSS MUTATED                                  33
  5Q LOSS WILD-TYPE                                73
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                   99
  5Q LOSS WILD-TYPE                                                221
                   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                               33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              99
  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                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               221
  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   102   3   0  10
  5Q LOSS WILD-TYPE 241   9   4  16
D51V13, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0             102               241
  R1               3                 9
  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   111
  5Q LOSS WILD-TYPE                        32   278
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                32
  WHITE                                        111               278
[1] 4 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     5 115
  5Q LOSS WILD-TYPE   2 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5  115
  5Q LOSS WILD-TYPE    2  267
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             115               267
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    59  44
  6P LOSS WILD-TYPE 266 123
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              103               389 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               44               123 
$`6P LOSS MUTATED`
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 TCGA-35-4123 
        3.98        45.01        37.02         0.00         2.99         5.98 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2662 TCGA-44-2666 TCGA-44-2668 
       11.64        44.61        14.73        42.08         3.19        25.02 
TCGA-44-3917 TCGA-44-3918 TCGA-44-5645 TCGA-44-6146 TCGA-44-6775 TCGA-44-6777 
       38.89        34.06        28.01         9.93        23.18        32.45 
TCGA-44-A47F TCGA-49-4486 TCGA-49-4488 TCGA-49-4505 TCGA-49-4512 TCGA-49-6745 
       11.08        76.21        28.57        14.07        29.75        17.16 
TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 TCGA-50-5068 TCGA-50-5932 TCGA-50-5935 
       40.41       123.58        15.72        49.28        40.60        21.47 
TCGA-50-6597 TCGA-53-7626 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6981 
       41.69        30.54        42.51         0.82        48.49        45.34 
TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7576 TCGA-55-7724 TCGA-55-7815 
       60.03        40.54         1.15         1.32        23.18         1.78 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 
        3.29        19.66        19.73         2.17         0.76         0.36 
TCGA-55-8508 TCGA-55-8616 TCGA-55-A494 TCGA-62-8402 TCGA-62-A46R TCGA-62-A46S 
        0.49         1.58        15.81        49.25        56.71        54.35 
TCGA-62-A472 TCGA-64-1676 TCGA-64-5781 TCGA-69-7760 TCGA-69-7974 TCGA-69-8253 
       29.92        56.81        51.25         6.64         6.05        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
       13.45        25.91        17.16         2.01        23.38        26.30 
TCGA-73-4675 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       30.31        11.18         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-86-8359 TCGA-86-8672 TCGA-93-7347 TCGA-93-7348 
       32.78        35.24        14.60         0.62        22.45        17.46 
TCGA-95-7043 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-8174 
       16.54        15.65         2.76        19.89        64.60         5.39 
TCGA-97-8547 TCGA-97-A4M0 TCGA-99-7458 TCGA-J2-8192 TCGA-MN-A4N1 TCGA-MP-A4SY 
       21.60        21.44        24.56        24.30        27.19        49.35 
TCGA-MP-A4T2 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       37.35         2.43        11.05        19.13        73.91        71.05 
TCGA-NJ-A4YI 
        0.13 

$`6P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 
       50.07        19.96        14.01         9.96        24.03        47.05 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 
        8.02        19.00        20.05        14.96         9.01        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
       12.00        30.02        21.99        26.01        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         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-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       26.30         4.37        43.53        46.98        44.42        44.94 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       38.10        42.77        37.15        38.24        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 
       33.30        28.37        23.77        19.56        27.78        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       21.63        63.72        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       13.74        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 
        9.44        11.54        13.64        13.45        28.11        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 
       35.54        46.72        32.84         8.81        29.46        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       16.04        53.29        55.33        11.64        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN 
      156.66        73.12        62.24        28.90         8.55        37.32 
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        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        31.04         8.09         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12         9.37        29.03        25.12        22.55 
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         7.59        27.25        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
       13.94        35.21        23.05        38.73        48.62        45.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
        2.86         0.07        32.65         0.79        40.73        15.25 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 TCGA-55-6984 
        3.88         5.49         7.79         2.20        32.71        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
      107.21        70.26         0.59         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 
        3.12         1.28         1.28         1.12         0.79        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51        22.16        15.42         1.45 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.95         0.26        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64        17.62         0.49         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        20.19        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-A46U 
       42.38        14.60        88.64        47.80        19.53        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 
       72.30        13.61        39.25        40.96        20.65        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-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        28.47         1.02        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 
       12.66        14.73         5.72         4.64        13.87         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         2.93 
TCGA-69-7980 TCGA-69-8255 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
       12.56         4.24        52.60        82.68        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        9.24         1.25        39.09        50.33       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7155 TCGA-78-7156 
       19.27        20.58       129.53        21.90        38.50        32.09 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       88.14        26.53        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
       12.36         5.88        34.39        20.55        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-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
       31.04        31.20        23.05        21.47         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       30.84        27.58        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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       10.19         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       19.82         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
       41.82         2.86        18.67        12.39        15.68        27.29 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       21.40        18.18        31.69        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        5.95         0.59         0.72        18.67        17.92        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 
       15.39        16.41        14.30        20.58        20.19        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 
       20.52        17.75        20.84        18.67        20.68        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        21.63        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.53         1.91        21.83        18.58        15.65        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
        2.76        86.14        58.45        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH 
        5.29        41.59        31.23        10.09        29.46        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       14.10        11.15        62.60         1.64        29.13         0.26 
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 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.00              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           123.58            238.29 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            22.45             19.82 
[1] "0.0 - 123.6 (22.4)" "0.1 - 238.3 (19.8)"
[1] "hr=" "1.3"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         0       19       35        0         9        15
  6P LOSS WILD-TYPE       5      116      104        1        43        57
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6P LOSS MUTATED           20          3        4
  6P LOSS WILD-TYPE         52          8       22
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                19               116
  STAGE IB                35               104
  STAGE II                 0                 1
  STAGE IIA                9                43
  STAGE IIB               15                57
  STAGE IIIA              20                52
  STAGE IIIB               3                 8
  STAGE IV                 4                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
  6P LOSS MUTATED    25  64  13   4
  6P LOSS WILD-TYPE 145 214  33  15
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              25               145
  T2              64               214
  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
  6P LOSS MUTATED    67  16    20
  6P LOSS WILD-TYPE 265  80    56
D52V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                 67               265
  N1                 16                80
  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"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    71   4
  6P LOSS WILD-TYPE 278  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     71    4
  6P LOSS WILD-TYPE  278   21
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              71               278
  1               4                21
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    57  49
  6P LOSS WILD-TYPE 218 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     57   49
  6P LOSS WILD-TYPE  218  191
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              57               218
  MALE                49               191
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    75  10
  6P LOSS WILD-TYPE 285  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     75   10
  6P LOSS WILD-TYPE  285   44
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               75               285
  YES              10                44
[1] 2 2
[1] FALSE
D52V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6P LOSS MUTATED                            3
  6P LOSS WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6P LOSS MUTATED                                  21
  6P LOSS WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                   68
  6P LOSS WILD-TYPE                                                252
                   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                              1                             7
  6P LOSS WILD-TYPE                            1                            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                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              68
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  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)               252
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  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    71   3   1   5
  6P LOSS WILD-TYPE 272   9   3  21
D52V13, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              71               272
  R1               3                 9
  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                          11    83
  6P LOSS WILD-TYPE                        40   306
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                     11                40
  WHITE                                         83               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"
D52V15, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  79
  6P LOSS WILD-TYPE   5 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   79
  6P LOSS WILD-TYPE    5  303
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              79               303
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   131  76
  6Q LOSS WILD-TYPE 194  91
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              207               285 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               76                91 
$`6Q LOSS MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4405 
        3.98        19.96        45.01        37.02         0.00        20.05 
TCGA-05-4415 TCGA-05-4425 TCGA-05-4430 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
        2.99        21.99        25.02        29.00        22.03         9.04 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2659 
        0.46         5.98        11.64        44.61        14.73        44.94 
TCGA-44-2662 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-5644 
       42.08         3.19        25.02        38.89        34.06        28.37 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       28.01         9.93        21.63        23.18        32.45        16.44 
TCGA-44-7659 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SU TCGA-49-4486 
       22.72        12.66         8.55        11.08        13.45        76.21 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       28.57        35.54        14.07         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AAR9 
       55.89        55.33        17.16        11.64       156.66         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-50-5051 TCGA-50-5068 TCGA-50-5932 
       40.41        37.32       123.58        15.72        49.28        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
       78.67        21.47         9.37        29.03        22.55        42.35 
TCGA-50-6594 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1595 TCGA-55-6543 
       12.16        34.29        30.54        13.94        48.62         0.07 
TCGA-55-6642 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6981 TCGA-55-6983 
       32.65        42.51         0.82        48.49        45.34        60.03 
TCGA-55-6985 TCGA-55-7283 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7815 
       40.54         1.15         1.32        23.18         1.28         1.78 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 
       18.64        17.65         6.15        19.82        29.72         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8203 TCGA-55-8207 TCGA-55-8302 
       19.66        19.73         0.13        17.98         2.17         0.76 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8616 TCGA-55-A48X TCGA-55-A48Y 
        0.36         0.49         0.10         1.58        22.65        20.71 
TCGA-55-A494 TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46R TCGA-62-A46S 
       15.81        39.98        14.60        49.25        56.71        54.35 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
       72.30        39.25        29.92        56.81        20.65        39.09 
TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-4679 
       87.98        28.41        51.25        28.47        20.05        14.73 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 
        4.64         6.64         7.56         6.05         4.41        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
       13.45        25.91        17.16         2.01        52.60        23.38 
TCGA-73-4666 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 
       26.30        30.31        39.09        50.33        11.18         5.69 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
      129.53        39.95       119.51        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
       64.90       104.19        31.20         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       10.55        50.24        77.59        27.09        12.36        31.13 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8279 
       38.04        20.55        32.78        35.24        37.74        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       23.05        21.47        14.60         0.62        26.50        29.46 
TCGA-91-6831 TCGA-91-7771 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 
       10.19        16.18        19.82        22.45        17.46        16.54 
TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
       18.67        15.65         2.76        18.18        19.89        64.60 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 
       25.48         5.95         0.59         5.39        15.39        21.60 
TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 
       21.44        20.52        17.75        20.84        20.68        24.56 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
       24.30        23.80        19.00         6.35        10.09        14.53 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
       27.19         2.76        86.14        49.35        37.35        58.85 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
        2.43        29.46        11.05        19.13        73.91        71.05 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
        0.13         1.64        29.13 

$`6Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
       50.07        14.01         9.96        24.03        47.05         8.02 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        26.01        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        4.96         2.04         7.40         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F 
       37.71        49.05        28.41        35.28        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       43.53        46.98        44.42        38.10        42.77        37.15 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 
       38.24        33.73        26.56        33.30        23.77        19.56 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6776 TCGA-44-6778 TCGA-44-7660 TCGA-44-7661 
       27.78        23.15        63.72        61.28        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        3.25        15.98        15.32         9.44        11.54        13.64 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4501 TCGA-49-4506 TCGA-49-6742 TCGA-49-6743 
       28.11        12.66        46.72        32.84        16.04        53.29 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ 
       22.26        22.26        73.12        62.24        28.90       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        70.55        60.16 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 
       31.04         8.09         9.27        14.27         8.45        15.12 
TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 
       25.12         3.91        25.55        11.05         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-A4EZ 
        0.72        10.13        36.99         7.59        27.25        35.21 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6712 TCGA-55-6969 
       23.05        38.73        45.21         2.86         0.79        40.73 
TCGA-55-6970 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 
       15.25         3.88         5.49         7.79         2.20        32.71 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
       24.99       107.21        70.26         0.59         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 
        0.13         3.12         1.28         1.12         0.79         0.53 
TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
        6.48         0.16        15.19         5.06        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
        1.08         1.51        22.16        15.42         1.45         0.95 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.26        17.72         0.30         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Z TCGA-55-A490 
        0.49         1.61         2.17        16.93        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B 
       20.58        19.59         0.92        20.19        19.99        17.95 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U 
        4.57        42.38        88.64        47.80        19.53        67.96 
TCGA-62-A46Y TCGA-62-A471 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
       13.61        40.96        81.80        37.02        38.37         2.04 
TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
       42.90         1.02        18.84        14.04        12.66         5.72 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 
       13.87         6.12        22.68        13.61         5.42         2.93 
TCGA-69-7980 TCGA-69-8255 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
       12.56         4.24        82.68        15.35         4.31         9.24 
TCGA-73-4677 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
        1.25       163.10        27.16        19.27        20.58        21.90 
TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       38.50        22.92         9.57       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7539 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
       26.53        26.01       232.18        39.75        10.55       110.50 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        5.88        34.39        19.89         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 TCGA-86-8668 
        0.79        22.82        32.65        31.04         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       30.84        27.58        28.34         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62        41.36         1.97         2.60        13.71 
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-A4BC TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        1.18         1.45         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
       17.29        41.82         2.86        12.39        15.68        27.29 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
       21.40        31.69        63.52        43.79         0.72        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX 
       17.92        18.12        16.41        14.30        20.58        20.19 
TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       19.76        18.67        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP 
       21.63        18.08        35.47        32.48        14.30         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T4 
       21.83        18.58        15.65        38.63        58.45        86.04 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TH 
        5.49         5.29        41.59        31.23        10.09        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       14.10        11.15        62.60         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.00              0.13 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           156.66            238.29 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            21.60             18.84 
[1] "0.0 - 156.7 (21.6)" "0.1 - 238.3 (18.8)"
[1] "hr=" "1"  
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         1       50       60        0        23        29
  6Q LOSS WILD-TYPE       4       85       79        1        29        43
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6Q LOSS MUTATED           35          6       10
  6Q LOSS WILD-TYPE         37          5       16
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                50                85
  STAGE IB                60                79
  STAGE II                 0                 1
  STAGE IIA               23                29
  STAGE IIB               29                43
  STAGE IIIA              35                37
  STAGE IIIB               6                 5
  STAGE IV                10                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
  6Q LOSS MUTATED    68 116  24   8
  6Q LOSS WILD-TYPE 102 162  22  11
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              68               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    35
  6Q LOSS WILD-TYPE 195  57    41
D53V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                137               195
  N1                 39                57
  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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   146  10
  6Q LOSS WILD-TYPE 203  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    146   10
  6Q LOSS WILD-TYPE  203   15
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             146               203
  1              10                15
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   112 104
  6Q LOSS WILD-TYPE 163 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    112  104
  6Q LOSS WILD-TYPE  163  136
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE             112               163
  MALE               104               136
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   155  21
  6Q LOSS WILD-TYPE 205  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    155   21
  6Q LOSS WILD-TYPE  205   33
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO              155               205
  YES              21                33
[1] 2 2
[1] FALSE
D53V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6Q LOSS MUTATED                            7
  6Q LOSS WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6Q LOSS MUTATED                                  51
  6Q LOSS WILD-TYPE                                55
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                  128
  6Q LOSS WILD-TYPE                                                192
                   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                              1                            13
  6Q LOSS WILD-TYPE                            1                            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                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             128
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    7
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  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                                 55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               192
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     12
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  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   151   4   1   9
  6Q LOSS WILD-TYPE 192   8   3  17
D53V13, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0             151               192
  R1               4                 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
  6Q LOSS MUTATED                                  0     3
  6Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          20   167
  6Q LOSS WILD-TYPE                        31   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                31
  WHITE                                        167               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     3 159
  6Q LOSS WILD-TYPE   4 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  159
  6Q LOSS WILD-TYPE    4  223
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             159               223
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    28  10
  7P LOSS WILD-TYPE 297 157
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               38               454 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               10               157 
$`7P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4427 TCGA-38-4630 TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 
       50.07        26.01        35.28        46.98        42.08        42.77 
TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 
       25.02        38.89        33.30        28.01        19.56        27.78 
TCGA-44-7670 TCGA-44-8119 TCGA-44-A47B TCGA-49-6742 TCGA-49-AAR9 TCGA-50-5931 
       29.00         3.25         9.44        16.04         8.55        14.27 
TCGA-53-7813 TCGA-55-1594 TCGA-55-8507 TCGA-62-A471 TCGA-67-3774 TCGA-69-7763 
       13.94        38.73         0.26        40.96        12.66        22.68 
TCGA-73-4659 TCGA-78-7167 TCGA-78-7220 TCGA-86-8278 TCGA-86-A4D0 TCGA-91-6828 
       23.38        88.14        26.53        31.04         3.81        10.62 
TCGA-91-6840 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 TCGA-95-A4VP TCGA-97-8174 
       12.23        16.18         1.18         6.12        19.89         5.39 
TCGA-97-A4M1 TCGA-97-A4M5 
       19.76        20.84 

$`7P LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        9.96        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         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-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
       26.30         4.37        43.53        44.42        44.94        38.10 
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-44-5644 TCGA-44-6144 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.37        23.77         9.93        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 
       12.03         7.17        36.07        18.87        29.23        13.74 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G 
       12.66         8.55        15.98        15.32        11.08        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-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       22.26        22.26       156.66        73.12        62.24        28.90 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       40.41        37.32       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        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.09         9.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12         9.37        29.03        25.12        22.55 
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-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       41.69         0.72        10.13        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 
       34.29        30.54        35.21        23.05        48.62        45.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        1.12         0.79         1.78        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65         6.15        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       15.81        20.19        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-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-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
       29.92        56.81        20.65        39.09        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-67-4679 
       28.47         1.02        20.05        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
        5.72         4.64        13.87         6.64         6.12        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         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 
       14.01        13.45         4.24        25.91        17.16         2.01 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
        9.24         1.25        39.09        50.33        11.18       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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       50.24       232.18        39.75        77.59        10.55       110.50 
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-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
        4.57        24.33         0.79        22.82        32.65        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         1.15        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-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       13.71        27.68         7.36         1.15        16.60        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
       19.00        17.29        41.82        16.54         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       18.18        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        5.95         0.59         0.72        18.67        17.92        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       21.44        20.52        17.75        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       34.85        36.76         1.45        21.57        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
        6.35        10.09        14.53         1.91        21.83        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       15.65        27.19        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-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        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 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.26              0.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            88.14            238.29 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           21.760            19.925 
[1] "0.3 - 88.1 (21.8)"  "0.0 - 238.3 (19.9)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0       10       11        0         4         7
  7P LOSS WILD-TYPE       5      125      128        1        48        65
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7P LOSS MUTATED            5          1        1
  7P LOSS WILD-TYPE         67         10       25
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                10               125
  STAGE IB                11               128
  STAGE II                 0                 1
  STAGE IIA                4                48
  STAGE IIB                7                65
  STAGE IIIA               5                67
  STAGE IIIB               1                10
  STAGE IV                 1                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
  7P LOSS MUTATED    11  24   3   1
  7P LOSS WILD-TYPE 159 254  43  18
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1              11               159
  T2              24               254
  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
  7P LOSS MUTATED    26   6     5
  7P LOSS WILD-TYPE 306  90    71
D54V5, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0                 26               306
  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"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    32   1
  7P LOSS WILD-TYPE 317  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     32    1
  7P LOSS WILD-TYPE  317   24
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              32               317
  1               1                24
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    17  22
  7P LOSS WILD-TYPE 258 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     17   22
  7P LOSS WILD-TYPE  258  218
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE              17               258
  MALE                22               218
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    33   3
  7P LOSS WILD-TYPE 327  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     33    3
  7P LOSS WILD-TYPE  327   51
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               33               327
  YES               3                51
[1] 2 2
[1] FALSE
D54V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7P LOSS MUTATED                            1
  7P LOSS WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7P LOSS MUTATED                                   5
  7P LOSS WILD-TYPE                               101
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                   28
  7P LOSS WILD-TYPE                                                292
                   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)              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                                    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                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               292
  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    21   1   0   2
  7P LOSS WILD-TYPE 322  11   4  24
D54V13, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              21               322
  R1               1                11
  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                           3    32
  7P LOSS WILD-TYPE                        48   357
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                      3                48
  WHITE                                         32               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"
D54V15, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  32
  7P LOSS WILD-TYPE   6 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   32
  7P LOSS WILD-TYPE    6  350
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              32               350
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    34  10
  7Q LOSS WILD-TYPE 291 157
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               44               448 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10               157 
$`7Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4417 TCGA-05-4427 TCGA-38-4630 TCGA-44-2656 
       50.07        45.01        14.96        26.01        35.28        46.98 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3917 TCGA-44-5645 TCGA-44-6147 
       42.08        42.77        25.02        38.89        28.01        27.78 
TCGA-44-7670 TCGA-44-8119 TCGA-44-A47B TCGA-49-6742 TCGA-49-AAR9 TCGA-50-5931 
       29.00         3.25         9.44        16.04         8.55        14.27 
TCGA-50-6673 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 TCGA-55-6982 TCGA-55-7727 
        0.72        13.94        38.73        48.62        32.71         1.12 
TCGA-55-8096 TCGA-55-A491 TCGA-55-A4DG TCGA-62-8402 TCGA-67-3770 TCGA-67-3771 
       23.64        20.58        19.99        49.25         1.02        20.05 
TCGA-67-3774 TCGA-86-8278 TCGA-91-6828 TCGA-91-6840 TCGA-91-7771 TCGA-93-8067 
       12.66        31.04        10.62        12.23        16.18         6.12 
TCGA-95-A4VP TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       19.89         5.39        16.41        19.76        20.84        18.67 
TCGA-97-A4M7 TCGA-99-8032 
       20.68         1.45 

$`7Q LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
        3.98        19.96        14.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         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-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-3396 
       43.53        44.42        44.94        38.10         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-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       23.77        19.56         9.93        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 
       12.03         7.17        36.07        18.87        29.23        13.74 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G 
       12.66         8.55        15.98        15.32        11.08        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-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        53.29        55.33        17.16        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       22.26        22.26       156.66        73.12        62.24        28.90 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       40.41        37.32       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        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.09         9.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12         9.37        29.03        25.12        22.55 
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-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       41.69        10.13        36.99         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
       30.54        35.21        23.05        45.21         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       23.18         1.28         1.28         0.79         1.78        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        0.53         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        0.13        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 
       16.93        22.65        20.71        21.40         1.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        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-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-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
       29.92        56.81        20.65        39.09        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-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        18.84        14.04        14.73         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
       13.45         4.24        25.91        17.16         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       23.38        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
        9.24         1.25        39.09        50.33        11.18       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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         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-86-8075 
       37.74         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       32.65        31.20        23.05        21.47        14.60         1.15 
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-91-6829 
       29.46         3.81        24.23        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        13.71        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       22.45        17.46        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       41.82        16.54         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 
       15.65        27.29         2.76        21.40        18.18        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
        0.72        18.67        17.92        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.58        20.19        21.44        20.52        17.75 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       24.56        34.85        36.76        21.57        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
        6.35        10.09        14.53         1.91        21.83        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       15.65        27.19        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-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        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 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.72              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            50.07            238.29 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           20.020            19.925 
[1] "0.7 - 50.1 (20.0)"  "0.0 - 238.3 (19.9)"
[1] "hr=" "1.3"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         1       15       15        0         3         7
  7Q LOSS WILD-TYPE       4      120      124        1        49        65
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7Q LOSS MUTATED            5          1        0
  7Q LOSS WILD-TYPE         67         10       26
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                15               120
  STAGE IB                15               124
  STAGE II                 0                 1
  STAGE IIA                3                49
  STAGE IIB                7                65
  STAGE IIIA               5                67
  STAGE IIIB               1                10
  STAGE IV                 0                26
[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    18  25   3   1
  7Q LOSS WILD-TYPE 152 253  43  18
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              18               152
  T2              25               253
  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
  7Q LOSS MUTATED    34   6     5
  7Q LOSS WILD-TYPE 298  90    71
D55V5, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0                 34               298
  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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    39   0
  7Q LOSS WILD-TYPE 310  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     39    0
  7Q LOSS WILD-TYPE  310   25
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              39               310
  1               0                25
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    26  21
  7Q LOSS WILD-TYPE 249 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     26   21
  7Q LOSS WILD-TYPE  249  219
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              26               249
  MALE                21               219
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    39   2
  7Q LOSS WILD-TYPE 321  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     39    2
  7Q LOSS WILD-TYPE  321   52
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               39               321
  YES               2                52
[1] 2 2
[1] FALSE
D55V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7Q LOSS MUTATED                            1
  7Q LOSS WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7Q LOSS MUTATED                                   9
  7Q LOSS WILD-TYPE                                97
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                   32
  7Q LOSS WILD-TYPE                                                288
                   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                                9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              32
  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                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               288
  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    28   1   0   2
  7Q LOSS WILD-TYPE 315  11   4  24
D55V13, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              28               315
  R1               1                11
  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    35
  7Q LOSS WILD-TYPE                        48   354
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                48
  WHITE                                         35               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"
D55V15, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  36
  7Q LOSS WILD-TYPE   6 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   36
  7Q LOSS WILD-TYPE    6  346
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              36               346
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   127  66
  8P LOSS WILD-TYPE 198 101
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              193               299 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               66               101 
$`8P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 
       50.07        45.01        37.02         0.00        47.05         8.02 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4427 TCGA-05-4433 TCGA-05-5425 
       29.98        12.00        21.99        26.01        24.00        29.00 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4628 TCGA-38-4631 TCGA-44-2656 TCGA-44-2657 
        7.40         5.98        49.05        11.64        46.98        44.42 
TCGA-44-2662 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 
       42.08        25.02        38.89        34.06        33.73        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6774 
       28.37        28.01        23.77        19.56         9.93        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 TCGA-44-7662 TCGA-44-7670 TCGA-44-8117 
       23.18        32.45        19.46         7.17        29.00        12.66 
TCGA-44-A479 TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 
       15.98        13.45        28.11        28.57        12.66        46.72 
TCGA-49-4505 TCGA-49-4510 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 
       14.07        29.46        53.29        55.33        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR4 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-50-5049 
       22.26        28.90        37.32       123.58       221.33        70.55 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5939 TCGA-50-5941 
       31.04        49.28        14.27        40.60        15.12         9.37 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-53-7624 
        3.91        11.05        12.16        41.69         0.72        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6979 
       30.54        35.21        38.73        48.62         2.86         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-7283 TCGA-55-7570 
        2.20        45.34        32.71        40.54         1.15         0.20 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 
        0.13         1.32         1.28         1.12        18.64         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 
       19.82         0.16         5.06        15.65         1.08         2.17 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8616 TCGA-55-A491 TCGA-55-A493 
        0.76         0.36        17.72         1.58        20.58         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-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
       67.96        56.81        39.09        81.80        38.37         2.04 
TCGA-64-5778 TCGA-64-5815 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7978 
       42.90        28.47        18.84        13.87         6.64         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4662 
        2.93        12.56         4.24        25.91        17.16        82.68 
TCGA-73-4668 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7150 TCGA-78-7152 
       15.35        39.09        50.33        11.18        21.90        39.95 
TCGA-78-7155 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-86-6851 
       38.50         8.02        10.55       232.18        10.55         5.88 
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-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-A456 TCGA-86-A4D0 
       22.82        31.20        14.60        13.91        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6836 TCGA-91-6847 TCGA-91-8499 TCGA-91-A4BD 
       24.23        13.64        13.71        27.68         1.18        19.82 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
        6.12        17.29        41.82        16.54         2.86        12.39 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 
       15.68        27.29         2.76        21.40        18.18        31.69 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M3 
       25.48         5.95         0.59        21.60        21.44        17.75 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
       20.68        24.56         1.45        24.30        23.80        35.47 
TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       19.00        14.53         1.91        18.58        15.65        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
        2.76        86.14        58.45        86.04         5.49        41.59 
TCGA-MP-A4TC TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ 
        2.43        11.15        19.13        71.05         0.13        29.13 
TCGA-O1-A52J 
       59.11 

$`8P LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 
        3.98        19.96        14.01         9.96        24.03        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4424 TCGA-05-4426 
       20.05         2.99        14.96         9.01        30.02        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 
       25.02        25.02        15.02        15.02         4.96        22.03 
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-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       37.71        28.41        35.28        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
        4.37        43.53        44.94        38.10        42.77         3.19 
TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-6147 TCGA-44-6148 TCGA-44-6776 
       37.15        38.24        26.56        27.78        23.15        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 
       61.28        16.44        22.72        12.03        36.07        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B 
       29.23        13.74         3.25         8.55        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 
       11.08        11.54        13.64        76.21        35.54        32.84 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 
        8.81        29.75        55.89        16.04        17.16       156.66 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARR TCGA-4B-A93V 
       73.12        62.24         8.55        40.41       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 
       20.52        71.47        15.72        60.16         8.09         9.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
       78.67        21.47         8.45        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       42.35        25.55         6.21        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
       27.25        13.94        23.05        45.21         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
        3.88         5.49        60.03        24.99       107.21        70.26 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 
        0.59         7.99         3.12        23.18         1.28         0.79 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 
        1.78         0.53         6.48        17.65        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 
        3.29        19.66        19.73         0.13        23.64        17.98 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 
        1.51        22.16        15.42         1.45         0.95         0.26 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.49         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8397 
       21.40         1.58        19.59        15.81        20.19        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V 
       14.60        88.64        19.53        56.71        54.35        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 
       13.61        39.25        40.96        29.92        20.65        37.02 
TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 
       87.98        28.41        51.25         1.02        20.05        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
       12.66        14.73         5.72         4.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 
       13.61         5.42         7.56         6.05        14.01        13.45 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
        2.01        52.60        23.38        26.30         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        9.24         1.25       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       20.58       129.53       119.51        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53        31.20        53.33        26.01        39.35 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       50.24        39.75        77.59       110.50        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 
       31.13        34.39        20.55        35.24         4.57        24.33 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 
       32.65        31.04        23.05        21.47         1.15        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P8 TCGA-91-6828 
       27.58         0.62        28.34        26.50        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 
       41.36         1.97        10.19         2.60        12.23         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-93-7347 
        1.15        16.18        16.60        14.27         1.45        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7948 
       17.46        23.61         1.08        19.00        18.67        15.65 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
       19.89        64.60        63.52        43.79         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 
       20.58        20.19        19.76        20.52        20.84        18.67 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG 
       34.85        36.76        21.57        21.63        18.08        32.48 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4SY 
       14.30         6.35        10.09        21.83        27.19        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE 
       37.35        58.85         5.29        31.23        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP 
       11.05        24.36        14.10        73.91        62.60         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.26         0.43        19.82        20.28        16.87 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.00              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           232.18            238.29 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            20.58             19.89 
[1] "0.0 - 232.2 (20.6)" "0.1 - 238.3 (19.9)"
[1] "hr=" "1"  
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         4       52       53        1        22        33
  8P LOSS WILD-TYPE       1       83       86        0        30        39
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8P LOSS MUTATED           27          3        7
  8P LOSS WILD-TYPE         45          8       19
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                52                83
  STAGE IB                53                86
  STAGE II                 1                 0
  STAGE IIA               22                30
  STAGE IIB               33                39
  STAGE IIIA              27                45
  STAGE IIIB               3                 8
  STAGE IV                 7                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 LOSS MUTATED    71 108  18   5
  8P LOSS WILD-TYPE  99 170  28  14
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              71                99
  T2             108               170
  T3              18                28
  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
  8P LOSS MUTATED   128  40    30
  8P LOSS WILD-TYPE 204  56    46
D56V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                128               204
  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   134   7
  8P LOSS WILD-TYPE 215  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    134    7
  8P LOSS WILD-TYPE  215   18
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             134               215
  1               7                18
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   120  82
  8P LOSS WILD-TYPE 155 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    120   82
  8P LOSS WILD-TYPE  155  158
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE             120               155
  MALE                82               158
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   140  22
  8P LOSS WILD-TYPE 220  32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    140   22
  8P LOSS WILD-TYPE  220   32
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              140               220
  YES              22                32
[1] 2 2
[1] FALSE
D56V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8P LOSS MUTATED                            8
  8P LOSS WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8P LOSS MUTATED                                  38
  8P LOSS WILD-TYPE                                68
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                  133
  8P LOSS WILD-TYPE                                                187
                   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                              1                             4
  8P LOSS WILD-TYPE                            1                            19
                   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                                       8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             133
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    7
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  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                                 68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               187
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     12
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     19
  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   135   2   1  14
  8P LOSS WILD-TYPE 208  10   3  12
D56V13, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             135               208
  R1               2                10
  R2               1                 3
  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
  8P LOSS MUTATED                                  1     3
  8P LOSS WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          22   148
  8P LOSS WILD-TYPE                        29   241
D56V14, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 4
  BLACK OR AFRICAN AMERICAN                     22                29
  WHITE                                        148               241
[1] 4 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     5 150
  8P LOSS WILD-TYPE   2 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  150
  8P LOSS WILD-TYPE    2  232
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             150               232
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    39  18
  8Q LOSS WILD-TYPE 286 149
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               57               435 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               18               149 
$`8Q LOSS MUTATED`
TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-44-2657 TCGA-44-2662 
        2.99        29.98        12.00        21.99        44.42        42.08 
TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
       25.02        38.89        34.06        28.01        19.56         9.93 
TCGA-44-6775 TCGA-44-7660 TCGA-49-4487 TCGA-49-4490 TCGA-49-6743 TCGA-49-6744 
       23.18        19.46        28.11        12.66        53.29        55.33 
TCGA-49-AAR4 TCGA-50-5049 TCGA-50-5068 TCGA-50-6594 TCGA-50-6597 TCGA-53-7626 
       28.90        70.55        49.28        12.16        41.69        30.54 
TCGA-55-7573 TCGA-55-7727 TCGA-55-7903 TCGA-55-8506 TCGA-55-A4DG TCGA-55-A57B 
        0.13         1.12        18.64         0.36        19.99        17.95 
TCGA-62-8394 TCGA-64-1676 TCGA-64-1679 TCGA-67-6217 TCGA-69-7980 TCGA-69-8453 
        4.57        56.81        81.80        13.87        12.56        25.91 
TCGA-73-4662 TCGA-73-4668 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7150 TCGA-78-8640 
       82.68        15.35        39.09        11.18        21.90       232.18 
TCGA-86-6851 TCGA-86-8055 TCGA-86-8074 TCGA-86-8279 TCGA-86-A4JF TCGA-95-7039 
        5.88         4.08         0.79        31.20        24.23        41.82 
TCGA-95-7944 TCGA-95-8494 TCGA-97-7546 TCGA-97-7554 TCGA-97-A4M7 TCGA-MP-A4T7 
       12.39         2.76        31.69        25.48        20.68         5.49 
TCGA-MP-A4TK TCGA-NJ-A4YI TCGA-O1-A52J 
       19.13         0.13        59.11 

$`8Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 
       20.05        14.96         9.01        30.02        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
        4.37        43.53        46.98        44.94        38.10        42.77 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        3.19        37.15        38.24        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
       28.37        23.77        27.78        23.15        21.63        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
       32.45        61.28        16.44        22.72        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       36.07        18.87        29.00        29.23        13.74        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
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-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       55.89        16.04        17.16        11.64        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
      156.66        73.12        62.24         8.55        40.41        37.32 
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        31.04         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        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         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       27.25        34.29        13.94        35.21        23.05        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       48.62        45.21         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
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         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.28         0.79         1.78         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       20.19        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-64-1677 TCGA-64-1678 
       13.61        39.25        40.96        29.92        20.65        39.09 
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         1.02        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-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        2.93        14.01        13.45         4.24        17.16         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       52.60        23.38        26.30         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1.25        50.33       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       20.58       129.53        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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        26.01        39.35        10.55        50.24        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       77.59        10.55       110.50        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        38.04        20.55        32.78        19.89        35.24 
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-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60         1.15        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-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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        2.60        13.71        12.23        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
       17.29        16.54         2.86        18.67        15.68        15.65 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       27.29        21.40        18.18        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       43.79         5.95         0.59         0.72        18.67        17.92 
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-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       21.57        21.63        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
       32.48        19.00        14.30         6.35        10.09        14.53 
TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
        1.91        21.83        18.58        15.65        27.19        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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.29        41.59        31.23         2.43        10.09 
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-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        62.60         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       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 
            21.99             19.82 
[1] "0.1 - 232.2 (22.0)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.2"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         1       16       11        0        10        10
  8Q LOSS WILD-TYPE       4      119      128        1        42        62
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8Q LOSS MUTATED            8          2        2
  8Q LOSS WILD-TYPE         64          9       24
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                16               119
  STAGE IB                11               128
  STAGE II                 0                 1
  STAGE IIA               10                42
  STAGE IIB               10                62
  STAGE IIIA               8                64
  STAGE IIIB               2                 9
  STAGE IV                 2                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
  8Q LOSS MUTATED    23  27   8   2
  8Q LOSS WILD-TYPE 147 251  38  17
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              23               147
  T2              27               251
  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
  8Q LOSS MUTATED    34  14    10
  8Q LOSS WILD-TYPE 298  82    66
D57V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0                 34               298
  N1                 14                82
  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"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    41   2
  8Q LOSS WILD-TYPE 308  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     41    2
  8Q LOSS WILD-TYPE  308   23
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              41               308
  1               2                23
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    35  25
  8Q LOSS WILD-TYPE 240 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     35   25
  8Q LOSS WILD-TYPE  240  215
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              35               240
  MALE                25               215
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    45   6
  8Q LOSS WILD-TYPE 315  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     45    6
  8Q LOSS WILD-TYPE  315   48
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               45               315
  YES               6                48
[1] 2 2
[1] FALSE
D57V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8Q LOSS MUTATED                            1
  8Q LOSS WILD-TYPE                         18
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8Q LOSS MUTATED                                   9
  8Q LOSS WILD-TYPE                                97
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                   41
  8Q LOSS WILD-TYPE                                                279
                   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                              1                             2
  8Q LOSS WILD-TYPE                            1                            21
                   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                                9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              41
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   8Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     21
  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    41   1   0   1
  8Q LOSS WILD-TYPE 302  11   4  25
D57V13, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              41               302
  R1               1                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
  8Q LOSS MUTATED                                  1     0
  8Q LOSS WILD-TYPE                                0     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           5    44
  8Q LOSS WILD-TYPE                        46   345
D57V14, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      5                46
  WHITE                                         44               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"
D57V15, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  45
  8Q LOSS WILD-TYPE   6 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   45
  8Q LOSS WILD-TYPE    6  337
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              45               337
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   164  95
  9P LOSS WILD-TYPE 161  72
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              259               233 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               95                72 
$`9P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        45.01         0.00         9.96 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 
        8.02        20.05         2.99         9.01        29.98        30.02 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
       24.00        15.02         4.96        29.00         9.04         2.04 
TCGA-35-4122 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        7.40        37.71        49.05        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
       14.73         4.37        44.42        44.94        38.10        42.08 
TCGA-44-2665 TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       42.77        25.02        38.89        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6146 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.77         9.93        23.18        32.45        61.28        16.44 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       19.46         7.17        36.07        18.87        29.00        29.23 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 
       12.66         8.55        13.64        13.45        28.11        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 
       35.54        46.72        14.07        32.84        29.46        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       16.04        53.29        22.26        22.26       156.66        73.12 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 
       62.24         8.55       123.58        60.16        49.28         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5939 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       15.12        25.12        22.55        25.55        11.05        12.16 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
        0.72        10.13         7.59        27.25        30.54        13.94 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
       23.05        38.73        45.21         2.86        32.65         0.79 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 
        0.82         3.88         2.20        45.34        32.71        40.54 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
      107.21         0.59         1.15         0.20         0.13         1.32 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 
       23.18         1.28         0.53         6.15        19.82         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         5.06         0.13        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 
        1.51         2.17         0.95         0.26        17.72         0.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-A48X TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
       17.62         0.49        22.65         1.58        19.59         0.92 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99        17.95        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       49.25        47.80        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-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 
       28.47         1.02        20.05        18.84        12.66         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7974 
       13.87         6.64         6.12        22.68        13.61         6.05 
TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
       12.56         4.24        25.91        82.68        15.35         4.31 
TCGA-73-4675 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       30.31        11.18       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 
       20.58       129.53        21.90        32.09        22.92         9.57 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.48        88.14        26.53        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 
      232.18        77.59        10.55        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         1.15        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-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP 
       18.67        15.65        27.29         2.76        21.40        19.89 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.95         5.39        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8032 
       20.58        21.44        19.76        18.67        20.68         1.45 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A7SV TCGA-L9-A8F4 
       21.57        24.30        18.08        32.48        18.58        15.65 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD 
       58.85         5.49         5.29        41.59        31.23        10.09 
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        29.13        20.28 
TCGA-O1-A52J 
       59.11 

$`9P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 
       19.96        37.02        24.03        47.05        19.00        14.96 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       12.00        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4434 TCGA-05-5428 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
       15.02        22.03         0.46         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2656 TCGA-44-2666 
      120.79        28.41        26.30        43.53        46.98         3.19 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-6145 
       37.15        38.24        34.06        33.73        26.56        19.56 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-7659 TCGA-44-7661 
       27.78        23.15        21.63        63.72        22.72        12.03 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       13.74         3.25        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-49-4486 TCGA-49-4488 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 
       11.54        76.21        28.57         8.81        29.75        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ 
       17.16        11.64        28.90        40.41        37.32       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        70.55        15.72 
TCGA-50-5066 TCGA-50-5941 TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 TCGA-50-6595 
       31.04         9.37        29.03        42.35         3.91         6.21 
TCGA-50-6597 TCGA-50-8457 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 
       41.69        36.99        34.29        35.21        48.62         0.07 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 
       42.51        40.73        15.25        48.49         5.49         7.79 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 
       60.03        24.99        70.26         7.99         3.12         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        1.12         0.79         1.78        18.64         6.48        17.65 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 
        0.16        29.72        15.19        23.64         1.08        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 
       15.42         1.45         0.76         0.36         0.49         0.30 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        4.80         6.64         1.58         1.61         2.17        16.93 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 
       20.71        21.40        20.58        15.81        20.19         4.57 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-64-1677 TCGA-64-5774 
       19.53        56.71        54.35        67.96        20.65        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-4679 
        2.04        42.90        28.41        51.25        14.04        14.73 
TCGA-67-6215 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
        5.72         5.42         7.56         4.41         2.93        14.01 
TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
       13.45        17.16         2.01        52.60        23.38        26.30 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7152 TCGA-78-7153 
        9.24         1.25        39.09        50.33        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 
       19.50        38.50         5.88        64.90       104.19       238.29 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-8648 TCGA-78-8662 
       31.20         8.02        53.33        26.01        39.75       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 
       27.09        12.36         5.88        31.13        20.55        32.78 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 
       24.33        32.65        31.04        14.60        30.84        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6836 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
       10.62        13.71        16.18        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       19.82        22.45         6.12         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VN 
       41.82        16.54         2.86        12.39        15.68        18.18 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       31.69        64.60        63.52        43.79        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-A4LX TCGA-97-A4M2 
        0.72        18.67        17.92        18.12        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R 
       17.75        20.84        24.56        34.85        36.76        21.63 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       23.80        35.47        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC 
       14.53         1.91        21.83        37.35        86.04         2.43 
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        62.60 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        1.64         0.26         0.43        19.82        16.87 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.00              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           232.18            238.29 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            19.89             20.19 
[1] "0.0 - 232.2 (19.9)" "0.1 - 238.3 (20.2)"
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         3       62       69        1        29        43
  9P LOSS WILD-TYPE       2       73       70        0        23        29
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9P LOSS MUTATED           43          6       14
  9P LOSS WILD-TYPE         29          5       12
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                62                73
  STAGE IB                69                70
  STAGE II                 1                 0
  STAGE IIA               29                23
  STAGE IIB               43                29
  STAGE IIIA              43                29
  STAGE IIIB               6                 5
  STAGE IV                14                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
  9P LOSS MUTATED    83 149  26  11
  9P LOSS WILD-TYPE  87 129  20   8
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              83                87
  T2             149               129
  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  60    44
  9P LOSS WILD-TYPE 171  36    32
D58V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                161               171
  N1                 60                36
  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"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   186  14
  9P LOSS WILD-TYPE 163  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    186   14
  9P LOSS WILD-TYPE  163   11
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             186               163
  1              14                11
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   134 136
  9P LOSS WILD-TYPE 141 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    134  136
  9P LOSS WILD-TYPE  141  104
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE             134               141
  MALE               136               104
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   182  33
  9P LOSS WILD-TYPE 178  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    182   33
  9P LOSS WILD-TYPE  178   21
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              182               178
  YES              33                21
[1] 2 2
[1] FALSE
D58V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9P LOSS MUTATED                           12
  9P LOSS WILD-TYPE                          7
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9P LOSS MUTATED                                  54
  9P LOSS WILD-TYPE                                52
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                  171
  9P LOSS WILD-TYPE                                                149
                   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                             9
  9P LOSS WILD-TYPE                            1                            14
                   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                                      12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             171
  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                                    9
  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                                 52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               149
  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                                     14
  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   178   6   2  15
  9P LOSS WILD-TYPE 165   6   2  11
D58V13, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             178               165
  R1               6                 6
  R2               2                 2
  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
  9P LOSS MUTATED                                  1     2
  9P LOSS WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          25   207
  9P LOSS WILD-TYPE                        26   182
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                26
  WHITE                                        207               182
[1] 4 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     4 194
  9P LOSS WILD-TYPE   3 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  194
  9P LOSS WILD-TYPE    3  188
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             194               188
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   158  85
  9Q LOSS WILD-TYPE 167  82
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              243               249 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               85                82 
$`9Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4402 TCGA-05-4415 
       50.07         3.98        19.96        45.01         8.02         2.99 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
        9.01        29.98        30.02        25.02        24.00        15.02 
TCGA-05-5425 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
       29.00         2.04         7.40         8.68        97.74        37.71 
TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F 
       49.05        35.28        11.64        44.61        14.73         4.37 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 
       44.42        44.94        38.10        42.08        42.77        25.02 
TCGA-44-3917 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6774 
       38.89        28.37        28.01        23.77         9.93        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       23.18        32.45        19.46         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-44-A4SU 
       29.00        29.23        12.66         8.55        13.64        13.45 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.11        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV 
       29.46        55.89        16.04        53.29        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO TCGA-50-5055 
      156.66        73.12        62.24         8.55       123.58        60.16 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.09        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5944 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 TCGA-50-7109 
        8.45        25.12        11.05        12.16         0.72        10.13 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
        7.59        27.25        13.94        23.05        38.73        45.21 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 
        2.86        32.65         0.79         0.82         3.88         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 
       45.34        32.71        40.54       107.21         0.59         1.15 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7911 
        0.20         0.13        23.18         1.28         0.53        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 
        6.15        19.82         3.29        19.66         5.06         0.13 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8505 
       15.65        17.98         1.51         2.17         1.45         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 
        0.26         0.49        17.72         0.10         6.64        17.62 
TCGA-55-8615 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
        0.49        22.65        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       20.19        19.99        17.95        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       49.25        47.80        56.71        72.30        13.61        39.25 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5779 
       56.81        81.80        37.02        38.37        87.98        28.41 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6217 TCGA-69-7760 
        1.02        20.05        18.84        12.66        13.87         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        12.56         4.24 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       17.16        23.38        82.68        15.35         4.31        30.31 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       11.18       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
      129.53        21.90        64.90         9.57        88.14        26.53 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8660 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 
       50.24       232.18        10.55        34.39        38.04        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
       35.24         4.08         0.79        22.82        31.20        23.05 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 
       21.47         1.15        13.91         0.62        29.46        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-91-8499 TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-8039 
        1.18        17.46        41.82        18.67        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7937 TCGA-97-8174 TCGA-97-8176 
        2.76        21.40        19.89         5.95         5.39        15.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 
       16.41        21.60        20.58        21.44        19.76        18.67 
TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG 
       20.68         1.45        21.57        24.30        18.08        32.48 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       18.58        15.65        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
       58.45        49.35        58.85         5.49        41.59        31.23 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YI 
       10.09        29.46        11.05        11.15        73.91         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13        20.28        59.11 

$`9Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 
       14.01        37.02         0.00         9.96        24.03        47.05 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       19.00        20.05        14.96        12.00        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4434 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       26.01        25.02        15.02         4.96        22.03         9.04 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 
        0.46         5.98       120.79        28.41        26.30        43.53 
TCGA-44-2656 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       46.98         3.19        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6776 
       26.56        33.30        19.56        27.78        23.15        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7672 TCGA-44-8119 
       61.28        16.44        22.72        12.03        13.74         3.25 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-49-4486 
       15.98        15.32         9.44        11.08        11.54        76.21 
TCGA-49-4488 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       28.57         8.81        29.75        55.33        17.16        11.64 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       28.90        40.41        37.32       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5930 
       20.52        71.47        70.55        15.72        31.04         9.27 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       15.12         9.37        29.03        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6595 TCGA-50-6597 TCGA-50-8457 TCGA-53-7624 TCGA-53-7626 
       25.55         6.21        41.69        36.99        34.29        30.54 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       35.21        48.62         0.07        42.51        40.73        15.25 
TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 
       48.49         5.49         7.79        60.03        24.99        70.26 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        7.99         3.12         1.32         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        1.78        18.64         6.48         0.16        29.72        15.19 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
       19.73        23.64         1.08        22.16        15.42         0.76 
TCGA-55-8506 TCGA-55-8511 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        0.36         0.30         4.80         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-62-8394 TCGA-62-8395 
       16.93        20.71        21.40         1.58         4.57        39.98 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
       19.53        54.35        67.96        40.96        29.92        20.65 
TCGA-64-1678 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 
       39.09         2.04        42.90        51.25        28.47        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 
       14.73         5.72         4.64        13.61         5.42         4.41 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 
        2.93        14.01        13.45        25.91         2.01        52.60 
TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7152 
       26.30         9.24         1.25        39.09        50.33        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-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      104.19       238.29         8.48        31.20         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-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 
       27.09        12.36         5.88        31.13        20.55        32.78 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 
       37.74         4.57        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-91-6836 TCGA-91-6849 TCGA-91-7771 
       13.64        26.47        10.62        13.71         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
       16.60        14.27         1.45        19.82        22.45         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29        16.54         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       12.39        15.68        18.18        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       43.79        25.48         0.59         0.72        18.67        17.92 
TCGA-97-8175 TCGA-97-8179 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       18.12        14.30        20.19        20.52        17.75        20.84 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE 
       24.56        34.85        36.76        21.63        23.80        35.47 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       19.00        14.30         6.35        10.09        14.53         1.91 
TCGA-L9-A743 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TH 
       21.83        37.35        86.04         5.29         2.43        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A 
       14.10        19.13        71.05        62.60         1.64         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        0.43        19.82        16.87 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              0.1               0.0 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           232.18            238.29 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            19.99             19.82 
[1] "0.1 - 232.2 (20.0)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1"  
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         3       62       69        1        27        37
  9Q LOSS WILD-TYPE       2       73       70        0        25        35
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9Q LOSS MUTATED           40          4       11
  9Q LOSS WILD-TYPE         32          7       15
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                62                73
  STAGE IB                69                70
  STAGE II                 1                 0
  STAGE IIA               27                25
  STAGE IIB               37                35
  STAGE IIIA              40                32
  STAGE IIIB               4                 7
  STAGE IV                11                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
  9Q LOSS MUTATED    83 140  24   6
  9Q LOSS WILD-TYPE  87 138  22  13
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              83                87
  T2             140               138
  T3              24                22
  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   155  53    40
  9Q LOSS WILD-TYPE 177  43    36
D59V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                155               177
  N1                 53                43
  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   172  11
  9Q LOSS WILD-TYPE 177  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    172   11
  9Q LOSS WILD-TYPE  177   14
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             172               177
  1              11                14
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   135 119
  9Q LOSS WILD-TYPE 140 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    135  119
  9Q LOSS WILD-TYPE  140  121
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE             135               140
  MALE               119               121
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   174  30
  9Q LOSS WILD-TYPE 186  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    174   30
  9Q LOSS WILD-TYPE  186   24
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              174               186
  YES              30                24
[1] 2 2
[1] FALSE
D59V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9Q LOSS MUTATED                           10
  9Q LOSS WILD-TYPE                          9
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9Q LOSS MUTATED                                  45
  9Q LOSS WILD-TYPE                                61
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                  166
  9Q LOSS WILD-TYPE                                                154
                   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                              1                             9
  9Q LOSS WILD-TYPE                            1                            14
                   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                                      10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             166
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    9
  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                                 61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               154
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     14
  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   171   6   2  13
  9Q LOSS WILD-TYPE 172   6   2  13
D59V13, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0             171               172
  R1               6                 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
  9Q LOSS MUTATED                                  1     2
  9Q LOSS WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          24   197
  9Q LOSS WILD-TYPE                        27   192
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                27
  WHITE                                        197               192
[1] 4 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     4 190
  9Q LOSS WILD-TYPE   3 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4  190
  9Q LOSS WILD-TYPE    3  192
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             190               192
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    61  48
  10P LOSS WILD-TYPE 264 119
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               109                383 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                48                119 
$`10P LOSS MUTATED`
TCGA-05-4402 TCGA-05-5429 TCGA-05-5715 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 
        8.02         9.04         2.04        37.71        49.05        11.64 
TCGA-38-6178 TCGA-44-2657 TCGA-44-2662 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 
       14.73        44.42        42.08         3.19        25.02        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-5645 TCGA-44-6775 TCGA-44-6779 
       38.89        34.06        33.73        28.01        23.18        16.44 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-A4SU TCGA-49-4488 
       19.46         7.17        18.87        29.00        13.45        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-6742 TCGA-49-6767 
       12.66        35.54        46.72        14.07        16.04        22.26 
TCGA-49-AAR0 TCGA-49-AARQ TCGA-50-5931 TCGA-50-5944 TCGA-50-6591 TCGA-50-6593 
      156.66       221.33        14.27        25.12         3.91        11.05 
TCGA-50-6597 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6986 TCGA-55-7281 
       41.69         2.20        45.34        32.71       107.21         0.59 
TCGA-55-7994 TCGA-55-8091 TCGA-55-8094 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48X 
       19.82        19.73         0.13         6.64        17.62        22.65 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8402 TCGA-62-A46Y TCGA-64-1676 
       20.19        19.99         4.57        49.25        13.61        56.81 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 
       81.80        38.37        87.98         2.04        28.41         1.02 
TCGA-67-3772 TCGA-69-7973 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       18.84         7.56        17.16        23.38        26.30        15.35 
TCGA-78-7147 TCGA-78-7540 TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       19.27        39.35       232.18        77.59        10.55        27.09 
TCGA-86-6851 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 
        5.88        19.89        37.74         4.08         0.79        22.82 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8669 TCGA-86-A4JF TCGA-91-6828 
       31.04        23.05        14.60        30.84        24.23        10.62 
TCGA-91-6835 TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JQ TCGA-95-7043 
        2.60        12.23         1.18        17.46        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-8494 TCGA-97-7546 TCGA-97-8547 TCGA-97-A4M1 
        2.86        15.68         2.76        31.69        21.60        19.76 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-MP-A4SY TCGA-MP-A4T2 
       20.68        24.30        18.08        32.48        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TJ TCGA-NJ-A4YI TCGA-NJ-A55A 
       86.04        58.85        41.59        11.15         0.13         0.26 
TCGA-O1-A52J 
       59.11 

$`10P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03        47.05        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-3615 
       15.02        15.02         4.96        29.00        22.03         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 
        7.40         5.98         8.68        97.74       120.79        28.41 
TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       35.28        44.61        26.30         4.37        43.53        46.98 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-4112 TCGA-44-5643 
       44.94        38.10        42.77        37.15        26.56        33.30 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.37        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 
       21.63        63.72        32.45        61.28        22.72        12.03 
TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       36.07        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       76.21        28.11        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV 
       55.89        53.29        55.33        17.16        11.64        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
       73.12        62.24        28.90         8.55        40.41        37.32 
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        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.09         9.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12         9.37 
TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       29.03        22.55        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         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
       30.54        13.94        35.21        23.05        38.73        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       45.21         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 
        7.79        60.03        24.99        40.54        70.26         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1.28         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
       15.19         3.29        19.66         5.06        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 
       17.72         0.30         0.10         4.80         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        1.61         2.17        16.93        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 
       20.58        19.59         0.92        15.81        17.95        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-A470 TCGA-62-A471 TCGA-62-A472 
       54.35        67.96        72.30        39.25        40.96        29.92 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
       20.65        39.09        37.02        42.90        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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4670 
        4.24        25.91         2.01        52.60        82.68         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
       30.31         9.24         1.25        39.09        50.33        11.18 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      163.10        27.16         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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
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-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 TCGA-86-6562 TCGA-86-7701 
       10.55        50.24        39.75       110.50        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 
       34.39        38.04        20.55        32.78        35.24         4.57 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
       24.33        32.65        31.20        21.47         1.15        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-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
       13.64        26.47        41.36         1.97        10.19        13.71 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82        22.45         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 
       19.00        41.82        18.67        12.39        15.65        27.29 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       21.40        18.18        19.89        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       25.48         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
        5.39        18.12        15.39        16.41        14.30        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       20.19        21.44        20.52        17.75        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-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       23.80        35.47        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
       14.53         1.91        21.83        18.58        15.65        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 
       38.63         2.76        86.14        58.45         5.49         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP 
       14.10        19.13        73.91        71.05        62.60         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       29.13         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 
             19.99              19.96 
[1] "0.1 - 232.2 (20.0)" "0.0 - 238.3 (20.0)"
[1] "hr=" "1.3"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         1       34       27        0        14        15
  10P LOSS WILD-TYPE       4      101      112        1        38        57
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10P LOSS MUTATED           17          1        5
  10P LOSS WILD-TYPE         55         10       21
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 34                101
  STAGE IB                 27                112
  STAGE II                  0                  1
  STAGE IIA                14                 38
  STAGE IIB                15                 57
  STAGE IIIA               17                 55
  STAGE IIIB                1                 10
  STAGE IV                  5                 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
  10P LOSS MUTATED    46  58   8   2
  10P LOSS WILD-TYPE 124 220  38  17
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               46                124
  T2               58                220
  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    69  24    18
  10P LOSS WILD-TYPE 263  72    58
D60V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  69                263
  N1                  24                 72
  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    79   5
  10P LOSS WILD-TYPE 270  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     79    5
  10P LOSS WILD-TYPE  270   20
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               79                270
  1                5                 20
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    74  40
  10P LOSS WILD-TYPE 201 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     74   40
  10P LOSS WILD-TYPE  201  200
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               74                201
  MALE                 40                200
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    91   7
  10P LOSS WILD-TYPE 269  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     91    7
  10P LOSS WILD-TYPE  269   47
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                91                269
  YES                7                 47
[1] 2 2
[1] FALSE
D60V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10P LOSS MUTATED                            5
  10P LOSS WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10P LOSS MUTATED                                  15
  10P LOSS WILD-TYPE                                91
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                   83
  10P LOSS WILD-TYPE                                                237
                    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)               83
  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                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  91
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                237
  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    83   1   1   6
  10P LOSS WILD-TYPE 260  11   3  20
D60V13, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               83                260
  R1                1                 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
  10P LOSS MUTATED                                  1     0
  10P LOSS WILD-TYPE                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           7    93
  10P LOSS WILD-TYPE                        44   296
D60V14, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                       7                 44
  WHITE                                          93                296
[1] 4 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     3  87
  10P LOSS WILD-TYPE   4 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3   87
  10P LOSS WILD-TYPE    4  295
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               87                295
[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 251 112
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               129                363 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                55                112 
$`10Q LOSS MUTATED`
TCGA-05-4397 TCGA-05-4402 TCGA-05-4420 TCGA-05-4424 TCGA-05-5429 TCGA-05-5715 
       24.03         8.02        29.98        30.02         9.04         2.04 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-44-2657 TCGA-44-2662 TCGA-44-2666 
       37.71        49.05        11.64        44.42        42.08         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-44-5645 TCGA-44-6775 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 
       28.01        23.18        16.44        19.46         7.17        18.87 
TCGA-44-7670 TCGA-44-A4SU TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-6742 
       29.00        13.45        12.66        35.54        14.07        16.04 
TCGA-49-AAR0 TCGA-49-AARE TCGA-49-AARQ TCGA-50-5931 TCGA-50-5944 TCGA-50-6591 
      156.66        40.41       221.33        14.27        25.12         3.91 
TCGA-50-6592 TCGA-50-6597 TCGA-50-6673 TCGA-55-5899 TCGA-55-6971 TCGA-55-6979 
       25.55        41.69         0.72         2.86         0.82         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 
        2.20        45.34        32.71       107.21         0.59        19.82 
TCGA-55-8091 TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 
       19.73         1.51         2.17         0.95         0.49         6.64 
TCGA-55-8614 TCGA-55-A48X TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8402 
       17.62        22.65        20.19        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         1.02        18.84         7.56         4.41         2.93 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4668 TCGA-73-A9RS TCGA-78-7147 
        4.24        17.16        26.30        15.35        11.18        19.27 
TCGA-78-7535 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 
       31.20        39.35        10.55       232.18        77.59        10.55 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 
       27.09         5.88        19.89        35.24         4.08         0.79 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8669 TCGA-86-A4JF 
       22.82        31.04        23.05        14.60        30.84        24.23 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 
       10.62        41.36         2.60        12.23        27.68         1.18 
TCGA-93-7348 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
       17.46        17.29        16.54         2.86        12.39        15.68 
TCGA-95-7948 TCGA-97-7546 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M1 TCGA-97-A4M7 
       15.65        31.69        18.12        21.60        19.76        20.68 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A443 TCGA-MP-A4SY TCGA-MP-A4T2 
       24.30        18.08        32.48         6.35        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        29.13        59.11 

$`10Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        0.00         9.96        47.05        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       14.96         9.01        12.00        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       29.00        22.03         0.46         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       97.74       120.79        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 
       26.30         4.37        43.53        46.98        44.94        38.10 
TCGA-44-2665 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
       42.77        26.56        33.30        28.37        23.77        19.56 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 
        9.93        27.78        23.15        21.63        63.72        32.45 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 
       61.28        22.72        12.03        36.07        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.08        11.54        13.64        76.21        28.11        28.57 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       46.72        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       53.29        55.33        17.16        11.64        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO 
       73.12        62.24        28.90         8.55        37.32       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        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
       60.16        31.04        49.28         8.09         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12         9.37        29.03 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 
       22.55        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         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 
       35.21        23.05        38.73        48.62        45.21         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       32.65         0.79        42.51        40.73        15.25        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 
        3.88         5.49        60.03        24.99        40.54        70.26 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        1.15         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
       18.64         0.53         6.48        17.65         6.15         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19         3.29        19.66         5.06         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 
       23.64        15.65        17.98         1.08        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
        1.45         0.76         0.36         0.26        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        0.10         4.80         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       16.93        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
        0.92        15.81        17.95        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
       72.30        39.25        40.96        29.92        20.65        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-67-6217 TCGA-69-7760 
       12.66        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7980 
        6.12        22.68        13.61         5.42         6.05        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
       14.01        13.45        25.91         2.01        52.60        23.38 
TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       82.68         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       50.33       163.10        27.16         5.69        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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        26.53         8.02        53.33        26.01 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       50.24        39.75       110.50        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         1.15        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-91-6836 TCGA-91-6848 TCGA-91-6849 
       26.47         1.97        10.19        13.71         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.45        19.82        22.45 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
        6.12        23.61         1.08        19.00        41.82        18.67 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
       27.29         2.76        21.40        18.18        19.89        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92         5.39        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.58        20.19        21.44        20.52        17.75        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-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 
       21.63        23.80        35.47        19.00        14.30        10.09 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
       14.53         1.91        21.83        18.58        15.65        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 
       38.63         2.76        86.14        58.45         5.49         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23         2.43        10.09        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        62.60         1.64         0.26         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 
             19.76              20.19 
[1] "0.1 - 232.2 (19.8)" "0.0 - 238.3 (20.2)"
[1] "hr=" "1.4"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         2       41       38        0        15        19
  10Q LOSS WILD-TYPE       3       94      101        1        37        53
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10Q LOSS MUTATED           16          1        4
  10Q LOSS WILD-TYPE         56         10       22
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 41                 94
  STAGE IB                 38                101
  STAGE II                  0                  1
  STAGE IIA                15                 37
  STAGE IIB                19                 53
  STAGE IIIA               16                 56
  STAGE IIIB                1                 10
  STAGE IV                  4                 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
  10Q LOSS MUTATED    54  71   9   2
  10Q LOSS WILD-TYPE 116 207  37  17
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               54                116
  T2               71                207
  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    88  28    17
  10Q LOSS WILD-TYPE 244  68    59
D61V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  88                244
  N1                  28                 68
  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    95   4
  10Q LOSS WILD-TYPE 254  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     95    4
  10Q LOSS WILD-TYPE  254   21
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               95                254
  1                4                 21
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    83  53
  10Q LOSS WILD-TYPE 192 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     83   53
  10Q LOSS WILD-TYPE  192  187
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               83                192
  MALE                 53                187
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    99  12
  10Q LOSS WILD-TYPE 261  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     99   12
  10Q LOSS WILD-TYPE  261   42
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                99                261
  YES               12                 42
[1] 2 2
[1] FALSE
D61V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10Q LOSS MUTATED                            6
  10Q LOSS WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10Q LOSS MUTATED                                  21
  10Q LOSS WILD-TYPE                                85
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                   94
  10Q LOSS WILD-TYPE                                                226
                    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)               94
  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                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                226
  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    96   1   1   9
  10Q LOSS WILD-TYPE 247  11   3  17
D61V13, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               96                247
  R1                1                 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
  10Q LOSS MUTATED                                  1     0
  10Q LOSS WILD-TYPE                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          11   106
  10Q LOSS WILD-TYPE                        40   283
D61V14, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                  7
  BLACK OR AFRICAN AMERICAN                      11                 40
  WHITE                                         106                283
[1] 4 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     4  99
  10Q LOSS WILD-TYPE   3 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4   99
  10Q LOSS WILD-TYPE    3  283
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO               99                283
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    74  39
  11P LOSS WILD-TYPE 251 128
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               113                379 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                39                128 
$`11P LOSS MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 
       19.96        45.01        37.02        26.01        24.00        15.02 
TCGA-05-5425 TCGA-05-5428 TCGA-35-5375 TCGA-38-4625 TCGA-38-4632 TCGA-44-2666 
       29.00        22.03         8.68        97.74        44.61         3.19 
TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-5643 TCGA-44-5645 TCGA-44-6146 
       25.02        38.89        34.06        33.30        28.01         9.93 
TCGA-44-6775 TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 TCGA-44-A47F TCGA-44-A4SS 
       23.18         7.17        36.07        29.23        11.08        13.64 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       28.11        12.66        14.07        32.84         8.81        29.46 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 
       22.26        22.26        62.24         8.09        14.27         8.45 
TCGA-50-5939 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 TCGA-53-7624 
       15.12        25.55        11.05        12.16         0.72        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
       30.54        35.21        48.62        45.21         2.86        32.65 
TCGA-55-6972 TCGA-55-7570 TCGA-55-7573 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
       48.49         0.20         0.13         1.12         1.78        18.64 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
       19.82         3.29         0.76         0.26        17.72         0.30 
TCGA-55-8615 TCGA-55-A490 TCGA-55-A492 TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46S 
        0.49         1.58        19.59        19.99        42.38        54.35 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-5774 TCGA-64-5778 
       40.96        29.92        56.81        81.80        87.98        42.90 
TCGA-64-5815 TCGA-69-7763 TCGA-69-A59K TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 
       28.47        22.68        17.16        23.38         4.31        30.31 
TCGA-73-7499 TCGA-73-A9RS TCGA-78-7145 TCGA-78-7148 TCGA-78-7154 TCGA-78-7160 
       50.33        11.18        27.16        20.58        19.50        22.92 
TCGA-78-7535 TCGA-78-8640 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
       31.20       232.18        31.13        34.39        38.04        32.78 
TCGA-86-8074 TCGA-86-8358 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6836 TCGA-91-6847 
        0.79        21.47         3.81        24.23        13.71        27.68 
TCGA-93-8067 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 TCGA-97-8174 
        6.12        15.65        27.29         2.76        43.79         5.39 
TCGA-97-A4M1 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
       19.76        18.08        19.00        18.58        15.65        27.19 
TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-NJ-A4YQ 
       37.35         5.29        29.46        11.05        29.13 

$`11P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       50.07         3.98        14.01         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
       25.02        25.02        15.02         4.96         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        0.46         7.40         5.98       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
       43.53        46.98        44.42        44.94        38.10        42.08 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       42.77        37.15        38.24        33.73        26.56        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
       23.77        19.56        27.78        23.15        21.63        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       18.87        29.00        13.74        12.66         3.25         8.55 
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-49-4488 TCGA-49-4494 TCGA-49-4501 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       28.57        35.54        46.72        29.75        55.89        16.04 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AAR2 
       53.29        55.33        17.16        11.64       156.66        73.12 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       28.90         8.55        40.41        37.32       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        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
       60.16        31.04        49.28         9.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       21.47         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6595 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        3.91         6.21        41.69        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 
       27.25        13.94        23.05        38.73         0.07         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 
       42.51        40.73        15.25         0.82         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
        3.12         1.32        23.18         1.28         1.28         0.79 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 
       15.42         1.45         0.95         0.36         0.49         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64        17.62         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 
       16.93        22.65        20.71        21.40        20.58         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
       15.81        20.19        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-A470 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
       72.30        13.61        39.25        20.65        39.09        37.02 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 
       38.37         2.04        28.41        51.25         1.02        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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       13.87         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         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 
        4.24        25.91         2.01        52.60        82.68        26.30 
TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7143 TCGA-78-7146 
       15.35         9.24         1.25        39.09       163.10         5.69 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
       19.27       129.53        21.90        39.95       119.51        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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        8.48        88.14        26.53         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        10.55        50.24        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7714 TCGA-86-7954 
      110.50        27.09        12.36         5.88        20.55        19.89 
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-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        31.20        23.05        14.60         1.15 
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-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-91-7771 
       10.19         2.60        12.23         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
       17.46        23.61         1.08        19.00        17.29        41.82 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
       16.54         2.86        18.67        12.39        15.68        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 
       18.18        19.89        31.69        64.60        63.52        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        5.95         0.59         0.72        18.67        17.92        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        20.52        17.75        20.84        18.67        20.68 
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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
       24.30        23.80        35.47        32.48        14.30         6.35 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N4 TCGA-MN-A4N5 
       10.09        14.53         1.91        21.83        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-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI 
       41.59        31.23         2.43        10.09        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        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        1.64         0.26         0.43        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.13               0.00 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            232.18             238.29 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             22.26              19.66 
[1] "0.1 - 232.2 (22.3)" "0.0 - 238.3 (19.7)"
[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       32        1        15        21
  11P LOSS WILD-TYPE       3      112      107        0        37        51
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11P LOSS MUTATED           15          0        7
  11P LOSS WILD-TYPE         57         11       19
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 23                112
  STAGE IB                 32                107
  STAGE II                  1                  0
  STAGE IIA                15                 37
  STAGE IIB                21                 51
  STAGE IIIA               15                 57
  STAGE IIIB                0                 11
  STAGE IV                  7                 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
  11P LOSS MUTATED    33  65  15   3
  11P LOSS WILD-TYPE 137 213  31  16
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               33                137
  T2               65                213
  T3               15                 31
  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    73  28    14
  11P LOSS WILD-TYPE 259  68    62
D62V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                  73                259
  N1                  28                 68
  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"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    78   7
  11P LOSS WILD-TYPE 271  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     78    7
  11P LOSS WILD-TYPE  271   18
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               78                271
  1                7                 18
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    47  69
  11P LOSS WILD-TYPE 228 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     47   69
  11P LOSS WILD-TYPE  228  171
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               47                228
  MALE                 69                171
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    77  15
  11P LOSS WILD-TYPE 283  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     77   15
  11P LOSS WILD-TYPE  283   39
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                77                283
  YES               15                 39
[1] 2 2
[1] FALSE
D62V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11P LOSS MUTATED                            2
  11P LOSS WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11P LOSS MUTATED                                  22
  11P LOSS WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                   84
  11P LOSS WILD-TYPE                                                236
                    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                              1                             3
  11P LOSS WILD-TYPE                            1                            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                                22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               84
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  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                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                236
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  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    79   2   1  10
  11P LOSS WILD-TYPE 264  10   3  16
D62V13, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               79                264
  R1                2                 10
  R2                1                  3
  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
  11P LOSS MUTATED                                  0     3
  11P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          14    85
  11P LOSS WILD-TYPE                        37   304
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                      14                 37
  WHITE                                          85                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"
D62V15, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5  88
  11P LOSS WILD-TYPE   2 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5   88
  11P LOSS WILD-TYPE    2  294
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  2
  NOT HISPANIC OR LATINO               88                294
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    60  29
  11Q LOSS WILD-TYPE 265 138
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                89                403 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                29                138 
$`11Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 
       19.96        45.01        37.02        26.01        24.00        15.02 
TCGA-05-5425 TCGA-05-5428 TCGA-35-5375 TCGA-38-4625 TCGA-38-4631 TCGA-44-2666 
       29.00        22.03         8.68        97.74        11.64         3.19 
TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-5643 TCGA-44-5645 TCGA-44-6146 
       25.02        38.89        34.06        33.30        28.01         9.93 
TCGA-44-6775 TCGA-44-7667 TCGA-44-7671 TCGA-44-A47F TCGA-44-A4SS TCGA-49-4487 
       23.18        36.07        29.23        11.08        13.64        28.11 
TCGA-49-4506 TCGA-49-4510 TCGA-49-6767 TCGA-49-AAQV TCGA-50-5072 TCGA-50-5931 
       32.84        29.46        22.26        22.26         8.09        14.27 
TCGA-50-5936 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 TCGA-53-7626 
        8.45        25.55        11.05        12.16         0.72        30.54 
TCGA-55-1595 TCGA-55-6972 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7995 
       48.62        48.49         1.12         1.78        18.64         0.16 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8302 TCGA-55-8507 TCGA-55-8511 TCGA-55-8615 
        3.29         0.13         0.76         0.26         0.30         0.49 
TCGA-62-8397 TCGA-62-A46S TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
       42.38        54.35        39.25        29.92        56.81        39.09 
TCGA-64-1679 TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 TCGA-69-7763 TCGA-69-8453 
       81.80        87.98        42.90        28.47        22.68        25.91 
TCGA-73-4662 TCGA-73-4675 TCGA-73-7499 TCGA-78-7145 TCGA-78-7148 TCGA-78-7160 
       82.68        30.31        50.33        27.16        20.58        22.92 
TCGA-78-8640 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8074 
      232.18        31.13        38.04        32.78        37.74         0.79 
TCGA-86-8358 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6847 TCGA-93-8067 TCGA-95-8039 
       21.47         3.81        24.23        27.68         6.12        27.29 
TCGA-95-8494 TCGA-95-A4VN TCGA-97-8174 TCGA-J2-A4AD TCGA-MN-A4N1 TCGA-MN-A4N5 
        2.76        18.18         5.39        18.08        27.19         2.76 
TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-NJ-A4YQ 
       37.35         5.29        29.46        11.05        29.13 

$`11Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       50.07         3.98        14.01         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
       25.02        25.02        15.02         4.96         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        0.46         7.40         5.98       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        44.61        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
       43.53        46.98        44.42        44.94        38.10        42.08 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       42.77        37.15        38.24        33.73        26.56        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
       23.77        19.56        27.78        23.15        21.63        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        22.72        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        7.17        18.87        29.00        13.74        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU 
        8.55        15.98        15.32         9.44        11.54        13.45 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       76.21        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
        8.81        29.75        55.89        16.04        53.29        55.33 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       17.16        11.64       156.66        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
        8.55        40.41        37.32       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        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       31.04        49.28         9.27        40.60        78.67        21.47 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6595 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        3.91         6.21        41.69        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       27.25        34.29        13.94        35.21        23.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       45.21         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        0.79         0.53         6.48        17.65         6.15        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 
       29.72        15.19        19.66        19.73         5.06        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
       15.42         1.45         0.95         0.36         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80         6.64        17.62         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        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-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-A471 TCGA-64-1677 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
       40.96        20.65        37.02        38.37         2.04        28.41 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       51.25         1.02        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45         4.24        17.16         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
       52.60        23.38        26.30        15.35         4.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 
        1.25        39.09        11.18       163.10         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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        8.48        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55        50.24        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 
       10.55       110.50        27.09        12.36         5.88        34.39 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       20.55        19.89        35.24         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-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        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-91-6836 TCGA-91-6840 TCGA-91-6848 
        1.97        10.19         2.60        13.71        12.23         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
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-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       17.29        41.82        16.54         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       15.68        15.65        21.40        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       36.76         1.45        21.57        21.63        24.30        23.80 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.53         1.91        21.83        18.58        15.65        38.63 
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-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI 
       41.59        31.23         2.43        10.09        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        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        1.64         0.26         0.43        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.13               0.00 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            232.18             238.29 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             25.02              19.53 
[1] "0.1 - 232.2 (25.0)" "0.0 - 238.3 (19.5)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         1       19       25        1        13        15
  11Q LOSS WILD-TYPE       4      116      114        0        39        57
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11Q LOSS MUTATED           13          0        4
  11Q LOSS WILD-TYPE         59         11       22
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 19                116
  STAGE IB                 25                114
  STAGE II                  1                  0
  STAGE IIA                13                 39
  STAGE IIB                15                 57
  STAGE IIIA               13                 59
  STAGE IIIB                0                 11
  STAGE IV                  4                 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
  11Q LOSS MUTATED    28  51  10   2
  11Q LOSS WILD-TYPE 142 227  36  17
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               28                142
  T2               51                227
  T3               10                 36
  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    59  18    13
  11Q LOSS WILD-TYPE 273  78    63
D63V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                  59                273
  N1                  18                 78
  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"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    69   4
  11Q LOSS WILD-TYPE 280  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     69    4
  11Q LOSS WILD-TYPE  280   21
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               69                280
  1                4                 21
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    37  54
  11Q LOSS WILD-TYPE 238 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     37   54
  11Q LOSS WILD-TYPE  238  186
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               37                238
  MALE                 54                186
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    64  10
  11Q LOSS WILD-TYPE 296  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     64   10
  11Q LOSS WILD-TYPE  296   44
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                64                296
  YES               10                 44
[1] 2 2
[1] FALSE
D63V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11Q LOSS MUTATED                            3
  11Q LOSS WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11Q LOSS MUTATED                                  16
  11Q LOSS WILD-TYPE                                90
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                   63
  11Q LOSS WILD-TYPE                                                257
                    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                              1                             3
  11Q LOSS WILD-TYPE                            1                            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)               63
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  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                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                257
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  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    64   2   0   8
  11Q LOSS WILD-TYPE 279  10   4  18
D63V13, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               64                279
  R1                2                 10
  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
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           7    69
  11Q LOSS WILD-TYPE                        44   320
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                       7                 44
  WHITE                                          69                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"
D63V15, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2  70
  11Q LOSS WILD-TYPE   5 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   70
  11Q LOSS WILD-TYPE    5  312
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               70                312
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    74  36
  12P LOSS WILD-TYPE 251 131
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               110                382 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                36                131 
$`12P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4405 TCGA-05-4426 TCGA-05-4434 TCGA-38-6178 TCGA-44-2657 
       50.07        20.05        26.01        15.02        14.73        44.42 
TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-6146 TCGA-44-6775 
       38.10         3.19        25.02        38.89         9.93        23.18 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47B 
       16.44         7.17        29.23        12.66         8.55         9.44 
TCGA-44-A47F TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-6743 
       11.08        13.45        28.57        12.66        46.72        53.29 
TCGA-49-6744 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-50-5049 TCGA-50-5051 
       55.33        40.41        37.32       221.33        70.55        15.72 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6591 
       49.28        40.60        15.12        29.03        22.55         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 TCGA-55-1592 TCGA-55-5899 TCGA-55-6979 
       11.05        12.16        36.99        23.05         2.86         7.79 
TCGA-55-6982 TCGA-55-6984 TCGA-55-7573 TCGA-55-7727 TCGA-55-7914 TCGA-55-8087 
       32.71        24.99         0.13         1.12         6.15        15.19 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
       17.72         0.30         6.64        17.62         1.58         1.61 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DG TCGA-62-A46R TCGA-62-A46S 
       22.65        21.40        20.58        19.99        56.71        54.35 
TCGA-64-1676 TCGA-64-5778 TCGA-67-3771 TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 
       56.81        42.90        20.05        13.87        22.68         5.42 
TCGA-69-7974 TCGA-69-8253 TCGA-71-6725 TCGA-73-4677 TCGA-73-7498 TCGA-78-7147 
        6.05        14.01         2.01         1.25        39.09        19.27 
TCGA-78-7153 TCGA-78-7535 TCGA-86-7701 TCGA-86-7955 TCGA-86-8073 TCGA-86-8074 
      119.51        31.20        31.13        35.24        24.33         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8672 TCGA-91-6840 TCGA-91-6847 
       22.82        31.20        21.47         0.62        12.23        27.68 
TCGA-91-6849 TCGA-91-7771 TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 
        1.15        16.18        41.82        16.54        15.68        15.65 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7938 TCGA-97-8177 TCGA-97-A4M1 
       31.69        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-A4TC TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55O 
        2.43        19.13        71.05         0.13        29.13         0.43 
TCGA-NJ-A7XG TCGA-O1-A52J 
       20.28        59.11 

$`12P LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 
        9.96        24.03        47.05         8.02        19.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        25.02        24.00        15.02         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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        44.61        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-3396 
       43.53        46.98        44.94        42.08        42.77        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-44-6147 TCGA-44-6148 TCGA-44-6774 
       28.01        23.77        19.56        27.78        23.15        21.63 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       63.72        32.45        61.28        22.72        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
       36.07        18.87        29.00        13.74         3.25        15.98 
TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 
       15.32        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-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       16.04        17.16        11.64        22.26        22.26       156.66 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARR 
       73.12        62.24        28.90         8.55       123.58       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        9.86        20.52        71.47        60.16        31.04         8.09 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 
        9.27        14.27        78.67        21.47         8.45         9.37 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.12        42.35        25.55         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       10.13         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
       35.21        38.73        48.62        45.21         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.79        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 
        3.88         5.49         2.20        45.34        60.03        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
      107.21        70.26         0.59         1.15         7.99         0.20 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
        3.12         1.32        23.18         1.28         1.28         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
        1.78        18.64         0.53         6.48        17.65        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        2.17        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
        0.36         0.26         0.49         0.10         4.80         0.49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
        2.17        16.93        20.71         1.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        20.19        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-64-1677 
       72.30        13.61        39.25        40.96        29.92        20.65 
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-67-3772 TCGA-67-3773 
       28.41        51.25        28.47         1.02        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-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
       13.61         7.56         4.41         2.93        12.56        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.24        25.91        17.16        52.60        23.38        82.68 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
       26.30        15.35         4.31        30.31         9.24        50.33 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       11.18       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-78-7166 
       64.90        22.92         9.57       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        50.24       232.18        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36         5.88        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-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       32.65        31.04        23.05        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       30.84        27.58        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-91-6836 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 
       10.19         2.60        13.71         7.36        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7567 
       23.61         1.08        19.00        17.29         2.86        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       12.39        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       63.52        43.79         5.95         0.72        18.67        17.92 
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-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 
       20.19        21.44        20.52        17.75        20.84        20.68 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       36.76         1.45        21.57        21.63        24.30        23.80 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        32.48        19.00        14.30         6.35        10.09 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        21.83        27.19        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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59        31.23        10.09        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        62.60 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R TCGA-S2-AA1A 
        1.64         0.26        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 
            19.875             20.075 
[1] "0.1 - 221.3 (19.9)" "0.0 - 238.3 (20.1)"
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         1       30       39        0         9        14
  12P LOSS WILD-TYPE       4      105      100        1        43        58
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12P LOSS MUTATED           16          1        4
  12P LOSS WILD-TYPE         56         10       22
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 30                105
  STAGE IB                 39                100
  STAGE II                  0                  1
  STAGE IIA                 9                 43
  STAGE IIB                14                 58
  STAGE IIIA               16                 56
  STAGE IIIB                1                 10
  STAGE IV                  4                 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
  12P LOSS MUTATED    37  65   8   4
  12P LOSS WILD-TYPE 133 213  38  15
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               37                133
  T2               65                213
  T3                8                 38
  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    77  21    15
  12P LOSS WILD-TYPE 255  75    61
D64V5, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                  77                255
  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    70   3
  12P LOSS WILD-TYPE 279  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     70    3
  12P LOSS WILD-TYPE  279   22
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               70                279
  1                3                 22
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    75  39
  12P LOSS WILD-TYPE 200 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     75   39
  12P LOSS WILD-TYPE  200  201
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               75                200
  MALE                 39                201
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    88  11
  12P LOSS WILD-TYPE 272  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     88   11
  12P LOSS WILD-TYPE  272   43
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                88                272
  YES               11                 43
[1] 2 2
[1] FALSE
D64V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12P LOSS MUTATED                            1
  12P LOSS WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12P LOSS MUTATED                                  23
  12P LOSS WILD-TYPE                                83
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                   75
  12P LOSS WILD-TYPE                                                245
                    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                              1                             5
  12P LOSS WILD-TYPE                            1                            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)               75
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  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                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                245
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  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    68   1   1   5
  12P LOSS WILD-TYPE 275  11   3  21
D64V13, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               68                275
  R1                1                 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
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                          17    88
  12P LOSS WILD-TYPE                        34   301
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                 34
  WHITE                                          88                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"
D64V15, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  94
  12P LOSS WILD-TYPE   5 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   94
  12P LOSS WILD-TYPE    5  288
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               94                288
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    61  37
  12Q LOSS WILD-TYPE 264 130
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                98                394 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                37                130 
$`12Q LOSS MUTATED`
TCGA-05-4426 TCGA-05-4434 TCGA-05-5428 TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 
       26.01        15.02        22.03        44.61        14.73        44.42 
TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-6146 TCGA-44-6775 
       38.10         3.19        25.02        38.89         9.93        23.18 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7671 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SU 
       16.44         7.17        29.23         8.55        11.08        13.45 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-6743 TCGA-49-6744 TCGA-49-AARE 
       28.57        12.66        46.72        53.29        55.33        40.41 
TCGA-49-AARN TCGA-49-AARQ TCGA-50-5049 TCGA-50-5068 TCGA-50-5932 TCGA-50-5939 
       37.32       221.33        70.55        49.28        40.60        15.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-8457 
       22.55         3.91        11.05        12.16        41.69        36.99 
TCGA-55-1592 TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 TCGA-55-6984 TCGA-55-7283 
       23.05         7.79         2.20        32.71        24.99         1.15 
TCGA-55-7727 TCGA-55-7914 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
        1.12         6.15        17.72         0.30         6.64        17.62 
TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A4DG TCGA-62-A46R 
        1.58         1.61        22.65        21.40        19.99        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-64-5778 TCGA-67-6217 TCGA-69-7763 
       54.35        67.96        13.61        42.90        13.87        22.68 
TCGA-69-7765 TCGA-69-7974 TCGA-69-8253 TCGA-71-6725 TCGA-73-4658 TCGA-73-4677 
        5.42         6.05        14.01         2.01        52.60         1.25 
TCGA-73-7498 TCGA-78-7147 TCGA-78-7153 TCGA-78-7535 TCGA-86-7955 TCGA-86-8074 
       39.09        19.27       119.51        31.20        35.24         0.79 
TCGA-86-8075 TCGA-86-8280 TCGA-91-6829 TCGA-91-6847 TCGA-91-7771 TCGA-95-7039 
       22.82        23.05        41.36        27.68        16.18        41.82 
TCGA-95-7043 TCGA-95-7948 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 
       16.54        15.65        27.29        31.69        64.60        25.48 
TCGA-97-8177 TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A8F4 
       16.41        19.76        24.56        34.85        18.08        15.65 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4TC TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A55O 
       27.19         2.76         2.43        19.13        71.05         0.43 
TCGA-NJ-A7XG TCGA-O1-A52J 
       20.28        59.11 

$`12Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       15.02         4.96        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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F 
       49.05        28.41        35.28        11.64        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-3396 
       43.53        46.98        44.94        42.08        42.77        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-44-6147 TCGA-44-6148 TCGA-44-6774 
       28.01        23.77        19.56        27.78        23.15        21.63 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       63.72        32.45        61.28        22.72        19.46        12.03 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       36.07        18.87        29.00        13.74        12.66         3.25 
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-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       28.11        35.54        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       29.75        55.89        16.04        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26       156.66        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        31.04         8.09         9.27        14.27        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       21.47         8.45         9.37        29.03        25.12        42.35 
TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
       25.55         6.21         0.72        10.13         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
       34.29        30.54        13.94        35.21        38.73        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       45.21         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       45.34        60.03        40.54       107.21        70.26         0.59 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1.28         1.28         0.79         1.78        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65        19.82         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        3.29        19.66        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 
        0.49         0.10         4.80         0.49         2.17        16.93 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        17.95         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46V TCGA-62-A470 
       88.64        49.25        47.80        19.53        72.30        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
       40.96        29.92        56.81        20.65        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-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       28.47         1.02        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         2.93        12.56        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
       25.91        17.16        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
        4.31        30.31         9.24        50.33        11.18       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-78-7166 TCGA-78-7167 TCGA-78-7220 
        9.57       104.19       238.29         8.48        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        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-86-8358 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        31.20        21.47        14.60         1.15 
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-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 
        1.97        10.19         2.60        13.71        12.23         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 
       17.29         2.86        18.67        12.39        15.68         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       21.40        18.18        19.89        63.52        43.79         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8028 
       20.52        17.75        20.84        18.67        20.68        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
        1.45        21.57        21.63        24.30        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
       32.48        19.00        14.30         6.35        10.09        14.53 
TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
        1.91        21.83        18.58        38.63        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59        31.23        10.09        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        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-S2-AA1A 
       29.13         0.26        19.82        16.87 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               0.3                0.0 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            221.33             238.29 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             22.29              19.82 
[1] "0.3 - 221.3 (22.3)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         1       22       35        0        10        14
  12Q LOSS WILD-TYPE       4      113      104        1        42        58
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12Q LOSS MUTATED           15          1        4
  12Q LOSS WILD-TYPE         57         10       22
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 22                113
  STAGE IB                 35                104
  STAGE II                  0                  1
  STAGE IIA                10                 42
  STAGE IIB                14                 58
  STAGE IIIA               15                 57
  STAGE IIIB                1                 10
  STAGE IV                  4                 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
  12Q LOSS MUTATED    30  60   8   4
  12Q LOSS WILD-TYPE 140 218  38  15
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               30                140
  T2               60                218
  T3                8                 38
  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    65  22    14
  12Q LOSS WILD-TYPE 267  74    62
D65V5, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                  65                267
  N1                  22                 74
  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"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    60   3
  12Q LOSS WILD-TYPE 289  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     60    3
  12Q LOSS WILD-TYPE  289   22
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               60                289
  1                3                 22
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    67  35
  12Q LOSS WILD-TYPE 208 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     67   35
  12Q LOSS WILD-TYPE  208  205
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               67                208
  MALE                 35                205
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    80  10
  12Q LOSS WILD-TYPE 280  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     80   10
  12Q LOSS WILD-TYPE  280   44
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                80                280
  YES               10                 44
[1] 2 2
[1] FALSE
D65V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12Q LOSS MUTATED                            2
  12Q LOSS WILD-TYPE                         17
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12Q LOSS MUTATED                                  23
  12Q LOSS WILD-TYPE                                83
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                   61
  12Q LOSS WILD-TYPE                                                259
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12Q LOSS MUTATED                                            0
  12Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12Q LOSS MUTATED                                               7
  12Q LOSS WILD-TYPE                                            12
                    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                              1                             4
  12Q LOSS WILD-TYPE                            1                            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)               61
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     7
  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                                      2
                                                    clus
vv                                                   12Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                259
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      12
  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                                        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    60   1   1   5
  12Q LOSS WILD-TYPE 283  11   3  21
D65V13, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               60                283
  R1                1                 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
  12Q LOSS MUTATED                                  0     1
  12Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                          16    78
  12Q LOSS WILD-TYPE                        35   311
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                      16                 35
  WHITE                                          78                311
[1] 4 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     2  83
  12Q LOSS WILD-TYPE   5 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   83
  12Q LOSS WILD-TYPE    5  299
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               83                299
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   165  83
  13Q LOSS WILD-TYPE 160  84
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               248                244 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                83                 84 
$`13Q LOSS MUTATED`
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-05-4402 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 
        8.02        20.05        14.96        29.98        30.02        21.99 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 TCGA-35-4123 
       25.02        25.02         4.96        29.00         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 
        8.68        97.74        49.05        28.41        44.61        14.73 
TCGA-44-2656 TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6146 
       46.98        25.02        38.89        33.30        28.37         9.93 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 
       23.18        32.45        61.28        16.44         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       18.87        29.00         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A4SU TCGA-49-4487 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       11.08        13.45        28.11        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 
        8.81        29.46        29.75        53.29        55.33        11.64 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO 
       22.26       156.66        62.24         8.55        37.32       123.58 
TCGA-4B-A93V TCGA-50-5045 TCGA-50-5051 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
        9.86        71.47        15.72        49.28         9.27        14.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
       78.67        21.47         8.45         9.37        25.12        22.55 
TCGA-50-6593 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ 
       11.05        41.69        10.13        27.25        13.94        35.21 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 
       48.62        45.21         2.86        32.65         0.79         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       48.49         3.88         5.49         2.20        45.34        32.71 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
       40.54       107.21        70.26         0.20         0.13         1.32 
TCGA-55-7724 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-8090 
       23.18         1.78        18.64        17.65        19.82        19.66 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8203 TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 
       19.73         0.13        17.98         2.17         1.45         0.76 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
        0.26         0.49        17.72         0.30         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG 
        0.49         1.58        21.40        20.58         0.92        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R 
        4.57        39.98        42.38        88.64        47.80        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-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 
       56.81        20.65        81.80        38.37        28.41        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
       28.47         1.02        13.87         6.64         6.12        13.61 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        5.42         4.41         2.93         4.24        17.16         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 
       52.60        23.38        82.68        15.35        30.31        50.33 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 
       27.16         5.69        19.27        19.50        38.50        22.92 
TCGA-78-7161 TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 TCGA-86-7701 
        9.57        26.01       232.18        10.55        27.09        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       34.39        38.04        32.78        19.89        37.74         4.08 
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-86-8669 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 
       30.84        28.34        29.46         3.81        24.23        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-8499 
       41.36        10.19         2.60        13.71        12.23         1.18 
TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        6.12         1.08        17.29        41.82         2.86        18.67 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       15.65        27.29         2.76        18.18        19.89        31.69 
TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       25.48         5.39        16.41        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.52        17.75        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.57        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       35.47        32.48        19.00         6.35        10.09        21.83 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       18.58        15.65        86.14        37.35        86.04        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59         2.43        10.09        11.05        14.10        19.13 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       71.05         0.13        29.13         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J 
       20.28        59.11 

$`13Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4415 
       50.07        19.96        14.01         9.96        19.00         2.99 
TCGA-05-4418 TCGA-05-4422 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 
        9.01        12.00        26.01        26.01        24.00        15.02 
TCGA-05-5420 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 
       15.02        22.03         9.04         2.04         0.46       120.79 
TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       37.71        35.28        11.64        26.30         4.37        43.53 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       44.42        44.94        38.10        42.08        42.77         3.19 
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-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
       23.77        19.56        27.78        23.15        21.63        63.72 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       22.72        19.46        12.03        29.23        13.74        12.66 
TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 
       15.32        11.54        13.64        76.21        28.57        12.66 
TCGA-49-4494 TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAR2 
       35.54        55.89        16.04        17.16        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        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5932 TCGA-50-5939 TCGA-50-5942 
       60.16        31.04         8.09        40.60        15.12        29.03 
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-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 
       36.99         7.59        34.29        30.54        23.05        38.73 
TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6979 TCGA-55-6983 
        0.07        42.51        40.73        15.25         7.79        60.03 
TCGA-55-6984 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 
       24.99         0.59         1.15         7.99         3.12         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 
        1.28         1.12         0.79         0.53         6.48         6.15 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 
        0.16        29.72        15.19         3.29         5.06        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 
       15.65         1.08         1.51        22.16        15.42         0.95 
TCGA-55-8506 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        0.36         0.10         4.80         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
       22.65        20.71         1.58        19.59        15.81        20.19 
TCGA-55-A57B TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P TCGA-62-A470 TCGA-64-1678 
       17.95        14.60        49.25        19.53        39.25        39.09 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-67-3771 TCGA-67-3772 
       37.02        87.98         2.04        42.90        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        12.56        14.01        13.45        25.91 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS 
       26.30         4.31         9.24         1.25        39.09        11.18 
TCGA-78-7143 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
      163.10        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       32.09         5.88        64.90       104.19       238.29         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
       88.14        26.53        31.20         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-6562 
       10.55        50.24        39.75        77.59       110.50        12.36 
TCGA-86-6851 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
        5.88        20.55        35.24         4.57        24.33         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
       32.65        31.04         1.15        27.58         0.62        26.50 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       13.64        26.47         1.97        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.18        16.60        14.27         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 
       17.46        23.61        19.00        16.54        12.39        15.68 
TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       21.40        64.60        63.52        43.79         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
        0.72        18.67        17.92        18.12        15.39        14.30 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-AA5R TCGA-L4-A4E6 TCGA-L9-A50W 
       20.84        18.67        20.68        21.63        14.30        14.53 
TCGA-L9-A5IP TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY 
        1.91        27.19        38.63         2.76        58.45        49.35 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TJ 
        5.49         5.29        31.23        29.46        24.36        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-S2-AA1A 
       73.91        62.60         1.64        16.87 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.00               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            232.18             238.29 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            20.400             19.545 
[1] "0.0 - 232.2 (20.4)" "0.1 - 238.3 (19.5)"
[1] "hr=" "1"  
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         2       63       70        1        26        43
  13Q LOSS WILD-TYPE       3       72       69        0        26        29
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  13Q LOSS MUTATED           36          6       10
  13Q LOSS WILD-TYPE         36          5       16
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 63                 72
  STAGE IB                 70                 69
  STAGE II                  1                  0
  STAGE IIA                26                 26
  STAGE IIB                43                 29
  STAGE IIIA               36                 36
  STAGE IIIB                6                  5
  STAGE IV                 10                 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    77 146  23  10
  13Q LOSS WILD-TYPE  93 132  23   9
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               77                 93
  T2              146                132
  T3               23                 23
  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   161  55    38
  13Q LOSS WILD-TYPE 171  41    38
D66V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                 161                171
  N1                  55                 41
  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   168   9
  13Q LOSS WILD-TYPE 181  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    168    9
  13Q LOSS WILD-TYPE  181   16
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0              168                181
  1                9                 16
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   140 117
  13Q LOSS WILD-TYPE 135 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    140  117
  13Q LOSS WILD-TYPE  135  123
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE              140                135
  MALE                117                123
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   185  27
  13Q LOSS WILD-TYPE 175  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    185   27
  13Q LOSS WILD-TYPE  175   27
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               185                175
  YES               27                 27
[1] 2 2
[1] FALSE
D66V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  13Q LOSS MUTATED                           12
  13Q LOSS WILD-TYPE                          7
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  13Q LOSS MUTATED                                  53
  13Q LOSS WILD-TYPE                                53
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                  162
  13Q LOSS WILD-TYPE                                                158
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  13Q LOSS MUTATED                                            1
  13Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  13Q LOSS MUTATED                                               9
  13Q LOSS WILD-TYPE                                            10
                    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                              1                            10
  13Q LOSS WILD-TYPE                            1                            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                                       12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              162
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     9
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  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                                  53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                158
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      10
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  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   168   7   2  15
  13Q LOSS WILD-TYPE 175   5   2  11
D66V13, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0              168                175
  R1                7                  5
  R2                2                  2
  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
  13Q LOSS MUTATED                                  1     5
  13Q LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          29   192
  13Q LOSS WILD-TYPE                        22   197
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                      29                 22
  WHITE                                         192                197
[1] 4 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     5 194
  13Q LOSS WILD-TYPE   2 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5  194
  13Q LOSS WILD-TYPE    2  188
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  2
  NOT HISPANIC OR LATINO              194                188
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    71  37
  14Q LOSS WILD-TYPE 254 130
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               108                384 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                130 
$`14Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 TCGA-05-4418 TCGA-05-4420 TCGA-05-4427 
        9.96        47.05        20.05         9.01        29.98        26.01 
TCGA-05-5425 TCGA-38-4625 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-44-2662 
       29.00        97.74        49.05        11.64        44.61        42.08 
TCGA-44-3398 TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 TCGA-44-6146 TCGA-44-6775 
       38.24        33.30        28.37        19.56         9.93        23.18 
TCGA-44-7669 TCGA-44-7671 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SS TCGA-49-4507 
       18.87        29.23         8.55        11.08        13.64         8.81 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-AARE TCGA-50-5068 TCGA-50-5931 
       29.46        55.89        16.04        40.41        49.28        14.27 
TCGA-50-5936 TCGA-50-6593 TCGA-50-6597 TCGA-50-8457 TCGA-55-1592 TCGA-55-1595 
        8.45        11.05        41.69        36.99        23.05        48.62 
TCGA-55-1596 TCGA-55-7281 TCGA-55-7283 TCGA-55-7727 TCGA-55-8092 TCGA-55-8094 
       45.21         0.59         1.15         1.12         5.06         0.13 
TCGA-55-8097 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 TCGA-55-A491 TCGA-55-A492 
       15.65         0.95         0.49         6.64        20.58        19.59 
TCGA-62-8398 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A471 TCGA-64-1680 
       14.60        47.80        54.35        67.96        40.96        37.02 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3774 TCGA-67-6217 TCGA-69-7761 
       42.90        28.41        51.25        12.66        13.87         6.12 
TCGA-69-7765 TCGA-69-7980 TCGA-69-A59K TCGA-73-4662 TCGA-73-4675 TCGA-73-A9RS 
        5.42        12.56        17.16        82.68        30.31        11.18 
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-86-8056 TCGA-86-8279 TCGA-86-8359 TCGA-86-8669 
       32.78        19.89         4.57        31.20        14.60        30.84 
TCGA-86-8672 TCGA-91-6830 TCGA-91-6848 TCGA-93-7347 TCGA-93-A4JO TCGA-95-7039 
        0.62         1.97         7.36        22.45         1.08        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7547 
       18.67        12.39        15.65         2.76        18.18        64.60 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-A4M0 TCGA-99-8025 TCGA-99-8032 
        5.39        15.39        16.41        21.44        34.85         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4SW 
       21.57        18.08        32.48        21.83        27.19        58.45 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A7XG 
        5.49         5.29         2.43        71.05        29.13        20.28 

$`14Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03         8.02        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-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02        15.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
        2.04         0.46         7.40         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       37.71        28.41        35.28        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
       43.53        46.98        44.42        44.94        38.10        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
        3.19        25.02        37.15        38.89        34.06        33.73 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       26.56        28.01        23.77        27.78        23.15        21.63 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
       12.03         7.17        36.07        29.00        13.74        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU 
        3.25        15.98        15.32         9.44        11.54        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       76.21        28.11        28.57        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       14.07        32.84        29.75        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       11.64        22.26        22.26       156.66        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        37.32       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        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       31.04         8.09         9.27        40.60        78.67        21.47 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12         9.37        29.03        25.12        22.55        42.35 
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-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        7.59        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         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
       40.54       107.21        70.26         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
        3.12         1.32        23.18         1.28         1.28         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.78        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       19.73        23.64        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42         1.45         0.76         0.36         0.26 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 
       17.72         0.30         0.10         4.80        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       21.40         1.58         0.92        15.81        20.19        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 
       17.95         4.57        39.98        42.38        88.64        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 
       19.53        56.71        72.30        13.61        39.25        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       56.81        20.65        39.09        81.80        38.37        87.98 
TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        2.04        28.47         1.02        20.05        18.84        14.04 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 
       14.73         5.72         4.64         6.64        22.68        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         4.41         2.93        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
        4.24        25.91         2.01        52.60        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31         9.24         1.25        39.09        50.33 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
      163.10        27.16        19.27        20.58       129.53        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-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        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-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
       50.24        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 
       12.36         5.88        31.13        20.55        35.24        37.74 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08        24.33         0.79        22.82        32.65        31.04 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 
       23.05        21.47         1.15        13.91        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-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP 
        1.45        19.82        17.46         6.12        23.61        19.00 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        27.29        21.40 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       19.89        31.69        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
        0.59         0.72        18.67        17.92        18.12        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.58        20.19        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R 
       20.84        18.67        20.68        24.56        36.76        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       24.30        23.80        35.47        19.00        14.30         6.35 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       10.09        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-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59        31.23        10.09        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        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        1.64         0.26         0.43        19.82        59.11        16.87 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.13               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            232.18             238.29 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            20.165             19.925 
[1] "0.1 - 232.2 (20.2)" "0.0 - 238.3 (19.9)"
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         1       23       28        0        14        19
  14Q LOSS WILD-TYPE       4      112      111        1        38        53
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  14Q LOSS MUTATED           21          2        6
  14Q LOSS WILD-TYPE         51          9       20
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 23                112
  STAGE IB                 28                111
  STAGE II                  0                  1
  STAGE IIA                14                 38
  STAGE IIB                19                 53
  STAGE IIIA               21                 51
  STAGE IIIB                2                  9
  STAGE IV                  6                 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    30  65  13   5
  14Q LOSS WILD-TYPE 140 213  33  14
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               30                140
  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
  14Q LOSS MUTATED    64  31    18
  14Q LOSS WILD-TYPE 268  65    58
D67V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                  64                268
  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 219 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     56   58
  14Q LOSS WILD-TYPE  219  182
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               56                219
  MALE                 58                182
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    90  11
  14Q LOSS WILD-TYPE 270  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     90   11
  14Q LOSS WILD-TYPE  270   43
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                90                270
  YES               11                 43
[1] 2 2
[1] FALSE
D67V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  14Q LOSS MUTATED                            3
  14Q LOSS WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  14Q LOSS MUTATED                                  25
  14Q LOSS WILD-TYPE                                81
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                   73
  14Q LOSS WILD-TYPE                                                247
                    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                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                25
  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                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                247
  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 265  12   4  19
D67V13, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               78                265
  R1                0                 12
  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                        33   311
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                 33
  WHITE                                          78                311
[1] 4 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   5 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   90
  14Q LOSS WILD-TYPE    5  292
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               90                292
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   154  73
  15Q LOSS WILD-TYPE 171  94
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               227                265 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                73                 94 
$`15Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4398 TCGA-05-4402 TCGA-05-4417 TCGA-05-4424 
       50.07        19.96        47.05         8.02        14.96        30.02 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
       25.02        25.02        29.00        22.03         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 
        8.68        97.74        37.71        49.05        35.28        11.64 
TCGA-38-6178 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-3917 TCGA-44-3918 
       14.73        44.42        44.94        42.08        38.89        34.06 
TCGA-44-3919 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 
       33.73        28.01        23.77         9.93        27.78        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       23.18        32.45        61.28        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47F 
       36.07        29.00        13.74        12.66         3.25        11.08 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4510 TCGA-49-4514 
       28.11        28.57        12.66        46.72        29.46        55.89 
TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AARE TCGA-49-AARN 
       55.33        11.64        22.26       156.66        40.41        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
      123.58       221.33        71.47        70.55        15.72        31.04 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       78.67        21.47         9.37        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       11.05        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 
       27.25        30.54        13.94        35.21        23.05        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 
       45.21         2.86        32.65        40.73         0.82         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 
       45.34        32.71        60.03         0.59         1.15         3.12 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 
        1.32         1.12         1.78        18.64         6.15        19.82 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8203 TCGA-55-8205 TCGA-55-8301 
        3.29        19.73         0.13        17.98         1.08         1.45 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8614 TCGA-55-8615 
        0.26         0.49        17.72         0.30        17.62         0.49 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        1.58         2.17        22.65        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-A46R 
        0.92        20.19        19.99         4.57        42.38        56.71 
TCGA-62-A46S TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
       54.35        13.61        29.92        56.81        81.80        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-69-7765 
       87.98        42.90        28.41         1.02        18.84         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-A59K TCGA-73-4659 
        7.56         6.05         4.41         2.93        17.16        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 TCGA-78-7143 
       82.68        26.30        15.35        30.31        50.33       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-86-6562 
       88.14        31.20         8.02        10.55       232.18        12.36 
TCGA-86-7701 TCGA-86-7954 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
       31.13        19.89        24.33         0.79        22.82        31.20 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       21.47        14.60        30.84        29.46         3.81        24.23 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       27.68         1.18         1.45        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
       23.61         1.08        17.29        41.82         2.86        18.67 
TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 
        2.76        18.18        19.89        31.69        25.48         5.95 
TCGA-97-8172 TCGA-97-8177 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M3 TCGA-99-7458 
       17.92        16.41        20.19        19.76        17.75        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
       34.85        36.76        24.30        18.08        32.48        19.00 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
        6.35        10.09        18.58        15.65        27.19        38.63 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC 
       86.14        58.45        37.35        86.04         5.29         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       10.09        29.46        11.05        14.10        11.15        19.13 
TCGA-NJ-A4YI TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.13         0.43        19.82        20.28        59.11 

$`15Q LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
        3.98        14.01        45.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 
       24.03        19.00        20.05         2.99         9.01        29.98 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 
       12.00        21.99        26.01        26.01        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 
       15.02         4.96         9.04         2.04         0.46       120.79 
TCGA-38-4629 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       28.41        44.61        26.30         4.37        43.53        46.98 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       38.10        42.77         3.19        25.02        37.15        38.24 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 TCGA-44-6148 TCGA-44-6776 
       26.56        33.30        28.37        19.56        23.15        63.72 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7669 TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 
       16.44        22.72        18.87        29.23         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-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 
       35.54        14.07        32.84         8.81        29.75        16.04 
TCGA-49-6743 TCGA-49-6745 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       53.29        17.16        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5055 TCGA-50-5068 
        8.55       164.12         9.86        20.52        60.16        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5936 TCGA-50-5939 
        8.09         9.27        14.27        40.60         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 
       29.03        25.12        42.35        36.99         7.59        34.29 
TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6970 TCGA-55-6972 
       38.73         0.07         0.79        42.51        15.25        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
        3.88         5.49         7.79        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
       70.26         7.99         0.20         0.13        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 
        1.28         0.79         0.53         6.48        17.65         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19        19.66         5.06        23.64        15.65 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 
        1.51         2.17        22.16        15.42         0.76         0.95 
TCGA-55-8506 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8619 TCGA-55-8621 
        0.36         0.10         4.80         6.64         1.61        16.93 
TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 
       20.71        19.59        15.81        17.95        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U TCGA-62-A46V 
       88.64        49.25        47.80        19.53        67.96        72.30 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 
       39.25        40.96        20.65        39.09        37.02         2.04 
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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
       13.61        12.56        14.01        13.45         4.24        25.91 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
        2.01        52.60         4.31         9.24         1.25        39.09 
TCGA-73-A9RS TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
       11.18        20.58       129.53        21.90        39.95        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       38.50        32.09        22.92         9.57       104.19       238.29 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        8.48        26.53        53.33        26.01        39.35        50.24 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 
       39.75        77.59        10.55       110.50        27.09         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
       34.39        38.04        20.55        32.78        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8585 
        4.08         4.57        32.65        31.04        23.05         1.15 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 
       13.91        27.58         0.62        28.34        26.50        13.64 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       26.47         1.97         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-A4JP TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 
       14.27        19.82        19.00        16.54        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       15.65        27.29        21.40        64.60        63.52        43.79 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        18.67         5.39        18.12        15.39 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        20.52        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 
       18.67        20.68         1.45        21.57        21.63        23.80 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N5 
       35.47        14.30        14.53         1.91        21.83         2.76 
TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH 
       49.35        58.85         5.49        41.59        31.23        24.36 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        62.60         1.64        29.13         0.26 
TCGA-S2-AA1A 
       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 
             19.99              19.82 
[1] "0.1 - 232.2 (20.0)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         3       63       67        0        27        29
  15Q LOSS WILD-TYPE       2       72       72        1        25        43
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  15Q LOSS MUTATED           35          6       11
  15Q LOSS WILD-TYPE         37          5       15
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 63                 72
  STAGE IB                 67                 72
  STAGE II                  0                  1
  STAGE IIA                27                 25
  STAGE IIB                29                 43
  STAGE IIIA               35                 37
  STAGE IIIB                6                  5
  STAGE IV                 11                 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    82 131  19   9
  15Q LOSS WILD-TYPE  88 147  27  10
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               82                 88
  T2              131                147
  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   152  45    38
  15Q LOSS WILD-TYPE 180  51    38
D68V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                 152                180
  N1                  45                 51
  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"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   163  10
  15Q LOSS WILD-TYPE 186  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    163   10
  15Q LOSS WILD-TYPE  186   15
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              163                186
  1               10                 15
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   135 106
  15Q LOSS WILD-TYPE 140 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    135  106
  15Q LOSS WILD-TYPE  140  134
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              135                140
  MALE                106                134
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   165  31
  15Q LOSS WILD-TYPE 195  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    165   31
  15Q LOSS WILD-TYPE  195   23
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               165                195
  YES               31                 23
[1] 2 2
[1] FALSE
D68V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  15Q LOSS MUTATED                            8
  15Q LOSS WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  15Q LOSS MUTATED                                  36
  15Q LOSS WILD-TYPE                                70
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                  167
  15Q LOSS WILD-TYPE                                                153
                    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                              1                            10
  15Q LOSS WILD-TYPE                            1                            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                                36
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              167
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     9
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  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                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                153
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      10
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  0
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  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   159   6   2  14
  15Q LOSS WILD-TYPE 184   6   2  12
D68V13, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              159                184
  R1                6                  6
  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   184
  15Q LOSS WILD-TYPE                        29   205
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                 29
  WHITE                                         184                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"
D68V15, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3 178
  15Q LOSS WILD-TYPE   4 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3  178
  15Q LOSS WILD-TYPE    4  204
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              178                204
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    75  37
  16P LOSS WILD-TYPE 250 130
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               112                380 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                37                130 
$`16P LOSS MUTATED`
TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 TCGA-05-4418 
       45.01         9.96        47.05         8.02         2.99         9.01 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-35-4122 TCGA-44-2656 TCGA-44-2668 
       29.98        30.02        26.01         7.40        46.98        25.02 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6146 TCGA-44-6775 
       34.06        26.56        33.30        28.01         9.93        23.18 
TCGA-44-6777 TCGA-44-7660 TCGA-44-7661 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       32.45        19.46        12.03        13.74        12.66         3.25 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
       28.57        35.54        29.46        16.04        53.29        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5066 TCGA-50-5068 TCGA-50-5936 TCGA-50-5946 
       11.64        22.26        31.04        49.28         8.45        22.55 
TCGA-50-6591 TCGA-50-6593 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
        3.91        11.05        34.29        13.94        35.21         2.86 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6986 TCGA-55-7576 
       42.51         0.82         5.49         7.79       107.21         1.32 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-8094 TCGA-55-8205 TCGA-55-8505 
        1.12        18.64         6.15         0.13         1.08         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8616 TCGA-55-A491 TCGA-62-8394 TCGA-62-8397 
        0.36         0.26         1.58        20.58         4.57        42.38 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       49.25        67.96        72.30        39.25        40.96        29.92 
TCGA-64-1677 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 TCGA-69-7974 
       20.65        28.41         1.02        20.05        22.68         6.05 
TCGA-69-7978 TCGA-69-8255 TCGA-69-A59K TCGA-73-4662 TCGA-73-A9RS TCGA-78-7143 
        4.41         4.24        17.16        82.68        11.18       163.10 
TCGA-78-7146 TCGA-78-7149 TCGA-78-7167 TCGA-78-7536 TCGA-83-5908 TCGA-86-6851 
        5.69       129.53        88.14         8.02        27.09         5.88 
TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8073 TCGA-86-8672 TCGA-91-6829 
       38.04        32.78        37.74        24.33         0.62        41.36 
TCGA-91-6831 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-93-A4JO TCGA-95-7562 
       10.19        27.68        16.18         1.18         1.08         2.86 
TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
       18.67         2.76        18.18        25.48         5.95        18.67 
TCGA-97-A4M3 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N1 
       17.75        19.00         6.35        10.09        18.58        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-NJ-A4YF 
        5.29        11.05        14.10        71.05 

$`16P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
       24.03        19.00        20.05        14.96        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
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-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        4.37        43.53        44.42        44.94        38.10        42.08 
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-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       28.37        23.77        19.56        27.78        23.15        21.63 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 
       63.72        61.28        16.44        22.72         7.17        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        29.00        29.23         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.11        12.66        46.72        14.07        32.84         8.81 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       29.75        55.89        55.33        22.26       156.66        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO 
       62.24        28.90         8.55        40.41        37.32       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        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       15.72        60.16         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67        21.47        15.12         9.37        29.03        25.12 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       42.35        25.55        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 
       10.13        36.99         7.59        27.25        30.54        23.05 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       38.73        48.62        45.21         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25        48.49         3.88         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
       32.71        60.03        24.99        40.54        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 
        1.15         7.99         0.20         0.13         3.12        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
        1.28         1.28         0.79         1.78         0.53         6.48 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         5.06        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
       17.62         0.49         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40         1.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
       20.19        19.99        17.95        39.98        14.60        88.64 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46Y TCGA-64-1676 
       47.80        19.53        56.71        54.35        13.61        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-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       42.90        51.25        28.47        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       14.73         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       13.61         5.42         7.56         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
       13.45        25.91         2.01        52.60        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       15.35         4.31        30.31         9.24         1.25        39.09 
TCGA-73-7499 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
       50.33        27.16        19.27        20.58        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-78-7166 TCGA-78-7220 
       22.92         9.57       104.19       238.29         8.48        26.53 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
       31.20        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 
      232.18        39.75        77.59        10.55       110.50        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       31.13        34.39        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         1.15        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-91-6836 
       13.64        26.47        10.62         1.97         2.60        13.71 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
       12.23         7.36         1.15        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP 
       19.82        22.45        17.46         6.12        23.61        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       17.29        41.82        16.54        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29        21.40        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
       43.79         0.59         0.72        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        20.84        18.67        20.68 
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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       24.30        23.80        18.08        35.47        32.48        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        21.83        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-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       24.36        11.15        19.13        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        29.13         0.26         0.43        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.13               0.00 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            163.10             238.29 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             18.61              20.40 
[1] "0.1 - 163.1 (18.6)" "0.0 - 238.3 (20.4)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         1       24       25        0        13        21
  16P LOSS WILD-TYPE       4      111      114        1        39        51
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16P LOSS MUTATED           20          6        7
  16P LOSS WILD-TYPE         52          5       19
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 24                111
  STAGE IB                 25                114
  STAGE II                  0                  1
  STAGE IIA                13                 39
  STAGE IIB                21                 51
  STAGE IIIA               20                 52
  STAGE IIIB                6                  5
  STAGE IV                  7                 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
  16P LOSS MUTATED    33  65  13   6
  16P LOSS WILD-TYPE 137 213  33  13
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               33                137
  T2               65                213
  T3               13                 33
  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
  16P LOSS MUTATED    69  21    24
  16P LOSS WILD-TYPE 263  75    52
D69V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                  69                263
  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"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    78   7
  16P LOSS WILD-TYPE 271  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     78    7
  16P LOSS WILD-TYPE  271   18
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               78                271
  1                7                 18
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    58  59
  16P LOSS WILD-TYPE 217 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     58   59
  16P LOSS WILD-TYPE  217  181
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               58                217
  MALE                 59                181
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    83  12
  16P LOSS WILD-TYPE 277  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     83   12
  16P LOSS WILD-TYPE  277   42
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                83                277
  YES               12                 42
[1] 2 2
[1] FALSE
D69V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16P LOSS MUTATED                            4
  16P LOSS WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16P LOSS MUTATED                                  28
  16P LOSS WILD-TYPE                                78
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                   70
  16P LOSS WILD-TYPE                                                250
                    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                              1                             3
  16P LOSS WILD-TYPE                            1                            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                                28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               70
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  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                                      2
                                                    clus
vv                                                   16P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  78
  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                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  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    73   1   1   5
  16P LOSS WILD-TYPE 270  11   3  21
D69V13, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               73                270
  R1                1                 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
  16P LOSS MUTATED                                  0     1
  16P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                          12    90
  16P LOSS WILD-TYPE                        39   299
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                      12                 39
  WHITE                                          90                299
[1] 4 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     4  86
  16P LOSS WILD-TYPE   3 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   86
  16P LOSS WILD-TYPE    3  296
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO               86                296
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    93  46
  16Q LOSS WILD-TYPE 232 121
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               139                353 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                46                121 
$`16Q LOSS MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 
       45.01        37.02        47.05         8.02        20.05         2.99 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-5428 
        9.01        29.98        30.02        26.01        25.02        22.03 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 TCGA-44-2656 TCGA-44-2661 
        7.40         5.98        97.74        49.05        46.98        38.10 
TCGA-44-2668 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       25.02        34.06        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 TCGA-44-7661 
       28.01         9.93        23.18        32.45        19.46        12.03 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47B TCGA-49-4488 
       18.87        13.74        12.66         3.25         9.44        28.57 
TCGA-49-4494 TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 
       35.54        29.46        16.04        53.29        17.16        11.64 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5936 TCGA-50-5946 TCGA-50-6591 
       70.55        31.04        49.28         8.45        22.55         3.91 
TCGA-50-6593 TCGA-50-8457 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 
       11.05        36.99        34.29        13.94        35.21        48.62 
TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6986 
        2.86        42.51         0.82         5.49         7.79       107.21 
TCGA-55-7281 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-8205 TCGA-55-8505 
        0.59         1.32         1.12        18.64         1.08         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 
        0.36         0.26         1.58         2.17        21.40        20.58 
TCGA-55-A493 TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46U TCGA-62-A470 
        0.92         4.57        42.38        47.80        67.96        39.25 
TCGA-62-A472 TCGA-64-1677 TCGA-64-5774 TCGA-64-5778 TCGA-67-3770 TCGA-67-3771 
       29.92        20.65        87.98        42.90         1.02        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         2.93         4.24        17.16 
TCGA-73-4658 TCGA-73-4662 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7146 TCGA-78-7149 
       52.60        82.68        11.18       163.10         5.69       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7159 TCGA-78-7167 TCGA-78-7536 TCGA-83-5908 
       21.90        39.95        64.90        88.14         8.02        27.09 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8073 
        5.88        34.39        38.04        32.78        37.74        24.33 
TCGA-86-8075 TCGA-86-8359 TCGA-86-8672 TCGA-91-6829 TCGA-91-6831 TCGA-91-6847 
       22.82        14.60         0.62        41.36        10.19        27.68 
TCGA-91-7771 TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7562 TCGA-95-7567 
       16.18         1.18        17.46         1.08         2.86        18.67 
TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
        2.76        18.18        31.69        25.48         5.95        18.67 
TCGA-97-A4M3 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV 
       17.75        32.48        19.00         6.35        10.09        18.58 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI TCGA-NJ-A4YI 
       27.19         5.29         2.43        11.05        14.10         0.13 
TCGA-NJ-A4YP 
        1.64 

$`16Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        19.96        14.01         0.00         9.96 
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-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 
        4.37        43.53        44.42        44.94        42.08        42.77 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-6144 TCGA-44-6145 
        3.19        37.15        38.24        38.89        23.77        19.56 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
       27.78        23.15        21.63        63.72        61.28        16.44 
TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-8120 
       22.72         7.17        36.07        29.00        29.23         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       76.21        28.11        12.66        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV 
        8.81        29.75        55.89        55.33        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
      156.66        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       37.32       123.58       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       71.47        15.72        60.16         8.09         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       40.60        78.67        21.47        15.12         9.37        29.03 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
       25.12        42.35        25.55        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 
        0.72        10.13         7.59        27.25        30.54        23.05 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       38.73        45.21         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       15.25        48.49         3.88         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 
       60.03        24.99        40.54        70.26         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.20         0.13         3.12        23.18         1.28         1.28 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        0.79         1.78         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.73         5.06         0.13        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
       17.62         0.49         1.61        16.93        22.65        20.71 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B 
        1.58        19.59        15.81        20.19        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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        4.64        13.87         6.64         6.12        13.61         5.42 
TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 
        7.56        12.56        14.01        13.45        25.91         2.01 
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-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
        1.25        39.09        50.33        27.16        19.27        20.58 
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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29         8.48        26.53        31.20 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-7701 
       39.75        77.59        10.55       110.50        12.36        31.13 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       20.55        19.89        35.24         4.08         4.57         0.79 
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         1.15 
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-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        13.71        12.23         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN 
       14.27         1.45        19.82        22.45         6.12        23.61 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 
       19.00        17.29        41.82        16.54        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       15.65        27.29        21.40        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
       43.79         0.59         0.72        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       15.39        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        19.76        20.52        20.84        18.67        20.68 
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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W 
       24.30        23.80        18.08        35.47        14.30        14.53 
TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        1.91        21.83        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-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TJ 
       41.59        31.23        10.09        29.46        24.36        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YQ TCGA-NJ-A55A 
       19.13        73.91        71.05        62.60        29.13         0.26 
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 

  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 
             19.46              19.99 
[1] "0.1 - 163.1 (19.5)" "0.0 - 238.3 (20.0)"
[1] "hr=" "1"  
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         1       34       37        0        15        23
  16Q LOSS WILD-TYPE       4      101      102        1        37        49
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16Q LOSS MUTATED           21          6        7
  16Q LOSS WILD-TYPE         51          5       19
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 34                101
  STAGE IB                 37                102
  STAGE II                  0                  1
  STAGE IIA                15                 37
  STAGE IIB                23                 49
  STAGE IIIA               21                 51
  STAGE IIIB                6                  5
  STAGE IV                  7                 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 LOSS MUTATED    46  80  13   5
  16Q LOSS WILD-TYPE 124 198  33  14
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               46                124
  T2               80                198
  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
  16Q LOSS MUTATED    88  26    26
  16Q LOSS WILD-TYPE 244  70    50
D70V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                  88                244
  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   101   7
  16Q LOSS WILD-TYPE 248  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    101    7
  16Q LOSS WILD-TYPE  248   18
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              101                248
  1                7                 18
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    73  71
  16Q LOSS WILD-TYPE 202 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     73   71
  16Q LOSS WILD-TYPE  202  169
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               73                202
  MALE                 71                169
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   105  15
  16Q LOSS WILD-TYPE 255  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    105   15
  16Q LOSS WILD-TYPE  255   39
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               105                255
  YES               15                 39
[1] 2 2
[1] FALSE
D70V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16Q LOSS MUTATED                            5
  16Q LOSS WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16Q LOSS MUTATED                                  32
  16Q LOSS WILD-TYPE                                74
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                   88
  16Q LOSS WILD-TYPE                                                232
                    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                              1                             5
  16Q LOSS WILD-TYPE                            1                            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                                32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               88
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  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                     2
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   16Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                232
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  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                       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    93   1   1   5
  16Q LOSS WILD-TYPE 250  11   3  21
D70V13, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               93                250
  R1                1                 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
  16Q LOSS MUTATED                                  0     2
  16Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                          13   111
  16Q LOSS WILD-TYPE                        38   278
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                 38
  WHITE                                         111                278
[1] 4 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     5 104
  16Q LOSS WILD-TYPE   2 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5  104
  16Q LOSS WILD-TYPE    2  278
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  2
  NOT HISPANIC OR LATINO              104                278
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   132  73
  17P LOSS WILD-TYPE 193  94
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               205                287 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                73                 94 
$`17P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 
       50.07        45.01         0.00         9.96        24.03         8.02 
TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       29.98        21.99        26.01        26.01        25.02        24.00 
TCGA-05-5420 TCGA-05-5428 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
       15.02        22.03         9.04         7.40         5.98        97.74 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-2659 TCGA-44-2666 
       11.64        44.61        14.73        44.42        44.94         3.19 
TCGA-44-3917 TCGA-44-3919 TCGA-44-5643 TCGA-44-6144 TCGA-44-6775 TCGA-44-6779 
       38.89        33.73        33.30        23.77        23.18        16.44 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 
       19.46        12.03         7.17        36.07        29.00        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47B TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 
        3.25         8.55         9.44        28.57        12.66        14.07 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
        8.81        29.46        29.75        53.29        55.33        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO 
       11.64        22.26         8.55        40.41        37.32       123.58 
TCGA-49-AARQ TCGA-50-5051 TCGA-50-5068 TCGA-50-5931 TCGA-50-5936 TCGA-50-5941 
      221.33        15.72        49.28        14.27         8.45         9.37 
TCGA-50-5944 TCGA-50-6591 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.12         3.91        12.16        41.69         0.72        10.13 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
       34.29        30.54        13.94        23.05        38.73        48.62 
TCGA-55-1596 TCGA-55-6712 TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       45.21         0.79        42.51        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-7281 
        7.79        45.34        32.71        24.99        40.54         0.59 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 
        0.13         1.32         1.28         1.12        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 
       17.65         6.15        19.82         3.29        19.73         5.06 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
       15.65         1.08        17.72         0.30         6.64        17.62 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-62-8397 TCGA-62-A46O 
       22.65        20.71        21.40        20.58        42.38        47.80 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
       56.71        54.35        67.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 
       38.37        87.98        28.47         1.02        20.05        14.04 
TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        5.72        13.87         6.64         6.12        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 
        6.05         4.41         4.24        25.91        17.16        52.60 
TCGA-73-4659 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       23.38        50.33        11.18       163.10        27.16         5.69 
TCGA-78-7150 TCGA-78-7159 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 
       21.90        64.90        31.20         8.02        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 
       10.55       232.18        77.59        31.13        34.39        32.78 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 
       19.89        37.74         4.57        24.33        22.82        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-A4JF TCGA-91-6831 
       31.20        23.05        21.47        13.91        24.23        10.19 
TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-93-7347 TCGA-93-A4JO TCGA-93-A4JQ 
       12.23        27.68        16.18        22.45         1.08        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       41.82         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 
       27.29         2.76        21.40        18.18        19.89        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-8175 TCGA-97-8547 TCGA-99-7458 TCGA-99-8025 
        5.95         0.59        18.12        21.60        24.56        34.85 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W 
       21.57        24.30        18.08        35.47        19.00        14.53 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TD 
       15.65        38.63        86.04        58.85         5.29        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ 
       29.46        11.05        73.91        71.05         0.13        29.13 
TCGA-O1-A52J 
       59.11 

$`17P LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 
        3.98        19.96        14.01        37.02        47.05        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4432 TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5715 TCGA-35-3615 
       25.02        15.02         4.96        29.00         2.04         0.46 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        8.68       120.79        37.71        49.05        28.41        35.28 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2661 TCGA-44-2662 
       26.30         4.37        43.53        46.98        38.10        42.08 
TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
       42.77        25.02        37.15        38.24        34.06        26.56 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.37        28.01        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7669 
       21.63        63.72        32.45        61.28        22.72        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G 
       29.23        13.74        15.98        15.32        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4501 
       13.64        13.45        76.21        28.11        35.54        46.72 
TCGA-49-4506 TCGA-49-4514 TCGA-49-6742 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       32.84        55.89        16.04        22.26       156.66        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
       62.24        28.90       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
       70.55        60.16        31.04         8.09         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
       78.67        21.47        15.12        29.03        22.55        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       25.55        11.05         6.21        36.99         7.59        27.25 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 
       35.21         2.86         0.07        32.65        40.73        15.25 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 
        0.82         2.20        60.03       107.21        70.26         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 
        7.99         0.20         3.12        23.18         1.28         0.79 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        1.78         0.53         0.16        29.72        15.19        19.66 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
        0.13        23.64        17.98         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        0.49         0.10         4.80         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
        2.17        16.93         1.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
       20.19        19.99        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       88.64        49.25        19.53        72.30        13.61        39.25 
TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 TCGA-64-5778 
       40.96        20.65        39.09        37.02         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 
       28.41        51.25        18.84        12.66        14.73         4.64 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
       22.68         7.56         2.93        12.56        14.01        13.45 
TCGA-71-6725 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        2.01        82.68        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        9.24         1.25        39.09        19.27        20.58       129.53 
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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.92         9.57       104.19       238.29         8.48        88.14 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
       26.53        53.33        50.24        39.75        10.55       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         1.15        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-91-6836 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       13.71         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP 
        1.45        19.82        17.46         6.12        23.61        19.00 
TCGA-95-7043 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
       16.54        31.69        64.60        63.52        43.79         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92         5.39        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       20.84        18.67        20.68        36.76         1.45        21.63 
TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP 
       23.80        32.48        14.30         6.35        10.09         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       21.83        18.58        27.19         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       49.35        37.35         5.49        41.59        31.23         2.43 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YP 
       24.36        14.10        11.15        19.13        62.60         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.26         0.43        19.82        20.28        16.87 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.00               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            232.18             238.29 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             21.40              19.76 
[1] "0.0 - 232.2 (21.4)" "0.1 - 238.3 (19.8)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         3       46       57        0        24        37
  17P LOSS WILD-TYPE       2       89       82        1        28        35
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17P LOSS MUTATED           35          4       10
  17P LOSS WILD-TYPE         37          7       16
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 46                 89
  STAGE IB                 57                 82
  STAGE II                  0                  1
  STAGE IIA                24                 28
  STAGE IIB                37                 35
  STAGE IIIA               35                 37
  STAGE IIIB                4                  7
  STAGE IV                 10                 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    63 125  20   7
  17P LOSS WILD-TYPE 107 153  26  12
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               63                107
  T2              125                153
  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   136  42    34
  17P LOSS WILD-TYPE 196  54    42
D71V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                 136                196
  N1                  42                 54
  N2+N3               34                 42
[1] 3 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   146   9
  17P LOSS WILD-TYPE 203  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    146    9
  17P LOSS WILD-TYPE  203   16
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              146                203
  1                9                 16
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   126  90
  17P LOSS WILD-TYPE 149 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    126   90
  17P LOSS WILD-TYPE  149  150
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              126                149
  MALE                 90                150
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   160  18
  17P LOSS WILD-TYPE 200  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    160   18
  17P LOSS WILD-TYPE  200   36
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               160                200
  YES               18                 36
[1] 2 2
[1] FALSE
D71V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17P LOSS MUTATED                            7
  17P LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17P LOSS MUTATED                                  40
  17P LOSS WILD-TYPE                                66
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                  146
  17P LOSS WILD-TYPE                                                174
                    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                                40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              146
  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                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                174
  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   146   4   1  13
  17P LOSS WILD-TYPE 197   8   3  13
D71V13, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              146                197
  R1                4                  8
  R2                1                  3
  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
  17P LOSS MUTATED                                  0     2
  17P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          22   162
  17P LOSS WILD-TYPE                        29   227
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                 29
  WHITE                                         162                227
[1] 4 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     6 153
  17P LOSS WILD-TYPE   1 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6  153
  17P LOSS WILD-TYPE    1  229
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  1
  NOT HISPANIC OR LATINO              153                229
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    32  21
  17Q LOSS WILD-TYPE 293 146
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                53                439 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                21                146 
$`17Q LOSS MUTATED`
TCGA-05-4396 TCGA-35-4122 TCGA-38-4631 TCGA-38-6178 TCGA-44-2657 TCGA-44-2666 
        9.96         7.40        11.64        14.73        44.42         3.19 
TCGA-44-7660 TCGA-49-4488 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 
       19.46        28.57        14.07         8.81        29.75        55.33 
TCGA-49-6761 TCGA-49-AARQ TCGA-50-5051 TCGA-50-5068 TCGA-50-5936 TCGA-53-7624 
       11.64       221.33        15.72        49.28         8.45        34.29 
TCGA-55-1596 TCGA-55-6712 TCGA-55-6972 TCGA-55-6975 TCGA-55-7576 TCGA-55-8091 
       45.21         0.79        48.49         3.88         1.32        19.73 
TCGA-55-8092 TCGA-55-8511 TCGA-55-8614 TCGA-62-8397 TCGA-64-1676 TCGA-67-6217 
        5.06         0.30        17.62        42.38        56.81        13.87 
TCGA-69-7764 TCGA-69-A59K TCGA-73-A9RS TCGA-78-7146 TCGA-78-7535 TCGA-78-8655 
       13.61        17.16        11.18         5.69        31.20        77.59 
TCGA-86-7701 TCGA-86-8280 TCGA-86-A4JF TCGA-91-6840 TCGA-91-7771 TCGA-95-7562 
       31.13        23.05        24.23        12.23        16.18         2.86 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-8547 TCGA-J2-8192 TCGA-J2-A4AD 
       15.65        21.40        19.89        21.60        24.30        18.08 
TCGA-L4-A4E5 TCGA-L9-A8F4 TCGA-MP-A4T6 TCGA-MP-A5C7 TCGA-NJ-A4YI 
       19.00        15.65        58.85        73.91         0.13 

$`17Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       15.02        15.02         4.96        29.00        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-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 
       37.71        49.05        28.41        35.28        44.61        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        4.37        43.53        46.98        44.94        38.10        42.08 
TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
       42.77        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-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       19.56         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
       63.72        32.45        61.28        16.44        22.72        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       11.08        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 
       12.66        35.54        46.72        32.84        29.46        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       16.04        53.29        17.16        22.26        22.26       156.66 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
       73.12        62.24        28.90         8.55        40.41        37.32 
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        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        31.04         8.09         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67        21.47        15.12         9.37        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       22.55        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        36.99         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       27.25        30.54        13.94        35.21        23.05        38.73 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 
       48.62         2.86         0.07        32.65        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       15.25         0.82         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
       18.64         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 
        0.16        29.72        15.19         3.29        19.66         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.26         0.49        17.72         0.10         4.80         6.64 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        0.49         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       20.71        21.40         1.58        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       15.81        20.19        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-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       29.92        20.65        39.09        81.80        37.02        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
        1.02        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-69-7765 
        5.72         4.64         6.64         6.12        22.68         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
       13.45         4.24        25.91         2.01        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       82.68        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
        1.25        39.09        50.33       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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
      104.19       238.29         8.48        88.14        26.53         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       53.33        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        10.55       110.50        27.09        12.36         5.88 
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-86-8075 
       37.74         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-86-8585 
       32.65        31.04        31.20        21.47        14.60         1.15 
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-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-91-6836 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        13.71        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       22.45        17.46         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29        41.82        16.54        18.67        12.39        15.68 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        18.18        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        21.57        21.63        23.80        35.47        32.48 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       14.30         6.35        10.09        14.53         1.91        21.83 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       18.58        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        86.04         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       31.23         2.43        10.09        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP 
       14.10        11.15        19.13        71.05        62.60         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.13               0.00 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            221.33             238.29 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             17.62              20.28 
[1] "0.1 - 221.3 (17.6)" "0.0 - 238.3 (20.3)"
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         2        7       15        0         7        10
  17Q LOSS WILD-TYPE       3      128      124        1        45        62
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17Q LOSS MUTATED           13          1        2
  17Q LOSS WILD-TYPE         59         10       24
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  7                128
  STAGE IB                 15                124
  STAGE II                  0                  1
  STAGE IIA                 7                 45
  STAGE IIB                10                 62
  STAGE IIIA               13                 59
  STAGE IIIB                1                 10
  STAGE IV                  2                 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
  17Q LOSS MUTATED    10  39   7   1
  17Q LOSS WILD-TYPE 160 239  39  18
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               10                160
  T2               39                239
  T3                7                 39
  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
  17Q LOSS MUTATED    32  12    12
  17Q LOSS WILD-TYPE 300  84    64
D72V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                  32                300
  N1                  12                 84
  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"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    36   2
  17Q LOSS WILD-TYPE 313  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     36    2
  17Q LOSS WILD-TYPE  313   23
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               36                313
  1                2                 23
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    34  23
  17Q LOSS WILD-TYPE 241 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     34   23
  17Q LOSS WILD-TYPE  241  217
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               34                241
  MALE                 23                217
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    45   5
  17Q LOSS WILD-TYPE 315  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     45    5
  17Q LOSS WILD-TYPE  315   49
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                45                315
  YES                5                 49
[1] 2 2
[1] FALSE
D72V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17Q LOSS MUTATED                            1
  17Q LOSS WILD-TYPE                         18
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17Q LOSS MUTATED                                  11
  17Q LOSS WILD-TYPE                                95
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                   40
  17Q LOSS WILD-TYPE                                                280
                    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                             2
  17Q LOSS WILD-TYPE                            2                            21
                    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                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               40
  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                                                   17Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         18
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                280
  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"
D72V11, continuous
D72V12, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    40   2   0   3
  17Q LOSS WILD-TYPE 303  10   4  23
D72V13, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               40                303
  R1                2                 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                           6    43
  17Q LOSS WILD-TYPE                        45   346
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                       6                 45
  WHITE                                          43                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"
D72V15, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2  42
  17Q LOSS WILD-TYPE   5 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   42
  17Q LOSS WILD-TYPE    5  340
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               42                340
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   110  59
  18P LOSS WILD-TYPE 215 108
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               169                323 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                59                108 
$`18P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 
       50.07         3.98        37.02         0.00        47.05         8.02 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       20.05        14.96         9.01        21.99        26.01        26.01 
TCGA-05-4434 TCGA-05-5425 TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
       15.02        29.00         2.04         5.98         8.68        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-44-2662 TCGA-44-2668 
       37.71        49.05        11.64        44.61        42.08        25.02 
TCGA-44-6145 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7667 TCGA-44-7669 
       19.56        32.45        61.28        16.44        36.07        18.87 
TCGA-44-7670 TCGA-44-A479 TCGA-44-A47F TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 
       29.00        15.98        11.08        13.45        28.57        12.66 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
       46.72        14.07        32.84        29.75        16.04        53.29 
TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN 
       22.26        73.12        62.24        28.90        40.41        37.32 
TCGA-49-AARO TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5946 
      123.58         8.09        78.67         8.45         9.37        22.55 
TCGA-50-6597 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
       41.69        36.99         7.59        34.29        30.54        38.73 
TCGA-55-1596 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 
       45.21        42.51         0.82        48.49         3.88         7.79 
TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
       40.54         0.59         1.15         0.13         3.12         1.32 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7910 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
        1.28         0.79         6.48        15.19        19.66        19.73 
TCGA-55-8097 TCGA-55-8207 TCGA-55-8507 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
       15.65         2.17         0.26         1.58         2.17        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A57B TCGA-62-8394 
        1.58        20.58        19.59         0.92        17.95         4.57 
TCGA-62-8397 TCGA-62-A46O TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       42.38        47.80        54.35        39.25        40.96        29.92 
TCGA-64-1679 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       81.80        51.25        28.47         1.02        20.05        18.84 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7765 TCGA-69-7979 TCGA-69-8453 TCGA-69-A59K 
        4.64        13.87         5.42         2.93        25.91        17.16 
TCGA-71-6725 TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 
        2.01        26.30         4.31        50.33        11.18         5.69 
TCGA-78-7150 TCGA-78-7161 TCGA-78-7167 TCGA-78-7535 TCGA-78-8660 TCGA-83-5908 
       21.90         9.57        88.14        31.20        10.55        27.09 
TCGA-86-6851 TCGA-86-7714 TCGA-86-7954 TCGA-86-8073 TCGA-86-8278 TCGA-86-8279 
        5.88        20.55        19.89        24.33        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8672 TCGA-91-6830 TCGA-91-6836 TCGA-91-6847 
       23.05        21.47         0.62         1.97        13.71        27.68 
TCGA-91-7771 TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       16.18        19.82        17.46        19.00        41.82        18.67 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 
       15.65        27.29         2.76        18.18        64.60        63.52 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4LX 
        5.95         0.72         5.39        15.39        21.60        20.19 
TCGA-97-A4M0 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
       21.44        24.30        23.80        18.08        35.47        19.00 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 
       14.53        18.58        15.65        58.45        37.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A55O 
        5.49        11.05        14.10        11.15        71.05         0.43 
TCGA-O1-A52J 
       59.11 

$`18P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 
       19.96        14.01        45.01         9.96        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-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 
       24.00        15.02         4.96        22.03         9.04         0.46 
TCGA-35-4122 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
        7.40       120.79        28.41        35.28        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        4.37        43.53        46.98        44.42        44.94        38.10 
TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
       42.77         3.19        37.15        38.24        38.89        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7671 TCGA-44-7672 
       22.72        19.46        12.03         7.17        29.23        13.74 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         3.25         8.55        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4507 TCGA-49-4510 
       13.64        76.21        28.11        35.54         8.81        29.46 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 
       55.89        55.33        17.16        11.64        22.26       156.66 
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 
       70.55        15.72        60.16        31.04        49.28         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       14.27        40.60        21.47        15.12        29.03        25.12 
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-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        0.72        10.13        27.25        13.94        35.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       48.62         2.86         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       15.25         5.49         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7724 
       24.99       107.21        70.26         7.99         0.20        23.18 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
        1.28         1.12         1.78        18.64         0.53        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
        6.15        19.82         0.16        29.72         3.29         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 
        0.13        23.64        17.98         1.08         1.51        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 
        0.49         1.61        16.93        22.65        20.71        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       20.19        19.99        39.98        14.60        88.64        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-64-1676 
       19.53        56.71        67.96        72.30        13.61        56.81 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       20.65        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-73-4658 
        4.41        12.56        14.01        13.45         4.24        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       23.38        82.68        15.35        30.31         9.24         1.25 
TCGA-73-7498 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       39.09       163.10        27.16        19.27        20.58       129.53 
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-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
       64.90        22.92       104.19       238.29         8.48        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        26.01        39.35        10.55        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-6562 TCGA-86-7701 
      232.18        39.75        77.59       110.50        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         1.15 
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-91-6848 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-A4BC TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN 
       14.27         1.18         1.45        22.45         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
        1.08        17.29        16.54         2.86        12.39        15.68 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       21.40        19.89        31.69        43.79        25.48         0.59 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
       18.67        17.92        18.12        16.41        14.30        20.58 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
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-A443 TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A743 
       32.48        14.30         6.35        10.09         1.91        21.83 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 
       27.19        38.63         2.76        86.14        49.35        86.04 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       24.36        19.13        73.91        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       29.13         0.26        19.82        20.28        16.87 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.00               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            123.58             238.29 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             19.73              20.28 
[1] "0.0 - 123.6 (19.7)" "0.1 - 238.3 (20.3)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         1       32       51        0        23        32
  18P LOSS WILD-TYPE       4      103       88        1        29        40
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18P LOSS MUTATED           20          5       13
  18P LOSS WILD-TYPE         52          6       13
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 32                103
  STAGE IB                 51                 88
  STAGE II                  0                  1
  STAGE IIA                23                 29
  STAGE IIB                32                 40
  STAGE IIIA               20                 52
  STAGE IIIB                5                  6
  STAGE IV                 13                 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    50 102  18   6
  18P LOSS WILD-TYPE 120 176  28  13
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               50                120
  T2              102                176
  T3               18                 28
  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   109  42    23
  18P LOSS WILD-TYPE 223  54    53
D73V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                 109                223
  N1                  42                 54
  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"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   108  12
  18P LOSS WILD-TYPE 241  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    108   12
  18P LOSS WILD-TYPE  241   13
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              108                241
  1               12                 13
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   107  70
  18P LOSS WILD-TYPE 168 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    107   70
  18P LOSS WILD-TYPE  168  170
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              107                168
  MALE                 70                170
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   120  18
  18P LOSS WILD-TYPE 240  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    120   18
  18P LOSS WILD-TYPE  240   36
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               120                240
  YES               18                 36
[1] 2 2
[1] FALSE
D73V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18P LOSS MUTATED                            7
  18P LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18P LOSS MUTATED                                  37
  18P LOSS WILD-TYPE                                69
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                  109
  18P LOSS WILD-TYPE                                                211
                    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                              6
  18P LOSS WILD-TYPE                            4
D73V10, multiclass
                                                    clus
vv                                                   18P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              109
  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                                      6
                                                    clus
vv                                                   18P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                211
  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                                        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"
D73V11, continuous
D73V12, continuous
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   117   5   3   5
  18P LOSS WILD-TYPE 226   7   1  21
D73V13, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              117                226
  R1                5                  7
  R2                3                  1
  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
  18P LOSS MUTATED                                  0     3
  18P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          23   123
  18P LOSS WILD-TYPE                        28   266
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                 28
  WHITE                                         123                266
[1] 4 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     2 130
  18P LOSS WILD-TYPE   5 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2  130
  18P LOSS WILD-TYPE    5  252
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              130                252
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   128  75
  18Q LOSS WILD-TYPE 197  92
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               203                289 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                75                 92 
$`18Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 
       50.07         3.98         0.00        47.05         8.02        20.05 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       26.01        24.00        15.02         4.96        29.00         9.04 
TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 
        2.04         5.98         8.68        37.71        49.05        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-2662 TCGA-44-2668 TCGA-44-6145 
       44.61        14.73        44.42        42.08        25.02        19.56 
TCGA-44-6146 TCGA-44-6777 TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 
        9.93        32.45        16.44         7.17        18.87        29.00 
TCGA-44-A479 TCGA-44-A47F TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       15.98        11.08        13.45        28.11        28.57        12.66 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
       46.72        14.07        32.84        29.75        16.04        53.29 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN 
       11.64        22.26        62.24        28.90        40.41        37.32 
TCGA-49-AARO TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 
      123.58        31.04        49.28         8.09        78.67         8.45 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-8457 
        9.37        22.55        11.05        12.16        41.69        36.99 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 
        7.59        34.29        30.54        38.73        45.21         0.79 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 TCGA-55-6980 
       42.51         0.82        48.49         3.88         7.79         2.20 
TCGA-55-6982 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 
       32.71        40.54         0.59         1.15         0.13         3.12 
TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7910 TCGA-55-7994 
        1.32         1.28         1.28         0.79         6.48        19.82 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8207 
       15.19        19.66        19.73         0.13        15.65         2.17 
TCGA-55-8507 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
        0.26         1.58        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46R 
        0.92        17.95         4.57        42.38        47.80        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 
       54.35        67.96        39.25        40.96        29.92        81.80 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       38.37         2.04        42.90        51.25        28.47         1.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 
       20.05        18.84         4.64        13.87         6.64         5.42 
TCGA-69-7979 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 
        2.93        13.45        25.91        17.16        82.68        26.30 
TCGA-73-4670 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        4.31        50.33        11.18       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 TCGA-78-7161 TCGA-78-7535 TCGA-78-7536 
       19.27        21.90        38.50         9.57        31.20         8.02 
TCGA-78-7539 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       26.01        10.55        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-91-6836 TCGA-91-6840 TCGA-91-6847 
        0.62        41.36         1.97        13.71        12.23        27.68 
TCGA-91-7771 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JP TCGA-93-A4JQ 
       16.18         1.45        19.82        17.46        19.00        17.29 
TCGA-95-7567 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7547 
       18.67        15.68        27.29         2.76        18.18        64.60 
TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 
       63.52         5.95         0.72         5.39        15.39        16.41 
TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M6 TCGA-J2-8192 TCGA-J2-8194 
       21.60        20.19        21.44        18.67        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 
       18.08        35.47        19.00        14.53        15.65        38.63 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI 
       58.45        37.35        58.85         5.49        11.05        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A55O TCGA-O1-A52J 
       11.15        19.13        71.05         0.43        59.11 

$`18Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4397 
       19.96        14.01        45.01        37.02         9.96        24.03 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 
       19.00         2.99        29.98        25.02        25.02        15.02 
TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 
       22.03         0.46         7.40        97.74       120.79        28.41 
TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 
       35.28        26.30         4.37        43.53        46.98        44.94 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       38.10        42.77         3.19        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-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       23.77        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7671 
       61.28        22.72        19.46        12.03        36.07        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B 
       13.74        12.66         3.25         8.55        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4507 TCGA-49-4510 
       11.54        13.64        76.21        35.54         8.81        29.46 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       55.89        55.33        17.16        22.26       156.66        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-50-5932 
       70.55        15.72        60.16         9.27        14.27        40.60 
TCGA-50-5935 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 
       21.47        15.12        29.03        25.12        42.35         3.91 
TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 
       25.55         6.21         0.72        10.13        27.25        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       35.21        23.05        48.62         2.86         0.07        32.65 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6978 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
       40.73        15.25         5.49        45.34        60.03        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7724 TCGA-55-7727 
      107.21        70.26         7.99         0.20        23.18         1.12 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
        1.78        18.64         0.53        17.65         6.15         0.16 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 
       29.72         3.29         5.06        23.64        17.98         1.08 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        1.51        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.36         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64        17.62         0.49         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
       22.65        20.71        15.81        20.19        19.99        39.98 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46V TCGA-62-A46Y 
       14.60        88.64        49.25        19.53        72.30        13.61 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 
       56.81        20.65        39.09        37.02        87.98        28.41 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-69-7761 TCGA-69-7763 
       14.04        12.66        14.73         5.72         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
       13.61         7.56         6.05         4.41        12.56        14.01 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 
        4.24         2.01        52.60        23.38        15.35        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
        9.24         1.25        39.09        20.58       129.53        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
      119.51        19.50        32.09         5.88        64.90        22.92 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 
      104.19       238.29         8.48        88.14        26.53        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        50.24       232.18        39.75        77.59 
TCGA-78-8662 TCGA-86-6562 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
      110.50        12.36        38.04        32.78        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8358 
        4.08         4.57        24.33        22.82        32.65        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       14.60         1.15        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-91-6831 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.62        10.19         2.60         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       14.27         1.18        22.45         6.12        23.61         1.08 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK 
       41.82        16.54         2.86        12.39        15.65        21.40 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-8171 
       19.89        31.69        43.79        25.48         0.59        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M2 
       17.92        18.12        14.30        20.58        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       17.75        20.84        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
        1.45        21.57        21.63        32.48        14.30         6.35 
TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 
       10.09         1.91        21.83        18.58        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.14        49.35        86.04         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG 
        2.43        10.09        29.46        24.36        73.91        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.13         1.64        29.13         0.26        19.82        20.28 
TCGA-S2-AA1A 
       16.87 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.00               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            163.10             238.29 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             19.13              20.68 
[1] "0.0 - 163.1 (19.1)" "0.1 - 238.3 (20.7)"
[1] "hr=" "1.3"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         1       41       56        0        27        40
  18Q LOSS WILD-TYPE       4       94       83        1        25        32
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18Q LOSS MUTATED           27          5       14
  18Q LOSS WILD-TYPE         45          6       12
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 41                 94
  STAGE IB                 56                 83
  STAGE II                  0                  1
  STAGE IIA                27                 25
  STAGE IIB                40                 32
  STAGE IIIA               27                 45
  STAGE IIIB                5                  6
  STAGE IV                 14                 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    61 120  22   8
  18Q LOSS WILD-TYPE 109 158  24  11
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               61                109
  T2              120                158
  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   128  50    29
  18Q LOSS WILD-TYPE 204  46    47
D74V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                 128                204
  N1                  50                 46
  N2+N3               29                 47
[1] 3 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   134  13
  18Q LOSS WILD-TYPE 215  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    134   13
  18Q LOSS WILD-TYPE  215   12
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              134                215
  1               13                 12
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   124  88
  18Q LOSS WILD-TYPE 151 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    124   88
  18Q LOSS WILD-TYPE  151  152
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              124                151
  MALE                 88                152
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   141  21
  18Q LOSS WILD-TYPE 219  33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    141   21
  18Q LOSS WILD-TYPE  219   33
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               141                219
  YES               21                 33
[1] 2 2
[1] FALSE
D74V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18Q LOSS MUTATED                            8
  18Q LOSS WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18Q LOSS MUTATED                                  48
  18Q LOSS WILD-TYPE                                58
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                  130
  18Q LOSS WILD-TYPE                                                190
                    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                                1
  18Q LOSS WILD-TYPE                              1
                    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                                        8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              130
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     7
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  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)                190
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      12
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  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   141   8   3   5
  18Q LOSS WILD-TYPE 202   4   1  21
D74V13, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              141                202
  R1                8                  4
  R2                3                  1
  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
  18Q LOSS MUTATED                                  0     2
  18Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          22   154
  18Q LOSS WILD-TYPE                        29   235
D74V14, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  5
  BLACK OR AFRICAN AMERICAN                      22                 29
  WHITE                                         154                235
[1] 4 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     3 151
  18Q LOSS WILD-TYPE   4 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3  151
  18Q LOSS WILD-TYPE    4  231
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              151                231
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED   146  88
  19P LOSS WILD-TYPE 179  79
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               234                258 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                88                 79 
$`19P LOSS MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
        3.98        19.96        14.01        45.01         0.00         9.96 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       47.05         8.02         2.99         9.01        29.98        12.00 
TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 
       26.01        25.02        24.00        15.02        15.02        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
       22.03         7.40         5.98         8.68        97.74        49.05 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 
       35.28        11.64        44.61        14.73        43.53        46.98 
TCGA-44-2662 TCGA-44-3917 TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 TCGA-44-6774 
       42.08        38.89        28.37        23.77         9.93        21.63 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       63.72        61.28        16.44        19.46        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A4SS 
       29.00        29.23        12.66         3.25         8.55        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 
       13.45        76.21        12.66        46.72        14.07         8.81 
TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6767 
       29.46        16.04        53.29        55.33        17.16        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       22.26       156.66        73.12         8.55        40.41       123.58 
TCGA-50-5051 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5936 TCGA-50-5939 
       15.72         8.09        14.27        40.60         8.45        15.12 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6597 
        9.37        25.12        22.55         3.91        11.05        41.69 
TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
       10.13        13.94        35.21        23.05        38.73        45.21 
TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
        2.86        42.51         0.82        48.49         3.88         5.49 
TCGA-55-6981 TCGA-55-6982 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7910 
       45.34        32.71         0.20         1.32         1.12         6.48 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
        6.15        19.82         0.16        29.72         3.29         5.06 
TCGA-55-8094 TCGA-55-8203 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
        0.13        17.98         0.76         0.26         0.49         0.10 
TCGA-55-8614 TCGA-55-8616 TCGA-55-A48X TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
       17.62         1.58        22.65        20.58         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 
       49.25        47.80        56.71        54.35        67.96        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       40.96        56.81        38.37        87.98        42.90        28.41 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        1.02        18.84        12.66         6.12        22.68        13.61 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 
        4.41        12.56         4.24        25.91        17.16         2.01 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 
       23.38        26.30        15.35         4.31         1.25        39.09 
TCGA-73-7499 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       50.33         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7159 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
      119.51        32.09        64.90       104.19         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-86-7701 TCGA-86-7713 
       31.20         8.02        26.01        10.55        31.13        38.04 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 
       32.78        19.89        35.24         4.08        24.33         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 
       22.82        31.20        23.05        30.84         0.62        29.46 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
        3.81        10.62        41.36         1.97        10.19        13.71 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-A4BC 
       12.23         7.36         1.15        16.18        14.27         1.45 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK 
       17.29        41.82        16.54        18.67        15.65        21.40 
TCGA-95-A4VN TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-A4LX 
       18.18        18.67        17.92         5.39        15.39        20.19 
TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 
       19.76        18.67        24.56        34.85        21.57        24.30 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 
       18.08        19.00         6.35        18.58        15.65         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       86.14        49.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       31.23         2.43        11.05        24.36        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        29.13        19.82        20.28        59.11 

$`19P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 
       50.07        37.02        24.03        19.00        20.05        14.96 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 
       30.02        21.99        26.01        25.02         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-7271 
        2.04         0.46       120.79        37.71        28.41        26.30 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
        4.37        44.42        44.94        38.10        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       25.02        37.15        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
       33.30        28.01        19.56        27.78        23.15        23.18 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7672 TCGA-44-A479 
       32.45        22.72        12.03         7.17        13.74        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-49-4487 TCGA-49-4488 
       15.32         9.44        11.08        11.54        28.11        28.57 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 TCGA-49-6761 TCGA-49-AAR3 
       35.54        32.84        29.75        55.89        11.64        62.24 
TCGA-49-AAR4 TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       28.90        37.32       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
       71.47        70.55        60.16        31.04        49.28         9.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 
       78.67        21.47        29.03        42.35        25.55        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        6.21         0.72        36.99         7.59        27.25        34.29 
TCGA-53-7626 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       30.54        48.62         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6979 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       15.25         7.79         2.20        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
      107.21        70.26         0.59         1.15         7.99         0.13 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
        3.12        23.18         1.28         1.28         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
       18.64         0.53        17.65        15.19        19.66        19.73 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 
       15.42         1.45         0.95         0.36        17.72         0.30 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        4.80         6.64         0.49         1.61         2.17        16.93 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A57B TCGA-62-8399 
       20.71        21.40         1.58        19.59        17.95        88.64 
TCGA-62-A46P TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
       19.53        72.30        13.61        29.92        20.65        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       81.80        37.02         2.04        51.25        28.47        20.05 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        14.73         5.72         4.64        13.87         6.64 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        5.42         7.56         6.05         2.93        14.01        13.45 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-78-7143 
       52.60        82.68        30.31         9.24        11.18       163.10 
TCGA-78-7145 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 
       27.16        39.95        19.50        38.50         5.88        22.92 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 
        9.57       238.29        26.53        53.33        39.35        50.24 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      232.18        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 
       12.36         5.88        34.39        20.55        37.74         4.57 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       32.65        31.04        21.47        14.60         1.15        13.91 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       27.58        28.34        26.50        24.23        13.64        26.47 
TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        2.60        27.68        16.60         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7562 
       17.46         6.12        23.61         1.08        19.00         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       12.39        15.68        27.29         2.76        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        0.72        18.12        16.41        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-8028 
       21.44        20.52        17.75        20.84        20.68        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
        1.45        21.63        23.80        35.47        32.48        14.30 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N4 
       10.09        14.53         1.91        21.83        27.19        38.63 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TJ 
       58.45        37.35        41.59        10.09        29.46        11.15 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
       62.60         0.13         1.64         0.26         0.43        16.87 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.00               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            156.66             238.29 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            19.365             20.615 
[1] "0.0 - 156.7 (19.4)" "0.1 - 238.3 (20.6)"
[1] "hr=" "1.2"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         2       58       62        1        27        38
  19P LOSS WILD-TYPE       3       77       77        0        25        34
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19P LOSS MUTATED           37          7       15
  19P LOSS WILD-TYPE         35          4       11
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 58                 77
  STAGE IB                 62                 77
  STAGE II                  1                  0
  STAGE IIA                27                 25
  STAGE IIB                38                 34
  STAGE IIIA               37                 35
  STAGE IIIB                7                  4
  STAGE IV                 15                 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
  19P LOSS MUTATED    76 139  20  11
  19P LOSS WILD-TYPE  94 139  26   8
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               76                 94
  T2              139                139
  T3               20                 26
  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
  19P LOSS MUTATED   153  53    37
  19P LOSS WILD-TYPE 179  43    39
D75V5, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                 153                179
  N1                  53                 43
  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"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   174  15
  19P LOSS WILD-TYPE 175  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    174   15
  19P LOSS WILD-TYPE  175   10
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              174                175
  1               15                 10
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   119 128
  19P LOSS WILD-TYPE 156 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    119  128
  19P LOSS WILD-TYPE  156  112
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE              119                156
  MALE                128                112
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   175  23
  19P LOSS WILD-TYPE 185  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    175   23
  19P LOSS WILD-TYPE  185   31
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO               175                185
  YES               23                 31
[1] 2 2
[1] FALSE
D75V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19P LOSS MUTATED                            9
  19P LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19P LOSS MUTATED                                  53
  19P LOSS WILD-TYPE                                53
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                  156
  19P LOSS WILD-TYPE                                                164
                    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                                        9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              156
  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)                164
  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   166   2   3  12
  19P LOSS WILD-TYPE 177  10   1  14
D75V13, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0              166                177
  R1                2                 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                          23   184
  19P LOSS WILD-TYPE                        28   205
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                      23                 28
  WHITE                                         184                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"
D75V15, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3 180
  19P LOSS WILD-TYPE   4 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3  180
  19P LOSS WILD-TYPE    4  202
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              180                202
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    93  59
  19Q LOSS WILD-TYPE 232 108
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               152                340 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                59                108 
$`19Q LOSS MUTATED`
TCGA-05-4250 TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 
        3.98         0.00         9.96        47.05         8.02         2.99 
TCGA-05-4420 TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 
       29.98        25.02        15.02        15.02        29.00        22.03 
TCGA-38-4625 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 
       97.74        35.28        44.61        14.73        43.53        46.98 
TCGA-44-3917 TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 TCGA-44-7667 TCGA-44-7670 
       38.89        28.37        61.28        16.44        36.07        29.00 
TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4486 
       29.23        12.66         3.25         8.55        13.45        76.21 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-6742 TCGA-49-6745 TCGA-49-6767 
       12.66        14.07         8.81        16.04        17.16        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 TCGA-50-5072 
       22.26       156.66        40.41       123.58        15.72         8.09 
TCGA-50-5932 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       40.60        15.12         9.37        25.12        22.55         3.91 
TCGA-50-6593 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       11.05        41.69        23.05        38.73        45.21         2.86 
TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6982 TCGA-55-7570 
       42.51        48.49         3.88         5.49        32.71         0.20 
TCGA-55-7727 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8203 TCGA-55-8507 
        1.12        19.82         0.16        29.72        17.98         0.26 
TCGA-55-8511 TCGA-55-8616 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DG TCGA-62-8394 
        0.30         1.58        22.65        20.58        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A470 
       39.98        42.38        49.25        47.80        56.71        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 TCGA-67-3770 TCGA-67-3772 TCGA-69-7978 
       40.96        56.81        38.37         1.02        18.84         4.41 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 
        4.24        17.16         2.01        23.38        26.30         4.31 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
        1.25        39.09        50.33         5.69        20.58       129.53 
TCGA-78-7153 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 
      119.51       104.19        88.14        31.20         8.02        10.55 
TCGA-86-7701 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8074 TCGA-86-8279 
       31.13        32.78        19.89        35.24         0.79        31.20 
TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
       30.84         0.62        29.46         3.81        10.62        41.36 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       10.19        13.71        12.23         7.36         1.15        16.18 
TCGA-91-8497 TCGA-91-A4BC TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 
       14.27         1.45        41.82        18.67        15.65         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8171 TCGA-97-8176 TCGA-97-A4LX TCGA-97-A4M1 
       21.40        18.18        18.67        15.39        20.19        19.76 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 
       18.67        24.56        21.57        24.30        18.08        19.00 
TCGA-L9-A7SV TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TA 
       18.58        86.14        49.35        58.85         5.29        31.23 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55R 
       14.10        19.13        73.91        71.05        29.13        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J 
       20.28        59.11 

$`19Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 
       50.07        19.96        14.01        45.01        37.02        24.03 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       19.00        20.05        14.96         9.01        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        26.01        25.02        24.00         4.96 
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-38-4629 TCGA-38-4631 TCGA-38-7271 
      120.79        37.71        49.05        28.41        11.64        26.30 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        4.37        44.42        44.94        38.10        42.08        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-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        28.01        23.77        19.56         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46        12.03         7.17        18.87        13.74 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 
       28.11        28.57        35.54        46.72        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-AAR2 
       29.75        55.89        53.29        55.33        11.64        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90         8.55        37.32       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        70.55        60.16        31.04 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
       49.28         9.27        14.27        78.67        21.47         8.45 
TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       29.03        42.35        25.55        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         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        48.62         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25         0.82         7.79         2.20        45.34 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        1.15         7.99         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1.28         1.28         0.79         1.78        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.48        17.65         6.15        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
       19.73         5.06         0.13        23.64        15.65         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.95         0.36         0.49        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64        17.62         0.49         1.61         2.17        16.93 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40         1.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A57B TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46S 
       20.19        17.95        14.60        88.64        19.53        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
       67.96        72.30        13.61        29.92        20.65        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        37.02        87.98         2.04        42.90        28.41 
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-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         7.56         6.05         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 
       14.01        13.45        25.91        52.60        82.68        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       30.31         9.24        11.18       163.10        27.16        19.27 
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-78-7163 TCGA-78-7166 TCGA-78-7220 
       64.90        22.92         9.57       238.29         8.48        26.53 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        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-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
       24.33        22.82        32.65        31.04        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
       14.60         1.15        13.91        27.58        28.34        26.50 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 
       24.23        13.64        26.47         1.97         2.60        27.68 
TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       16.60         1.18        19.82        22.45        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29        16.54         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        15.68        27.29        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       17.92         5.39        18.12        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 
       20.58        21.44        20.52        17.75        20.84        20.68 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE 
       34.85        36.76         1.45        21.63        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       32.48        14.30         6.35        10.09        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
       21.83        15.65        27.19        38.63         2.76        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD 
       37.35        86.04         5.49        41.59         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A4YI 
       29.46        11.05        24.36        11.15        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
        1.64         0.26         0.43        16.87 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.00               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            156.66             238.29 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            20.090             19.925 
[1] "0.0 - 156.7 (20.1)" "0.1 - 238.3 (19.9)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         1       39       37        1        15        24
  19Q LOSS WILD-TYPE       4       96      102        0        37        48
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19Q LOSS MUTATED           26          6       11
  19Q LOSS WILD-TYPE         46          5       15
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 39                 96
  STAGE IB                 37                102
  STAGE II                  1                  0
  STAGE IIA                15                 37
  STAGE IIB                24                 48
  STAGE IIIA               26                 46
  STAGE IIIB                6                  5
  STAGE IV                 11                 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
  19Q LOSS MUTATED    48  88  14   9
  19Q LOSS WILD-TYPE 122 190  32  10
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               48                122
  T2               88                190
  T3               14                 32
  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    97  35    26
  19Q LOSS WILD-TYPE 235  61    50
D76V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                  97                235
  N1                  35                 61
  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   113  11
  19Q LOSS WILD-TYPE 236  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    113   11
  19Q LOSS WILD-TYPE  236   14
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0              113                236
  1               11                 14
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    82  78
  19Q LOSS WILD-TYPE 193 162
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     82   78
  19Q LOSS WILD-TYPE  193  162
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               82                193
  MALE                 78                162
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   115  16
  19Q LOSS WILD-TYPE 245  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    115   16
  19Q LOSS WILD-TYPE  245   38
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO               115                245
  YES               16                 38
[1] 2 2
[1] FALSE
D76V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19Q LOSS MUTATED                            3
  19Q LOSS WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19Q LOSS MUTATED                                  37
  19Q LOSS WILD-TYPE                                69
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                  103
  19Q LOSS WILD-TYPE                                                217
                    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)              103
  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                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                217
  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   103   2   3   7
  19Q LOSS WILD-TYPE 240  10   1  19
D76V13, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0              103                240
  R1                2                 10
  R2                3                  1
  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
  19Q LOSS MUTATED                                  0     4
  19Q LOSS WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                          14   119
  19Q LOSS WILD-TYPE                        37   270
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                 37
  WHITE                                         119                270
[1] 4 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     2 118
  19Q LOSS WILD-TYPE   5 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2  118
  19Q LOSS WILD-TYPE    5  264
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              118                264
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    62  43
  20P LOSS WILD-TYPE 263 124
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               105                387 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                43                124 
$`20P LOSS MUTATED`
TCGA-05-4395 TCGA-05-4405 TCGA-05-4415 TCGA-05-4422 TCGA-05-5423 TCGA-05-5428 
        0.00        20.05         2.99        12.00         4.96        22.03 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3917 TCGA-44-3919 TCGA-44-6779 
       42.08        42.77        25.02        38.89        33.73        16.44 
TCGA-44-A47A TCGA-44-A47G TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-6743 
       15.32        11.54        46.72        14.07        29.75        53.29 
TCGA-49-6745 TCGA-49-AARE TCGA-49-AARQ TCGA-50-5051 TCGA-50-5072 TCGA-50-5933 
       17.16        40.41       221.33        15.72         8.09        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 
        8.45        15.12        25.12        11.05        12.16        41.69 
TCGA-53-7624 TCGA-55-1594 TCGA-55-1595 TCGA-55-6712 TCGA-55-6968 TCGA-55-6980 
       34.29        38.73        48.62         0.79        42.51         2.20 
TCGA-55-6984 TCGA-55-7283 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 
       24.99         1.15         1.28         1.12        18.64         0.53 
TCGA-55-7994 TCGA-55-8090 TCGA-55-8092 TCGA-55-8207 TCGA-55-8506 TCGA-55-8616 
       19.82        19.66         5.06         2.17         0.36         1.58 
TCGA-62-8397 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       42.38        47.80        19.53        67.96        72.30        13.61 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1681 TCGA-64-5781 
       40.96        29.92        56.81        39.09        38.37        51.25 
TCGA-67-3770 TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 TCGA-69-7974 TCGA-69-8453 
        1.02        14.04         4.64         6.12         6.05        25.91 
TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-78-7143 
       17.16        26.30         4.31        30.31        50.33       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7158 TCGA-78-7537 TCGA-78-8660 
       27.16         5.69        20.58         5.88        53.33        10.55 
TCGA-86-6851 TCGA-86-7953 TCGA-86-7955 TCGA-86-8280 TCGA-86-8673 TCGA-91-6828 
        5.88        32.78        35.24        23.05        28.34        10.62 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6848 TCGA-93-7347 TCGA-95-7039 TCGA-95-7562 
       10.19         2.60         7.36        22.45        41.82         2.86 
TCGA-97-8177 TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8033 TCGA-L4-A4E5 TCGA-L9-A444 
       16.41        21.44        24.56        21.57        19.00        10.09 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TI 
       38.63        86.14        58.45         5.29         2.43        14.10 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-O1-A52J 
       71.05         0.13        59.11 

$`20P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4417 
        9.96        24.03        47.05         8.02        19.00        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        9.01        29.98        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 
       25.02        25.02        24.00        15.02        15.02        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-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       11.64        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-3396 
       46.98        44.42        44.94        38.10         3.19        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24        34.06        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       23.18        63.72        32.45        61.28        22.72        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        29.23 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       13.74        12.66         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.08        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 
       12.66        35.54        32.84         8.81        29.46        55.89 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       16.04        55.33        11.64        22.26        22.26       156.66 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO 
       73.12        62.24        28.90         8.55        37.32       123.58 
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        70.55        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
       31.04        49.28         9.27        14.27        40.60        21.47 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
        9.37        29.03        22.55        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         7.59        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 
       30.54        13.94        35.21        23.05        45.21         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.07        32.65        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        3.88         5.49         7.79        45.34        32.71        60.03 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
       40.54       107.21        70.26         0.59         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 
        0.13         3.12         1.32        23.18         1.28         0.79 
TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        1.78         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19         3.29        19.73         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
        0.10         4.80         6.64        17.62         0.49         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        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-A46R TCGA-62-A46S TCGA-62-A470 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 
       56.71        54.35        39.25        20.65        81.80        37.02 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
       87.98         2.04        42.90        28.41        28.47        20.05 
TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 
       18.84        12.66        14.73         5.72        13.87         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         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 
       12.56        14.01        13.45         4.24         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       23.38        82.68        15.35         9.24         1.25        39.09 
TCGA-73-A9RS TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       11.18        19.27       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        38.50        32.09        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       238.29         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        26.01        39.35        10.55        50.24       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       39.75        77.59       110.50        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       34.39        38.04        20.55        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-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.20        21.47        14.60         1.15        13.91        30.84 
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-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 
       13.64        26.47        41.36         1.97        13.71        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82        17.46         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       19.00        17.29        16.54        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.65        27.29         2.76        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 
       15.39        14.30        21.60        20.58        20.19        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 
       20.52        17.75        20.84        18.67        20.68        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       36.76         1.45        21.63        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP 
       35.47        32.48        14.30         6.35        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SY 
       21.83        18.58        15.65        27.19         2.76        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.35        86.04        58.85         5.49        41.59        31.23 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK 
       10.09        29.46        11.05        24.36        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       73.91        62.60         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       19.82        20.28        16.87 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.00               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            221.33             238.29 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             19.82              19.99 
[1] "0.0 - 221.3 (19.8)" "0.1 - 238.3 (20.0)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         2       21       29        0         9        19
  20P LOSS WILD-TYPE       3      114      110        1        43        53
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20P LOSS MUTATED           23          4        6
  20P LOSS WILD-TYPE         49          7       20
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 21                114
  STAGE IB                 29                110
  STAGE II                  0                  1
  STAGE IIA                 9                 43
  STAGE IIB                19                 53
  STAGE IIIA               23                 49
  STAGE IIIB                4                  7
  STAGE IV                  6                 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
  20P LOSS MUTATED    30  64  12   6
  20P LOSS WILD-TYPE 140 214  34  13
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               30                140
  T2               64                214
  T3               12                 34
  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  20    25
  20P LOSS WILD-TYPE 265  76    51
D77V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                  67                265
  N1                  20                 76
  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"
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    64  49
  20P LOSS WILD-TYPE 211 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     64   49
  20P LOSS WILD-TYPE  211  191
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               64                211
  MALE                 49                191
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    84  11
  20P LOSS WILD-TYPE 276  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     84   11
  20P LOSS WILD-TYPE  276   43
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                84                276
  YES               11                 43
[1] 2 2
[1] FALSE
D77V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20P LOSS MUTATED                            3
  20P LOSS WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20P LOSS MUTATED                                  26
  20P LOSS WILD-TYPE                                80
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                   70
  20P LOSS WILD-TYPE                                                250
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20P LOSS MUTATED                                            0
  20P LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20P LOSS MUTATED                                               6
  20P LOSS WILD-TYPE                                            13
                    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                             2
  20P LOSS WILD-TYPE                            2                            21
                    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                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   20P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                250
  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                                      21
  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    79   3   1   4
  20P LOSS WILD-TYPE 264   9   3  22
D77V13, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               79                264
  R1                3                  9
  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
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           6    88
  20P LOSS WILD-TYPE                        45   301
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                       6                 45
  WHITE                                          88                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"
D77V15, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  81
  20P LOSS WILD-TYPE   6 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   81
  20P LOSS WILD-TYPE    6  301
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               81                301
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    38  27
  20Q LOSS WILD-TYPE 287 140
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                65                427 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                27                140 
$`20Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4422 TCGA-05-5428 
       50.07         8.02        20.05         2.99        12.00        22.03 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3919 TCGA-44-A47B TCGA-44-A47G 
       42.08        42.77        25.02        33.73         9.44        11.54 
TCGA-49-4501 TCGA-49-4512 TCGA-49-6743 TCGA-49-6745 TCGA-49-AARE TCGA-50-5051 
       46.72        29.75        53.29        17.16        40.41        15.72 
TCGA-50-5072 TCGA-50-5936 TCGA-50-6593 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1595 
        8.09         8.45        11.05        34.29        35.21        48.62 
TCGA-55-7283 TCGA-55-8087 TCGA-55-8090 TCGA-55-8207 TCGA-62-8397 TCGA-62-A46O 
        1.15        15.19        19.66         2.17        42.38        47.80 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
       19.53        54.35        67.96        29.92        56.81        39.09 
TCGA-67-3770 TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 TCGA-69-8453 TCGA-73-4675 
        1.02        14.04         4.64         6.12        25.91        30.31 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7146 TCGA-78-7158 TCGA-78-7160 TCGA-78-7537 
       50.33       163.10         5.69         5.88        22.92        53.33 
TCGA-86-6851 TCGA-86-7953 TCGA-86-7955 TCGA-86-8280 TCGA-86-8358 TCGA-91-6828 
        5.88        32.78        35.24        23.05        21.47        10.62 
TCGA-91-6831 TCGA-93-7347 TCGA-97-8174 TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8033 
       10.19        22.45         5.39        21.44        24.56        21.57 
TCGA-L4-A4E5 TCGA-MP-A4SW TCGA-MP-A4TC TCGA-MP-A4TI TCGA-NJ-A4YF 
       19.00        58.45         2.43        14.10        71.05 

$`20Q LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4418 
        9.96        24.03        47.05        19.00        14.96         9.01 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
       29.98        30.02        21.99        26.01        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         4.96        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-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       11.64        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-3396 
       46.98        44.42        44.94        38.10         3.19        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-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       21.63        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       22.72        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        29.23        13.74        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.98        15.32        11.08        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-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6761 
        8.81        29.46        55.89        16.04        55.33        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       22.26        22.26       156.66        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        37.32       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        70.55        60.16        31.04        49.28 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 
        9.27        14.27        40.60        78.67        21.47        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        9.37        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
       36.99         7.59        27.25        30.54        13.94        23.05 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       38.73        45.21         2.86         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        5.49         7.79         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 
       24.99        40.54       107.21        70.26         0.59         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1.28         1.12         0.79         1.78        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
        3.29        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       17.98         1.08         1.51        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
       20.19        19.99        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       88.64        49.25        56.71        72.30        13.61        39.25 
TCGA-62-A471 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       40.96        20.65        81.80        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 
       18.84        12.66        14.73         5.72        13.87         6.64 
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-A59K 
        2.93        12.56        14.01        13.45         4.24        17.16 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01        52.60        23.38        82.68        26.30        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7145 
        4.31         9.24         1.25        39.09        11.18        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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      238.29         8.48        88.14        26.53        31.20         8.02 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       26.01        39.35        10.55        50.24       232.18        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       77.59        10.55       110.50        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       34.39        38.04        20.55        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-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       31.20        14.60         1.15        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-91-6835 TCGA-91-6836 
       13.64        26.47        41.36         1.97         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 
       14.27         1.18         1.45        19.82        17.46         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
       23.61         1.08        19.00        17.29        41.82        16.54 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.76        21.40        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.58        20.19        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        34.85        36.76         1.45 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.63        24.30        23.80        18.08        35.47        32.48 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       14.30         6.35        10.09        14.53         1.91        21.83 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       18.58        15.65        27.19        38.63         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59        31.23        10.09        29.46        11.05        24.36 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       11.15        19.13        73.91        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13         0.26         0.43        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              1.02               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            163.10             238.29 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             22.03              19.82 
[1] "1.0 - 163.1 (22.0)" "0.0 - 238.3 (19.8)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         1       12       24        0         8         6
  20Q LOSS WILD-TYPE       4      123      115        1        44        66
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20Q LOSS MUTATED           12          2        4
  20Q LOSS WILD-TYPE         60          9       22
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 12                123
  STAGE IB                 24                115
  STAGE II                  0                  1
  STAGE IIA                 8                 44
  STAGE IIB                 6                 66
  STAGE IIIA               12                 60
  STAGE IIIB                2                  9
  STAGE IV                  4                 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
  20Q LOSS MUTATED    18  41   5   4
  20Q LOSS WILD-TYPE 152 237  41  15
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1               18                152
  T2               41                237
  T3                5                 41
  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    45   9    13
  20Q LOSS WILD-TYPE 287  87    63
D78V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                  45                287
  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"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    54   4
  20Q LOSS WILD-TYPE 295  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     54    4
  20Q LOSS WILD-TYPE  295   21
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               54                295
  1                4                 21
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    37  32
  20Q LOSS WILD-TYPE 238 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     37   32
  20Q LOSS WILD-TYPE  238  208
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               37                238
  MALE                 32                208
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    55   6
  20Q LOSS WILD-TYPE 305  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     55    6
  20Q LOSS WILD-TYPE  305   48
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                55                305
  YES                6                 48
[1] 2 2
[1] FALSE
D78V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20Q LOSS MUTATED                            3
  20Q LOSS WILD-TYPE                         16
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20Q LOSS MUTATED                                  18
  20Q LOSS WILD-TYPE                                88
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q LOSS MUTATED                                                   36
  20Q LOSS WILD-TYPE                                                284
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20Q LOSS MUTATED                                            0
  20Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20Q LOSS MUTATED                                               4
  20Q LOSS WILD-TYPE                                            15
                    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                             2
  20Q LOSS WILD-TYPE                            2                            21
                    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                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               36
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  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)                284
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      21
  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    49   2   1   4
  20Q LOSS WILD-TYPE 294  10   3  22
D78V13, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               49                294
  R1                2                 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
  20Q LOSS MUTATED                                  0     1
  20Q LOSS WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           2    55
  20Q LOSS WILD-TYPE                        49   334
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                       2                 49
  WHITE                                          55                334
[1] 4 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  49
  20Q LOSS WILD-TYPE   5 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2   49
  20Q LOSS WILD-TYPE    5  333
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               49                333
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   106  56
  21Q LOSS WILD-TYPE 219 111
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               162                330 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                56                111 
$`21Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
       50.07        19.96        45.01        37.02         0.00         9.96 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       47.05         8.02        14.96        29.98        12.00        30.02 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5429 TCGA-35-4122 
       26.01        25.02        25.02        15.02         9.04         7.40 
TCGA-35-4123 TCGA-38-4627 TCGA-44-2659 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 
        5.98        37.71        44.94        38.89        33.30        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 
       23.77        19.56        61.28        16.44        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47B 
        7.17        36.07        29.00        13.74        15.98         9.44 
TCGA-44-A47F TCGA-44-A4SS TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-6745 
       11.08        13.64        32.84         8.81        29.46        17.16 
TCGA-49-6761 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-4B-A93V 
       11.64        73.12        28.90         8.55        40.41         9.86 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 TCGA-50-5933 
       71.47        15.72        49.28         8.09        40.60        78.67 
TCGA-50-5935 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 TCGA-50-6595 TCGA-50-7109 
       21.47        25.12        22.55        25.55         6.21        10.13 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 
       13.94        23.05        38.73        45.21         2.86        42.51 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        0.82        48.49         5.49        60.03        40.54       107.21 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 
        1.32        23.18         0.79         1.78         6.48        17.65 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8203 TCGA-55-8205 
       19.82         3.29        19.66         5.06        17.98         1.08 
TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 TCGA-55-A490 
        0.76         0.26         0.49        17.72         6.64         1.58 
TCGA-55-A491 TCGA-55-A4DF TCGA-62-8402 TCGA-62-A46O TCGA-62-A46S TCGA-62-A470 
       20.58        20.19        49.25        47.80        54.35        39.25 
TCGA-62-A471 TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 
       40.96        20.65        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 
        1.02         6.64         6.12         6.05         2.93        12.56 
TCGA-69-8255 TCGA-69-8453 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
        4.24        25.91        52.60        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7148 TCGA-78-7153 
        4.31        30.31        11.18         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-78-8660 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8359 
       10.55        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-91-7771 
        1.15        30.84        24.23        10.62        12.23        16.18 
TCGA-95-7043 TCGA-95-7562 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-8172 
       16.54         2.86         2.76        19.89        64.60        17.92 
TCGA-97-8174 TCGA-97-8175 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
        5.39        18.12        34.85        36.76         1.45        21.57 
TCGA-J2-A4AE TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4TE 
       35.47        15.65        38.63        86.14        49.35        29.46 
TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       11.05        11.15        29.13         0.43        19.82        20.28 

$`21Q LOSS WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4397 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        3.98        14.01        24.03        19.00        20.05         2.99 
TCGA-05-4418 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 
        9.01        21.99        26.01        24.00        15.02         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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
      120.79        49.05        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       38.10        42.08        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6146 
       38.24        34.06        33.73        26.56        28.01         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
       27.78        23.15        21.63        23.18        63.72        32.45 
TCGA-44-7659 TCGA-44-7669 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       22.72        18.87        29.23        12.66         3.25         8.55 
TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       15.32        11.54        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-4514 
       12.66        35.54        46.72        14.07        29.75        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       16.04        53.29        55.33        22.26        22.26       156.66 
TCGA-49-AAR3 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 
       62.24        37.32       123.58       221.33       164.12        20.52 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 
       70.55        60.16        31.04         9.27        14.27         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 
       15.12         9.37        29.03        42.35         3.91        11.05 
TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       12.16        41.69         0.72        36.99         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 
       34.29        30.54        35.21        48.62         0.07        32.65 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6975 TCGA-55-6979 TCGA-55-6980 
        0.79        40.73        15.25         3.88         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
       45.34        32.71        24.99        70.26         0.59         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 
        7.99         0.20         0.13         3.12         1.28         1.28 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        1.12        18.64         0.53         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19        19.73         0.13        23.64        15.65         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16        15.42         1.45         0.95         0.36 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
        0.30         0.10         4.80        17.62         0.49         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       19.59         0.92        15.81        19.99        17.95         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R 
       39.98        42.38        14.60        88.64        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-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
       13.87        22.68        13.61         5.42         7.56         4.41 
TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 TCGA-73-4676 
       14.01        13.45        17.16         2.01        82.68         9.24 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
        1.25        39.09        50.33       163.10        27.16        19.27 
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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
       22.92         9.57       104.19       238.29         8.48        31.20 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        26.01        39.35        10.55        50.24        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-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       20.55        19.89        35.24         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-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       21.47        13.91        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       29.46         3.81        13.64        26.47        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        13.71        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       17.46         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
       41.82        18.67        12.39        15.68        15.65        27.29 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       21.40        18.18        31.69        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8176 TCGA-97-8177 
        5.95         0.59         0.72        18.67        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
       21.63        24.30        23.80        18.08        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       14.30         6.35        10.09        14.53         1.91        21.83 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
       18.58        27.19         2.76        58.45        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       10.09        24.36        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-O1-A52J TCGA-S2-AA1A 
       62.60         0.13         1.64         0.26        59.11        16.87 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.00               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            232.18             238.29 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            19.855             20.050 
[1] "0.0 - 232.2 (19.9)" "0.1 - 238.3 (20.1)"
[1] "hr=" "1"  
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         1       40       46        0        14        28
  21Q LOSS WILD-TYPE       4       95       93        1        38        44
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  21Q LOSS MUTATED           26          5        7
  21Q LOSS WILD-TYPE         46          6       19
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 40                 95
  STAGE IB                 46                 93
  STAGE II                  0                  1
  STAGE IIA                14                 38
  STAGE IIB                28                 44
  STAGE IIIA               26                 46
  STAGE IIIB                5                  6
  STAGE IV                  7                 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
  21Q LOSS MUTATED    48  95  16   7
  21Q LOSS WILD-TYPE 122 183  30  12
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               48                122
  T2               95                183
  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   109  30    25
  21Q LOSS WILD-TYPE 223  66    51
D79V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                 109                223
  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   117   7
  21Q LOSS WILD-TYPE 232  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    117    7
  21Q LOSS WILD-TYPE  232   18
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              117                232
  1                7                 18
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    81  86
  21Q LOSS WILD-TYPE 194 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     81   86
  21Q LOSS WILD-TYPE  194  154
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               81                194
  MALE                 86                154
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   110  22
  21Q LOSS WILD-TYPE 250  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    110   22
  21Q LOSS WILD-TYPE  250   32
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               110                250
  YES               22                 32
[1] 2 2
[1] FALSE
D79V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  21Q LOSS MUTATED                            9
  21Q LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  21Q LOSS MUTATED                                  25
  21Q LOSS WILD-TYPE                                81
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                  116
  21Q LOSS WILD-TYPE                                                204
                    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                                        9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              116
  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)                204
  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   112   2   1   6
  21Q LOSS WILD-TYPE 231  10   3  20
D79V13, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              112                231
  R1                2                 10
  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                        31   271
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                 31
  WHITE                                         118                271
[1] 4 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   5 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2  120
  21Q LOSS WILD-TYPE    5  262
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              120                262
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   138  69
  22Q LOSS WILD-TYPE 187  98
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               207                285 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                69                 98 
$`22Q LOSS MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4415 
       45.01        37.02         0.00         9.96        24.03         2.99 
TCGA-05-4418 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
        9.01        30.02        26.01        26.01        25.02        24.00 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       15.02        29.00        22.03         7.40         5.98         8.68 
TCGA-38-4628 TCGA-38-6178 TCGA-44-2659 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 
       49.05        14.73        44.94        38.89        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-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4501 TCGA-49-4505 
       29.23        12.66         8.55        13.64        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 
       32.84         8.81        29.46        55.33        11.64        22.26 
TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-50-5051 
       73.12         8.55        40.41        37.32       123.58        15.72 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        9.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6597 TCGA-50-6673 
        9.37        42.35         3.91        25.55        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
       10.13        36.99        34.29        13.94        35.21         2.86 
TCGA-55-6642 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       32.65        42.51         0.82        48.49         3.88         2.20 
TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       40.54         0.59         1.15         0.20         3.12         1.32 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 
       18.64         6.48        17.65         5.06         0.13        17.98 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        1.08         2.17         0.95         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
        0.30         0.10         0.49         1.58         2.17        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-A46S TCGA-62-A46U 
        1.58         0.92        20.19        19.99        54.35        67.96 
TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       13.61        29.92        56.81        20.65        81.80        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-6217 TCGA-69-7760 
       87.98        42.90        28.41        51.25        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
        6.12        22.68        13.61         7.56         4.41         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       12.56        14.01        25.91        17.16         2.01        23.38 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-73-A9RS TCGA-78-7143 
       82.68        15.35         4.31         1.25        11.18       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-78-8660 TCGA-83-5908 TCGA-86-6851 
       31.20         8.02       232.18        10.55        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         1.15        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-91-6836 TCGA-91-6840 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC 
       10.19        13.71        12.23        16.18         1.18         1.45 
TCGA-93-A4JN TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VN 
       23.61        41.82         2.86        18.67         2.76        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       19.89        31.69        63.52        25.48         5.95         0.59 
TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M3 TCGA-99-7458 TCGA-99-8032 
       18.12        21.60        21.44        17.75        24.56         1.45 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 
       32.48        19.00        10.09        18.58        15.65         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TA 
       86.14        49.35        37.35        58.85         5.29        31.23 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ 
       29.46        11.05        11.15        71.05         0.13        29.13 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       19.82        20.28        59.11 

$`22Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4398 TCGA-05-4402 
       50.07         3.98        19.96        14.01        47.05         8.02 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
       19.00        20.05        14.96        29.98        12.00        21.99 
TCGA-05-4430 TCGA-05-4434 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       25.02        15.02         4.96         9.04         2.04         0.46 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       97.74       120.79        37.71        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       44.61        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       38.10        42.08        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       38.24        34.06        28.01         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        63.72        32.45        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 
       19.46        12.03         7.17        18.87        29.00        13.74 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25        15.98        15.32         9.44        11.08        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-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-AAQV 
       29.75        55.89        16.04        53.29        17.16        22.26 
TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
      156.66        62.24        28.90       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        70.55        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6593 
        8.09        14.27        29.03        25.12        22.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 
       12.16         6.21         7.59        27.25        30.54        23.05 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 
       38.73        48.62        45.21         0.07         0.79        40.73 
TCGA-55-6970 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       15.25         5.49         7.79        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       24.99       107.21        70.26         7.99         0.13        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
        1.28         1.28         1.12         0.79         1.78         0.53 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
        6.15        19.82         0.16        29.72        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       19.66        19.73        23.64        15.65         1.51        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8513 TCGA-55-8514 
       15.42         1.45         0.76         0.36         4.80         6.64 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A491 
       17.62         1.61        16.93        22.65        20.71        20.58 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       19.59        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-A46R 
       14.60        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 
       72.30        39.25        40.96        39.09        37.02         2.04 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       28.47         1.02        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7765 TCGA-69-7974 TCGA-69-8254 
       14.73         5.72         4.64         5.42         6.05        13.45 
TCGA-69-8255 TCGA-73-4658 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 
        4.24        52.60        26.30        30.31         9.24        39.09 
TCGA-73-7499 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
       50.33        19.27        20.58       129.53        21.90       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 
       19.50        38.50        32.09         5.88        22.92         9.57 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
      104.19         8.48        26.53        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-6562 
       10.55        50.24        39.75        77.59       110.50        12.36 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 
       31.13        38.04        20.55        35.24         4.08        24.33 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 
       32.65        31.04        23.05        13.91        27.58        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6847 
       26.50        29.46        13.64        26.47         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-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
       17.46         6.12         1.08        19.00        17.29        16.54 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-97-7547 
       12.39        15.68        15.65        27.29        21.40        64.60 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 
       43.79         0.72        18.67        17.92         5.39        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 
       16.41        14.30        20.58        20.19        19.76        20.52 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 
       20.84        18.67        20.68        34.85        36.76        21.57 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 
       21.63        24.30        23.80        18.08        35.47        14.30 
TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N4 
        6.35        14.53         1.91        21.83        27.19        38.63 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD 
       58.45        86.04         5.49        41.59         2.43        10.09 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP 
       24.36        14.10        19.13        73.91        62.60         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
        0.26         0.43        16.87 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.00               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            238.29             221.33 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             18.67              20.55 
[1] "0.0 - 238.3 (18.7)" "0.1 - 221.3 (20.6)"
[1] "hr=" "1.1"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         3       52       56        0        22        33
  22Q LOSS WILD-TYPE       2       83       83        1        30        39
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  22Q LOSS MUTATED           34          6       11
  22Q LOSS WILD-TYPE         38          5       15
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 52                 83
  STAGE IB                 56                 83
  STAGE II                  0                  1
  STAGE IIA                22                 30
  STAGE IIB                33                 39
  STAGE IIIA               34                 38
  STAGE IIIB                6                  5
  STAGE IV                 11                 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
  22Q LOSS MUTATED    69 119  20   9
  22Q LOSS WILD-TYPE 101 159  26  10
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               69                101
  T2              119                159
  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   140  41    35
  22Q LOSS WILD-TYPE 192  55    41
D80V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                 140                192
  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   149  11
  22Q LOSS WILD-TYPE 200  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    149   11
  22Q LOSS WILD-TYPE  200   14
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              149                200
  1               11                 14
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   109 108
  22Q LOSS WILD-TYPE 166 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    109  108
  22Q LOSS WILD-TYPE  166  132
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE              109                166
  MALE                108                132
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   145  25
  22Q LOSS WILD-TYPE 215  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    145   25
  22Q LOSS WILD-TYPE  215   29
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               145                215
  YES               25                 29
[1] 2 2
[1] FALSE
D80V9, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  22Q LOSS MUTATED                           11
  22Q LOSS WILD-TYPE                          8
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  22Q LOSS MUTATED                                  40
  22Q LOSS WILD-TYPE                                66
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                  137
  22Q LOSS WILD-TYPE                                                183
                    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                                       11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              137
  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)                183
  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   144   5   1   9
  22Q LOSS WILD-TYPE 199   7   3  17
D80V13, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              144                199
  R1                5                  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
  22Q LOSS MUTATED                                  1     1
  22Q LOSS WILD-TYPE                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          23   161
  22Q LOSS WILD-TYPE                        28   228
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                 28
  WHITE                                         161                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"
D80V15, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3 162
  22Q LOSS WILD-TYPE   4 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3  162
  22Q LOSS WILD-TYPE    4  220
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              162                220
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    70  30
  XP LOSS WILD-TYPE 255 137
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              100               392 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               30               137 
$`XP LOSS MUTATED`
TCGA-05-4396 TCGA-05-4405 TCGA-05-4426 TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 
        9.96        20.05        26.01        22.03         2.04         7.40 
TCGA-35-4123 TCGA-38-6178 TCGA-44-2659 TCGA-44-5643 TCGA-44-6778 TCGA-44-8120 
        5.98        14.73        44.94        33.30        61.28         8.55 
TCGA-49-4507 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARQ TCGA-50-5066 
        8.81        22.26        73.12        62.24       221.33        31.04 
TCGA-50-5932 TCGA-50-5936 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6597 
       40.60         8.45         9.37        22.55        42.35        41.69 
TCGA-50-7109 TCGA-53-7626 TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
       10.13        30.54        23.05        48.62        45.21         2.86 
TCGA-55-6968 TCGA-55-6985 TCGA-55-7281 TCGA-55-7570 TCGA-55-7726 TCGA-55-7903 
       42.51        40.54         0.59         0.20         1.28        18.64 
TCGA-55-7994 TCGA-55-8090 TCGA-55-8203 TCGA-55-8510 TCGA-55-8616 TCGA-55-A48Z 
       19.82        19.66        17.98        17.72         1.58        21.40 
TCGA-55-A492 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 
       19.59        42.38        47.80        67.96        29.92        56.81 
TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 
       42.90        28.47         1.02        18.84        14.04        14.73 
TCGA-67-6217 TCGA-69-7764 TCGA-71-6725 TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 
       13.87        13.61         2.01        26.30         4.31        50.33 
TCGA-73-A9RS TCGA-78-7146 TCGA-78-7154 TCGA-78-7166 TCGA-78-7535 TCGA-78-7542 
       11.18         5.69        19.50         8.48        31.20        10.55 
TCGA-78-8655 TCGA-78-8660 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       77.59        10.55        19.89        35.24        37.74         4.08 
TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 TCGA-86-A4P7 TCGA-91-6848 TCGA-91-8496 
       22.82        21.47        14.60        13.64         7.36        16.60 
TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-8039 
        1.08        17.29        41.82        16.54        18.67        27.29 
TCGA-95-8494 TCGA-97-7937 TCGA-97-8172 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M6 
        2.76         5.95        17.92        21.60        21.44        18.67 
TCGA-97-A4M7 TCGA-L4-A4E5 TCGA-L9-A50W TCGA-MN-A4N5 TCGA-MP-A4T4 TCGA-MP-A4TI 
       20.68        19.00        14.53         2.76        86.04        14.10 
TCGA-MP-A4TK TCGA-NJ-A4YI TCGA-NJ-A55A TCGA-NJ-A7XG 
       19.13         0.13         0.26        20.28 

$`XP LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 
        0.00        24.03        47.05         8.02        19.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
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-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       44.61        26.30         4.37        43.53        46.98        44.42 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       38.10        42.08        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-44-6146 TCGA-44-6147 TCGA-44-6148 
       28.01        23.77        19.56         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        63.72        32.45        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
       29.23        13.74        12.66         3.25        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       32.84        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR4 
       55.33        17.16        11.64        22.26       156.66        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41        37.32       123.58       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 
       20.52        71.47        70.55        15.72        60.16        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 
        8.09         9.27        14.27        78.67        21.47        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       29.03        25.12         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        6.21         0.72        36.99         7.59        27.25        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        38.73         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 
      107.21        70.26         1.15         7.99         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1.32        23.18         1.28         1.12         0.79         1.78 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.53         6.48        17.65         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        1.45         0.76         0.95         0.36         0.26         0.49 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.30         0.10         4.80         6.64        17.62         0.49 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
        1.61         2.17        16.93        22.65        20.71         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B 
       20.58         0.92        15.81        20.19        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
        4.57        39.98        14.60        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-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       20.65        39.09        81.80        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3774 TCGA-67-6215 
        2.04        28.41        51.25        20.05        12.66         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 
        4.64         6.64         6.12        22.68         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         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.24        25.91        17.16        52.60        23.38        82.68 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7143 
       15.35        30.31         9.24         1.25        39.09       163.10 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16        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-78-7536 
        9.57       104.19       238.29        88.14        26.53         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        50.24       232.18        39.75 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      110.50        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         1.15        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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
       10.19         2.60        13.71        12.23        27.68         1.15 
TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.18        14.27         1.18         1.45        19.82        22.45 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7562 TCGA-95-7944 
       17.46         6.12        23.61        19.00         2.86        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       15.68        15.65        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79        25.48         0.59         0.72 
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-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.58        20.19        19.76        20.52        17.75        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-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       24.30        23.80        18.08        35.47        32.48        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
        6.35        10.09         1.91        21.83        18.58        15.65 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19        38.63        86.14        58.45        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 
       10.09        29.46        11.05        24.36        11.15        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       71.05        62.60         1.64        29.13         0.43        19.82 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  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 
           19.065            20.535 
[1] "0.1 - 221.3 (19.1)" "0.0 - 238.3 (20.5)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED         2       27       31        0         7        19
  XP LOSS WILD-TYPE       3      108      108        1        45        53
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XP LOSS MUTATED           12          2        3
  XP LOSS WILD-TYPE         60          9       23
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                27               108
  STAGE IB                31               108
  STAGE II                 0                 1
  STAGE IIA                7                45
  STAGE IIB               19                53
  STAGE IIIA              12                60
  STAGE IIIB               2                 9
  STAGE IV                 3                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
  XP LOSS MUTATED    34  58  10   2
  XP LOSS WILD-TYPE 136 220  36  17
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              34               136
  T2              58               220
  T3              10                36
  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
  XP LOSS MUTATED    67  24    11
  XP LOSS WILD-TYPE 265  72    65
D81V5, multiclass
       clus
vv      XP LOSS MUTATED XP LOSS WILD-TYPE
  N0                 67               265
  N1                 24                72
  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"
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    49  55
  XP LOSS WILD-TYPE 226 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     49   55
  XP LOSS WILD-TYPE  226  185
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              49               226
  MALE                55               185
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    68  10
  XP LOSS WILD-TYPE 292  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     68   10
  XP LOSS WILD-TYPE  292   44
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               68               292
  YES              10                44
[1] 2 2
[1] FALSE
D81V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XP LOSS MUTATED                            5
  XP LOSS WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XP LOSS MUTATED                                  23
  XP LOSS WILD-TYPE                                83
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XP LOSS MUTATED                                                   68
  XP LOSS WILD-TYPE                                                252
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XP LOSS MUTATED                                            0
  XP LOSS WILD-TYPE                                          5
                   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                              0                             2
  XP LOSS WILD-TYPE                            2                            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                               23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              68
  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                                    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                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               252
  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                                     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    70   1   0   5
  XP LOSS WILD-TYPE 273  11   4  21
D81V13, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              70               273
  R1               1                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
  XP LOSS MUTATED                                  0     3
  XP LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          11    78
  XP LOSS WILD-TYPE                        40   311
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                40
  WHITE                                         78               311
[1] 4 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  79
  XP LOSS WILD-TYPE   7 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   79
  XP LOSS WILD-TYPE    7  303
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              79               303
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    39  22
  XQ LOSS WILD-TYPE 286 145
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               61               431 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               22               145 
$`XQ LOSS MUTATED`
TCGA-05-4396 TCGA-05-5428 TCGA-05-5715 TCGA-35-4123 TCGA-44-5643 TCGA-44-8120 
        9.96        22.03         2.04         5.98        33.30         8.55 
TCGA-49-4507 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-50-5066 TCGA-50-5932 
        8.81        73.12        62.24         8.55        31.04        40.60 
TCGA-50-5936 TCGA-50-6590 TCGA-50-6597 TCGA-50-7109 TCGA-55-1592 TCGA-55-1595 
        8.45        42.35        41.69        10.13        23.05        48.62 
TCGA-55-1596 TCGA-55-6968 TCGA-55-7570 TCGA-55-7576 TCGA-55-7903 TCGA-55-8090 
       45.21        42.51         0.20         1.32        18.64        19.66 
TCGA-55-8203 TCGA-55-A48Z TCGA-55-A491 TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O 
       17.98        21.40        20.58         4.57        42.38        47.80 
TCGA-62-A46U TCGA-62-A472 TCGA-64-5778 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
       67.96        29.92        42.90        28.47        18.84        14.04 
TCGA-69-7764 TCGA-69-7973 TCGA-69-8255 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 
       13.61         7.56         4.24        50.33        11.18         5.69 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-8655 TCGA-86-7954 TCGA-86-7955 
        8.48        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-97-A4M7 TCGA-L9-A50W 
        2.76        21.60        21.44        18.67        20.68        14.53 
TCGA-NJ-A4YI 
        0.13 

$`XQ LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00        24.03        47.05         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-35-3615 
       15.02        15.02         4.96        29.00         9.04         0.46 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        4.37        43.53        46.98        44.42        44.94        38.10 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       42.08        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-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        19.56         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       19.46        12.03         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
       29.23        13.74        12.66         3.25        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       28.11        28.57        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       32.84        29.46        29.75        55.89        16.04        53.29 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       55.33        17.16        11.64        22.26        22.26       156.66 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90        40.41        37.32       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        70.55        15.72        60.16 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
       49.28         8.09         9.27        14.27        78.67        21.47 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       15.12         9.37        29.03        25.12        22.55         3.91 
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 
        7.59        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-55-6969 
       38.73         2.86         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       15.25         0.82        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
      107.21        70.26         0.59         1.15         7.99         0.13 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        3.12        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.78         0.53         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19         3.29        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        0.13        23.64        15.65         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        6.64        17.62         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
       16.93        22.65        20.71         1.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 
       15.81        20.19        19.99        17.95        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-64-1677 TCGA-64-1678 
       13.61        39.25        40.96        56.81        20.65        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-67-3770 TCGA-67-3771 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       51.25         1.02        20.05        12.66        14.73         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 
        4.64        13.87         6.64         6.12        22.68         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41         2.93        12.56        14.01        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
       25.91        17.16         2.01        52.60        23.38        82.68 
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-73-7498 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       39.09       163.10        27.16        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-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       88.14        31.20        53.33        26.01        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
       50.24       232.18        39.75        10.55       110.50        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-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       32.78         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         1.15 
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-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.18        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82        22.45        17.46         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
        1.08        19.00        17.29        16.54         2.86        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       15.68        15.65        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 
       16.41        14.30        20.58        20.19        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       17.75        20.84        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       21.57        21.63        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP 
       32.48        19.00        14.30         6.35        10.09         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       21.83        18.58        15.65        27.19        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-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        5.49         5.29        41.59        31.23         2.43        10.09 
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-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        62.60         1.64        29.13         0.26 
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 

  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 
            19.89             19.99 
[1] "0.1 - 77.6 (19.9)"  "0.0 - 238.3 (20.0)"
[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       17        0         3        13
  XQ LOSS WILD-TYPE       5      119      122        1        49        59
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XQ LOSS MUTATED            9          3        1
  XQ LOSS WILD-TYPE         63          8       25
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                16               119
  STAGE IB                17               122
  STAGE II                 0                 1
  STAGE IIA                3                49
  STAGE IIB               13                59
  STAGE IIIA               9                63
  STAGE IIIB               3                 8
  STAGE IV                 1                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
  XQ LOSS MUTATED    19  34   7   2
  XQ LOSS WILD-TYPE 151 244  39  17
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              19               151
  T2              34               244
  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
  XQ LOSS MUTATED    37  13    10
  XQ LOSS WILD-TYPE 295  83    66
D82V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                 37               295
  N1                 13                83
  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"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    49   1
  XQ LOSS WILD-TYPE 300  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     49    1
  XQ LOSS WILD-TYPE  300   24
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              49               300
  1               1                24
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    26  36
  XQ LOSS WILD-TYPE 249 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     26   36
  XQ LOSS WILD-TYPE  249  204
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              26               249
  MALE                36               204
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    42  10
  XQ LOSS WILD-TYPE 318  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     42   10
  XQ LOSS WILD-TYPE  318   44
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               42               318
  YES              10                44
[1] 2 2
[1] FALSE
D82V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XQ LOSS MUTATED                            3
  XQ LOSS WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XQ LOSS MUTATED                                  21
  XQ LOSS WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                   31
  XQ LOSS WILD-TYPE                                                289
                   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                              0                             1
  XQ LOSS WILD-TYPE                            2                            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                               21
  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                                     0
  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                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               289
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  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                      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    39   0   0   2
  XQ LOSS WILD-TYPE 304  12   4  24
D82V13, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              39               304
  R1               0                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
  XQ LOSS MUTATED                                  0     2
  XQ LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                          10    45
  XQ LOSS WILD-TYPE                        41   344
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                41
  WHITE                                         45               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"
D82V15, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1  51
  XQ LOSS WILD-TYPE   6 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   51
  XQ LOSS WILD-TYPE    6  331
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              51               331
[1] 2 2
[1] FALSE
